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Conserved domains on  [gi|568977806|ref|XP_006515179|]
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ATPase family AAA domain-containing protein 2B isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 399-568 6.56e-116

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


:

Pssm-ID: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 360.67  E-value: 6.56e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  399 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFMRKGADCLSKWV 478
Cdd:cd19517     1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  479 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 558
Cdd:cd19517    81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                         170
                  ....*....|
gi 568977806  559 PGRFDREFLF 568
Cdd:cd19517   161 PGRFDREFYF 170
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 958-1069 2.32e-61

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


:

Pssm-ID: 99957  Cd Length: 112  Bit Score: 204.90  E-value: 2.32e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  958 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:cd05528     1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 568977806 1038 DKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 1069
Cdd:cd05528    81 DRDPADKLIRSRACELRDEVHAMIEAELDPLF 112
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 593-633 1.11e-09

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


:

Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 55.24  E-value: 1.11e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 568977806   593 DAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQIYAS 633
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
COG5076 super family cl34891
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 839-1084 2.32e-08

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


The actual alignment was detected with superfamily member COG5076:

Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 57.89  E-value: 2.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  839 DAVSDTVRATFLTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILHQAS 914
Cdd:COG5076    31 NDSSPFPNAPEEEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAI 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  915 MAPPRRKHTALRAMEVLPLalPSPPRQLSESEKNRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDY 993
Cdd:COG5076   110 ESVTPESGLGSLLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDY 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  994 LEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNpdkDPGDKIIRHrACTLKDTahaiiaaeLDPEFNKLC 1073
Cdd:COG5076   182 YEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVD-AKELEKY--------FLKLIEEIP 249

                         250
                  ....*....|.
gi 568977806 1074 EEIKEARIKRG 1084
Cdd:COG5076   250 EEMLELSIKPG 260
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 757-893 3.32e-04

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19507:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 161  Bit Score: 42.74  E-value: 3.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  757 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 834
Cdd:cd19507    26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  835 ---------GDwwDAVSDTVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 893
Cdd:cd19507   101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 399-568 6.56e-116

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 360.67  E-value: 6.56e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  399 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFMRKGADCLSKWV 478
Cdd:cd19517     1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  479 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 558
Cdd:cd19517    81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                         170
                  ....*....|
gi 568977806  559 PGRFDREFLF 568
Cdd:cd19517   161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 394-630 8.59e-90

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 294.61  E-value: 8.59e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  394 SVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADC 473
Cdd:COG1222    74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGEL-----GAPFIRVRGSEL 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  474 LSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSI 552
Cdd:COG1222   149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  553 DPALRRPGRFDREFLFNLPDQRARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQI 630
Cdd:COG1222   229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDTV 305
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 395-667 1.29e-75

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 267.54  E-value: 1.29e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   395 VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCL 474
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   475 SKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDP 554
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   555 ALRRPGRFDREFLFNLPDQRARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQiyass 634
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIRE----- 403

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 568977806   635 HKLQLDVTSI---VL-----SAHDFYHAMQNIVPASQRAVM 667
Cdd:TIGR01243  404 GKINFEAEEIpaeVLkelkvTMKDFMEALKMVEPSAIREVL 444
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 368-630 5.40e-68

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 234.73  E-value: 5.40e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  368 LASGILRERVKVGASLA---------DV-----DP----MNIDKS--VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKF 427
Cdd:PRK03992   81 VSPFIDREKLKPGARVAlnqqslaivEVlpsekDPrvqaMEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEV 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  428 KIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEID 506
Cdd:PRK03992  161 GIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEID 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  507 GLApvrSSRQDQIHS---SIVST---LLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHIL 580
Cdd:PRK03992  235 AIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEIL 311

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 568977806  581 QIHTRDWNPKlSDAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQI 630
Cdd:PRK03992  312 KIHTRKMNLA-DDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEV 360
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 958-1069 2.32e-61

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 204.90  E-value: 2.32e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  958 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:cd05528     1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 568977806 1038 DKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 1069
Cdd:cd05528    81 DRDPADKLIRSRACELRDEVHAMIEAELDPLF 112
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 436-570 3.97e-47

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 165.07  E-value: 3.97e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   436 LFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSR 515
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKEL-----GAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806   516 QDQIHSSIVSTLLALMDGLDNR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFNL 570
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 431-572 8.74e-19

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 84.73  E-value: 8.74e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806    431 PPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYLMRPS 498
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568977806    499 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPgRFDREFLFNLPD 572
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
BROMO smart00297
bromo domain;
958-1056 1.20e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 82.71  E-value: 1.20e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806    958 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:smart00297    5 QKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90
                    ....*....|....*....
gi 568977806   1038 DkdpgDKIIRHRACTLKDT 1056
Cdd:smart00297   85 P----DSEVYKDAKKLEKF 99
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 980-1037 7.21e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 73.89  E-value: 7.21e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806   980 IFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:pfam00439   16 PFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 593-633 1.11e-09

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 55.24  E-value: 1.11e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 568977806   593 DAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQIYAS 633
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 839-1084 2.32e-08

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 57.89  E-value: 2.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  839 DAVSDTVRATFLTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILHQAS 914
Cdd:COG5076    31 NDSSPFPNAPEEEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAI 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  915 MAPPRRKHTALRAMEVLPLalPSPPRQLSESEKNRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDY 993
Cdd:COG5076   110 ESVTPESGLGSLLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDY 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  994 LEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNpdkDPGDKIIRHrACTLKDTahaiiaaeLDPEFNKLC 1073
Cdd:COG5076   182 YEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVD-AKELEKY--------FLKLIEEIP 249

                         250
                  ....*....|.
gi 568977806 1074 EEIKEARIKRG 1084
Cdd:COG5076   250 EEMLELSIKPG 260
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 757-893 3.32e-04

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 42.74  E-value: 3.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  757 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 834
Cdd:cd19507    26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  835 ---------GDwwDAVSDTVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 893
Cdd:cd19507   101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 435-511 1.22e-03

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 42.07  E-value: 1.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  435 CLFYGPPGTGKTLVARALANE-CSQGdKKVAFFmrKGADCLSKWvGESERQLRL--LFDQayLMRPSIIFFDEIdGLAPV 511
Cdd:NF038214   93 VLLLGPPGTGKTHLAIALGYAaCRQG-YRVRFT--TAADLVEQL-AQARADGRLgrLLRR--LARYDLLIIDEL-GYLPF 165
 
Name Accession Description Interval E-value
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 399-568 6.56e-116

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 360.67  E-value: 6.56e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  399 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFMRKGADCLSKWV 478
Cdd:cd19517     1 DIGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSKGGQKVSFFMRKGADCLSKWV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  479 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 558
Cdd:cd19517    81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRR 160

                         170
                  ....*....|
gi 568977806  559 PGRFDREFLF 568
Cdd:cd19517   161 PGRFDREFYF 170
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 394-630 8.59e-90

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 294.61  E-value: 8.59e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  394 SVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADC 473
Cdd:COG1222    74 DVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGEL-----GAPFIRVRGSEL 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  474 LSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSI 552
Cdd:COG1222   149 VSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQRTVNQLLAELDGFESRGDVLIIAATNRPDLL 228

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  553 DPALRRPGRFDREFLFNLPDQRARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQI 630
Cdd:COG1222   229 DPALLRPGRFDRVIEVPLPDEEAREEILKIHLRD-MPLADDVDLDKLAKLTEGFSGADLKAIVTEAGMFAIREGRDTV 305
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 399-568 4.15e-78

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 254.91  E-value: 4.15e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  399 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWV 478
Cdd:cd19503     1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEA-----GANFLSISGPSIVSKYL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  479 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRR 558
Cdd:cd19503    76 GESEKNLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRR 155

                         170
                  ....*....|
gi 568977806  559 PGRFDREFLF 568
Cdd:cd19503   156 PGRFDREVEI 165
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 395-667 1.29e-75

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 267.54  E-value: 1.29e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   395 VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCL 474
Cdd:TIGR01243  175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAG-----AYFISINGPEIM 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   475 SKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDP 554
Cdd:TIGR01243  250 SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDP 329

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   555 ALRRPGRFDREFLFNLPDQRARKHILQIHTRDwNPKLSDAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQiyass 634
Cdd:TIGR01243  330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRN-MPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIRE----- 403

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 568977806   635 HKLQLDVTSI---VL-----SAHDFYHAMQNIVPASQRAVM 667
Cdd:TIGR01243  404 GKINFEAEEIpaeVLkelkvTMKDFMEALKMVEPSAIREVL 444
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 364-630 2.01e-72

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 247.90  E-value: 2.01e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  364 RAEDLASGILRERVKVGASLADVDPMNIDKSVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGT 443
Cdd:COG0464   123 RESAEALALAAPLVTYEDIGGLEEELLELREAILDDLGGLEEVKEELRELVALPLKRPELREEYGLPPPRGLLLYGPPGT 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  444 GKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSI 523
Cdd:COG0464   203 GKTLLARALAGEL-----GLPLIEVDLSDLVSKYVGETEKNLREVFDKARGLAPCVLFIDEADALAGKRGEVGDGVGRRV 277

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  524 VSTLLALMDGLdnRGEIVVIGATNRLDSIDPALRRpgRFDREFLFNLPDQRARKHILQIHTRDwNPKLSDAFLGELAEKC 603
Cdd:COG0464   278 VNTLLTEMEEL--RSDVVVIAATNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIHLRK-RPLDEDVDLEELAEAT 352

                         250       260
                  ....*....|....*....|....*..
gi 568977806  604 VGYCGADIKALCTEAALTALRRRYPQI 630
Cdd:COG0464   353 EGLSGADIRNVVRRAALQALRLGREPV 379
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 347-667 3.63e-72

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 257.14  E-value: 3.63e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   347 KSKSMARARnRCLP---MNFRAEDLASGILRErVKVGA-----SLADVDPMNIDK------SVRFDSIGGLSHHIHALKE 412
Cdd:TIGR01243  390 KEAAMAALR-RFIRegkINFEAEEIPAEVLKE-LKVTMkdfmeALKMVEPSAIREvlvevpNVRWSDIGGLEEVKQELRE 467

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   413 MVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGdkkvaFFMRKGADCLSKWVGESERQLRLLFDQA 492
Cdd:TIGR01243  468 AVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGAN-----FIAVRGPEILSKWVGESEKAIREIFRKA 542

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   493 YLMRPSIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLP 571
Cdd:TIGR01243  543 RQAAPAIIFFDEIDAIAPARGARFDTsVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPP 622

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   572 DQRARKHILQIHTRDWnPKLSDAFLGELAEKCVGYCGADIKALCTEAALTALRRrypqIYASSHKLQLDVTS------IV 645
Cdd:TIGR01243  623 DEEARKEIFKIHTRSM-PLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRE----SIGSPAKEKLEVGEeeflkdLK 697

                          330       340
                   ....*....|....*....|..
gi 568977806   646 LSAHDFYHAMQNIVPASQRAVM 667
Cdd:TIGR01243  698 VEMRHFLEALKKVKPSVSKEDM 719
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 368-630 5.40e-68

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 234.73  E-value: 5.40e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  368 LASGILRERVKVGASLA---------DV-----DP----MNIDKS--VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKF 427
Cdd:PRK03992   81 VSPFIDREKLKPGARVAlnqqslaivEVlpsekDPrvqaMEVIESpnVTYEDIGGLEEQIREVREAVELPLKKPELFEEV 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  428 KIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEID 506
Cdd:PRK03992  161 GIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEID 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  507 GLApvrSSRQDQIHS---SIVST---LLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHIL 580
Cdd:PRK03992  235 AIA---AKRTDSGTSgdrEVQRTlmqLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEIL 311

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 568977806  581 QIHTRDWNPKlSDAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQI 630
Cdd:PRK03992  312 KIHTRKMNLA-DDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEV 360
26Sp45 TIGR01242
26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an ...
 367-626 4.87e-62

26S proteasome subunit P45 family; Many proteins may score above the trusted cutoff because an internal


Pssm-ID: 130309 [Multi-domain]  Cd Length: 364  Bit Score: 216.59  E-value: 4.87e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   367 DLASGILRERVKVGASLA---------DVDPMNID-----------KSVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEK 426
Cdd:TIGR01242   71 NVSAFIDRKSLKPGARVAlnqqtltivDVLPTSKDplvkgmeveerPNVSYEDIGGLEEQIREIREAVELPLKHPELFEE 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   427 FKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEI 505
Cdd:TIGR01242  151 VGIEPPKGVLLYGPPGTGKTLLAKAVAHETN------ATFIRvVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEI 224

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   506 DGLAPVR---SSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHILQI 582
Cdd:TIGR01242  225 DAIAAKRtdsGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKI 304

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....
gi 568977806   583 HTRDWNPKlSDAFLGELAEKCVGYCGADIKALCTEAALTALRRR 626
Cdd:TIGR01242  305 HTRKMKLA-EDVDLEAIAKMTEGASGADLKAICTEAGMFAIREE 347
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 958-1069 2.32e-61

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 204.90  E-value: 2.32e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  958 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:cd05528     1 LRELRLFLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 568977806 1038 DKDPGDKIIRHRACTLKDTAHAIIAAELDPEF 1069
Cdd:cd05528    81 DRDPADKLIRSRACELRDEVHAMIEAELDPLF 112
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 400-565 4.04e-61

first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 206.52  E-value: 4.04e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  400 IGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVG 479
Cdd:cd19519     2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETG-----AFFFLINGPEIMSKLAG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  480 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRP 559
Cdd:cd19519    77 ESESNLRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF 156


                  ....*.
gi 568977806  560 GRFDRE 565
Cdd:cd19519   157 GRFDRE 162
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 409-564 9.39e-61

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 205.21  E-value: 9.39e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  409 ALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLL 488
Cdd:cd19511     4 ELKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEA-----GLNFISVKGPELFSKYVGESERAVREI 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568977806  489 FDQAYLMRPSIIFFDEIDGLAPVRSSRQD-QIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 564
Cdd:cd19511    79 FQKARQAAPCIIFFDEIDSLAPRRGQSDSsGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDK 155
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 379-630 3.27e-58

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 208.09  E-value: 3.27e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  379 VGASLADVDP----MNIDKSV--RFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARAL 452
Cdd:PTZ00361  158 VGILLDEVDPlvsvMKVDKAPleSYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAV 237

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  453 ANECSqgdkkvAFFMR-KGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL- 530
Cdd:PTZ00361  238 ANETS------ATFLRvVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELl 311

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  531 --MDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHILQIHTRDWNPKlSDAFLGELAEKCVGYCG 608
Cdd:PTZ00361  312 nqLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLA-EDVDLEEFIMAKDELSG 390

                         250       260
                  ....*....|....*....|..
gi 568977806  609 ADIKALCTEAALTALRRRYPQI 630
Cdd:PTZ00361  391 ADIKAICTEAGLLALRERRMKV 412
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 392-630 2.16e-54

ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273520 [Multi-domain]  Cd Length: 495  Bit Score: 198.66  E-value: 2.16e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   392 DKSVRFDSIGGLSHHIHALKEMVVFpLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALAnecsqGDKKVAFFMRKGA 471
Cdd:TIGR01241   49 KPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVA-----GEAGVPFFSISGS 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   472 DCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGlapVRSSRQDQI---HSSIVSTL---LALMDGLDNRGEIVVIGA 545
Cdd:TIGR01241  123 DFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDA---VGRQRGAGLgggNDEREQTLnqlLVEMDGFGTNTGVIVIAA 199

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   546 TNRLDSIDPALRRPGRFDREFLFNLPDQRARKHILQIHTRdwNPKLS-DAFLGELAEKCVGYCGADIKALCTEAALTALR 624
Cdd:TIGR01241  200 TNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAK--NKKLApDVDLKAVARRTPGFSGADLANLLNEAALLAAR 277


                   ....*.
gi 568977806   625 RRYPQI 630
Cdd:TIGR01241  278 KNKTEI 283
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 410-564 2.29e-54

second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 186.93  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  410 LKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGdkkvaFFMRKGADCLSKWVGESERQLRLLF 489
Cdd:cd19529     5 LKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATESNAN-----FISVKGPELLSKWVGESEKAIREIF 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  490 DQAYLMRPSIIFFDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 564
Cdd:cd19529    80 RKARQVAPCVIFFDEIDSIAPRRGTTGDSgVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDR 155
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 368-666 1.67e-51

proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 200312 [Multi-domain]  Cd Length: 512  Bit Score: 190.69  E-value: 1.67e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   368 LASGILRERVKVGASLAdVDPMN------IDKS------------VRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKI 429
Cdd:TIGR03689  135 LAGALADEGLRPGDTLL-VDPRAgyafeaIPRTevedlvleevpdVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGL 213

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   430 QPPRGCLFYGPPGTGKTLVARALANECSQ-----GDKKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLM----RPSII 500
Cdd:TIGR03689  214 KPPKGVLLYGPPGCGKTLIAKAVANSLAArigaeGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKasegRPVIV 293

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   501 FFDEIDGLAPVRSS-RQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHI 579
Cdd:TIGR03689  294 FFDEMDSLFRTRGSgVSSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADI 373

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   580 LQIHTRDWNPklsdaFLGELAEKcVGYCGADIKALcteaaltaLRRRYPQIYASSHKLQ-LDVTSI-----VLSAHDFYH 653
Cdd:TIGR03689  374 FAKYLTDDLP-----LPEDLAAH-DGDREATAAAL--------IQRVVDALYARSEANRyVEVTYAngsteVLYFADFVS 439

                          330
                   ....*....|....*.
gi 568977806   654 -AM-QNIVP-ASQRAV 666
Cdd:TIGR03689  440 gAMlANIVDrAKKRAI 455
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 397-564 1.90e-51

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 179.07  E-value: 1.90e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  397 FDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkvAFFMR-KGADCLS 475
Cdd:cd19502     2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTD------ATFIRvVGSELVQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  476 KWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLAL---MDGLDNRGEIVVIGATNRLDSI 552
Cdd:cd19502    76 KYIGEGARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTGGDREVQRTMLELlnqLDGFDPRGNIKVIMATNRPDIL 155

                         170
                  ....*....|..
gi 568977806  553 DPALRRPGRFDR 564
Cdd:cd19502   156 DPALLRPGRFDR 167
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 410-564 5.19e-50

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 174.24  E-value: 5.19e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  410 LKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLF 489
Cdd:cd19528     5 LQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC-----QANFISVKGPELLTMWFGESEANVRDIF 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  490 DQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSS---IVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 564
Cdd:cd19528    80 DKARAAAPCVLFFDELDSIAKARGGNIGDAGGAadrVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQ 157
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 399-565 5.35e-50

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 174.52  E-value: 5.35e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  399 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWV 478
Cdd:cd19518     1 DIGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGEL-----KVPFLKISATEIVSGVS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  479 GESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGL----DNRGEIVVIGATNRLDSIDP 554
Cdd:cd19518    76 GESEEKIRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELnnekTAGGPVLVIGATNRPDSLDP 155

                         170
                  ....*....|.
gi 568977806  555 ALRRPGRFDRE 565
Cdd:cd19518   156 ALRRAGRFDRE 166
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 370-627 5.23e-49

26S protease regulatory subunit 6B-like protein; Provisional


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 179.96  E-value: 5.23e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  370 SGILRERVKVGASLA---------DVDPMNIDKSVR-----------FDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKI 429
Cdd:PTZ00454   97 STLNRELLKPNASVAlhrhshavvDILPPEADSSIQllqmsekpdvtYSDIGGLDIQKQEIREAVELPLTCPELYEQIGI 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  430 QPPRGCLFYGPPGTGKTLVARALANEcsqgdKKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLA 509
Cdd:PTZ00454  177 DPPRGVLLYGPPGTGKTMLAKAVAHH-----TTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIA 251

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  510 PVRSSRQ---DQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHILQIHTRD 586
Cdd:PTZ00454  252 TKRFDAQtgaDREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSK 331

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 568977806  587 WNpkLSDAF-LGELAEKCVGYCGADIKALCTEAALTALRR-RY 627
Cdd:PTZ00454  332 MN--LSEEVdLEDFVSRPEKISAADIAAICQEAGMQAVRKnRY 372
ftsH CHL00176
cell division protein; Validated
 364-630 3.09e-47

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 180.63  E-value: 3.09e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  364 RAEDLASGILRERVKVGASLADVDpMNIDKSVRFDSIGGlshhIHALK---EMVVFPLLYPEIFEKFKIQPPRGCLFYGP 440
Cdd:CHL00176  150 RSSNFKGGPGQNLMNFGKSKARFQ-MEADTGITFRDIAG----IEEAKeefEEVVSFLKKPERFTAVGAKIPKGVLLVGP 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  441 PGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSR----Q 516
Cdd:CHL00176  225 PGTGKTLLAKAIAGEAE-----VPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGigggN 299

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  517 DQiHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHILQIHTRdwNPKL-SDAF 595
Cdd:CHL00176  300 DE-REQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHAR--NKKLsPDVS 376

                         250       260       270
                  ....*....|....*....|....*....|....*
gi 568977806  596 LGELAEKCVGYCGADIKALCTEAALTALRRRYPQI 630
Cdd:CHL00176  377 LELIARRTPGFSGADLANLLNEAAILTARRKKATI 411
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 410-568 3.16e-47

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 166.30  E-value: 3.16e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  410 LKEMVVFPLLYPEiFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLF 489
Cdd:cd19481     5 LREAVEAPRRGSR-LRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL-----GLPLIVVKLSSLLSKYVGESEKNLRKIF 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  490 DQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSS-IVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLF 568
Cdd:cd19481    79 ERARRLAPCILFIDEIDAIGRKRDSSGESGELRrVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVIEF 158
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 436-570 3.97e-47

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 165.07  E-value: 3.97e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   436 LFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSR 515
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKEL-----GAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806   516 QDQIHSSIVSTLLALMDGLDNR-GEIVVIGATNRLDSIDPALRrpGRFDREFLFNL 570
Cdd:pfam00004   77 GDSESRRVVNQLLTELDGFTSSnSKVIVIAATNRPDKLDPALL--GRFDRIIEFPL 130
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 403-564 1.55e-46

second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 164.58  E-value: 1.55e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  403 LSHHIHALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESE 482
Cdd:cd19530     1 LDHVREELTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANES-----GANFISVKGPELLNKYVGESE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  483 RQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRF 562
Cdd:cd19530    76 RAVRQVFQRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRL 155


                  ..
gi 568977806  563 DR 564
Cdd:cd19530   156 DK 157
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
422-624 3.61e-46

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 166.60  E-value: 3.61e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  422 EIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVGESERQLRLLFDQAYLmRPSIIF 501
Cdd:COG1223    25 ENLRKFGLWPPRKILFYGPPGTGKTMLAEALAGEL-----KLPLLTVRLDSLIGSYLGETARNLRKLFDFARR-APCVIF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  502 FDEIDGLAPVRSSRQD--QIHsSIVSTLLALMDGLdnRGEIVVIGATNRLDSIDPALRRpgRFDREFLFNLPDQRARKHI 579
Cdd:COG1223    99 FDEFDAIAKDRGDQNDvgEVK-RVVNALLQELDGL--PSGSVVIAATNHPELLDSALWR--RFDEVIEFPLPDKEERKEI 173

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 568977806  580 LQIHTRDWNPKLSDAfLGELAEKCVGYCGADIKALCTEAALTALR 624
Cdd:COG1223   174 LELNLKKFPLPFELD-LKKLAKKLEGLSGADIEKVLKTALKKAIL 217
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
388-626 6.08e-45

ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 172.53  E-value: 6.08e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  388 PMNIDKS-----------VRFDSIGGLSHHIHALKEMVVFpLLYPEIFEKF--KIqpPRGCLFYGPPGTGKTLVARALAN 454
Cdd:COG0465   121 AMSFGKSkaklydedkpkVTFDDVAGVDEAKEELQEIVDF-LKDPEKFTRLgaKI--PKGVLLVGPPGTGKTLLAKAVAG 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  455 ECsqgdkKVAFF---------MRKGadclskwVGESeRqLRLLFDQAYLMRPSIIFFDEIDGLAPVRSS--------RqD 517
Cdd:COG0465   198 EA-----GVPFFsisgsdfveMFVG-------VGAS-R-VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAglggghdeR-E 262

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  518 QihssivsTL---LALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHILQIHTRdwNPKLS-D 593
Cdd:COG0465   263 Q-------TLnqlLVEMDGFEGNEGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDVKGREAILKVHAR--KKPLApD 333

                         250       260       270
                  ....*....|....*....|....*....|...
gi 568977806  594 AFLGELAEKCVGYCGADIKALCTEAALTALRRR 626
Cdd:COG0465   334 VDLEVIARRTPGFSGADLANLVNEAALLAARRN 366
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 400-567 7.62e-45

ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 159.83  E-value: 7.62e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  400 IGGLSHHIHALKEMVVFPLLYPEIFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVG 479
Cdd:cd19509     1 IAGLDDAKEALKEAVILPSLRPDLF-PGLRGPPRGILLYGPPGTGKTLLARAVASESG-----STFFSISASSLVSKWVG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  480 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE--IVVIGATNRLDSIDPALR 557
Cdd:cd19509    75 ESEKIVRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVLNKPEdrVLVLGATNRPWELDEAFL 154

                         170
                  ....*....|
gi 568977806  558 RpgRFDREFL 567
Cdd:cd19509   155 R--RFEKRIY 162
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 395-565 2.92e-44

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 158.16  E-value: 2.92e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  395 VRFDSIGGLSHHIHALKEMVVFpLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCL 474
Cdd:cd19501     1 VTFKDVAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA-----GVPFFSISGSDFV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  475 SKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDNRGEIVVIGATNRLDS 551
Cdd:cd19501    75 EMFVGVGASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDEREQTLnqlLVEMDGFESNTGVIVIAATNRPDV 154

                         170
                  ....*....|....
gi 568977806  552 IDPALRRPGRFDRE 565
Cdd:cd19501   155 LDPALLRPGRFDRQ 168
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 412-564 4.36e-41

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 148.82  E-value: 4.36e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  412 EMVVFPLLYPEIFEKfKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVGESERQLRLLFDQ 491
Cdd:cd19527     7 DTIQLPLEHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAIATECS-----LNFLSVKGPELINMYIGESEANVREVFQK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  492 AYLMRPSIIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDNRGE-IVVIGATNRLDSIDPALRRPGRFDR 564
Cdd:cd19527    81 ARDAKPCVIFFDELDSLAPSRGNSGDSggVMDRVVSQLLAELDGMSSSGQdVFVIGATNRPDLLDPALLRPGRFDK 156
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
397-624 7.03e-41

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 161.74  E-value: 7.03e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  397 FDSIGGLSHHIHALKEMVVFpLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALAnecsqGDKKVAFFMRKGADCLSK 476
Cdd:PRK10733  151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIA-----GEAKVPFFTISGSDFVEM 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  477 WVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTL---LALMDGLDNRGEIVVIGATNRLDSID 553
Cdd:PRK10733  225 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLnqmLVEMDGFEGNEGIIVIAATNRPDVLD 304

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568977806  554 PALRRPGRFDREFLFNLPDQRARKHILQIHTRDWnPKLSDAFLGELAEKCVGYCGADIKALCTEAALTALR 624
Cdd:PRK10733  305 PALLRPGRFDRQVVVGLPDVRGREQILKVHMRRV-PLAPDIDAAIIARGTPGFSGADLANLVNEAALFAAR 374
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 409-564 2.81e-40

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 146.42  E-value: 2.81e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  409 ALKEMVVFPLLYPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVGESERQLRLL 488
Cdd:cd19526     4 ALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECG-----LNFISVKGPELLNKYIGASEQNVRDL 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  489 FDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 564
Cdd:cd19526    79 FSRAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDK 154
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 399-562 2.87e-37

ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 137.94  E-value: 2.87e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  399 SIGGLSHHIHALKEMVVFPLLYPEIFEKFKI-QPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKW 477
Cdd:cd19520     1 DIGGLDEVITELKELVILPLQRPELFDNSRLlQPPKGVLLYGPPGCGKTMLAKATAKEAG-----ARFINLQVSSLTDKW 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  478 VGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRG--EIVVIGATNRLDSIDPA 555
Cdd:cd19520    76 YGESQKLVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLSTDGncRVIVMGATNRPQDLDEA 155


                  ....*....
gi 568977806  556 LRR--PGRF 562
Cdd:cd19520   156 ILRrmPKRF 164
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 382-558 3.74e-37

ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 138.58  E-value: 3.74e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  382 SLADVDPMNIDKSVRFDSIGGLSHHIHALKEMVVFPLLYPEIFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdk 461
Cdd:cd19525     6 ELIMSEIMDHGPPINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQS----- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  462 KVAFFMRKGADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE-- 539
Cdd:cd19525    80 GATFFSISASSLTSKWVGEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSSEdr 159

                         170
                  ....*....|....*....
gi 568977806  540 IVVIGATNRLDSIDPALRR 558
Cdd:cd19525   160 ILVVGATNRPQEIDEAARR 178
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 394-564 3.30e-35

ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 132.29  E-value: 3.30e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  394 SVRFDSIGGLSHHIHALKEMVVFPLLYPEIFeKFKIQPPRGCLFYGPPGTGKTLVARALANECSQgdkkvAFFMRKGADC 473
Cdd:cd19521     3 NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-TGNRKPWSGILLYGPPGTGKSYLAKAVATEANS-----TFFSVSSSDL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  474 LSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE-IVVIGATNRLDSI 552
Cdd:cd19521    77 VSKWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVGNDSQgVLVLGATNIPWQL 156

                         170
                  ....*....|..
gi 568977806  553 DPALRRpgRFDR 564
Cdd:cd19521   157 DSAIRR--RFEK 166
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 415-563 5.42e-35

first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410912 [Multi-domain]  Cd Length: 177  Bit Score: 131.84  E-value: 5.42e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  415 VFPllyPEIFEKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAffmrKGADCLSKWVGESERQLRLLF----- 489
Cdd:cd19504    21 VFP---PEIVEQLGCKHVKGILLYGPPGTGKTLMARQIGKMLNAREPKIV----NGPEILNKYVGESEANIRKLFadaee 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568977806  490 DQAYLMRPS---IIFFDEIDGLAPVRSSRQDQ--IHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFD 563
Cdd:cd19504    94 EQRRLGANSglhIIIFDEIDAICKQRGSMAGStgVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 400-558 1.48e-33

Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 127.79  E-value: 1.48e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  400 IGGLSHHIHALKEMVVFPLLYPEIFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVG 479
Cdd:cd19522     2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATEC-----GTTFFNVSSSTLTSKYRG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  480 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIV-STLLALMDGLDNRGE-------IVVIGATNRLDS 551
Cdd:cd19522    76 ESEKLVRLLFEMARFYAPTTIFIDEIDSICSRRGTSEEHEASRRVkSELLVQMDGVGGASEnddpskmVMVLAATNFPWD 155


                  ....*..
gi 568977806  552 IDPALRR 558
Cdd:cd19522   156 IDEALRR 162
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 400-558 3.57e-32

ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in microtubule dynamics; it specifically recognizes and cuts microtubules that are polyglutamylated. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410932 [Multi-domain]  Cd Length: 164  Bit Score: 123.42  E-value: 3.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  400 IGGLSHHIHALKEMVVFPLLYPEIFEKFKiQPPRGCLFYGPPGTGKTLVARALANECsqgdkKVAFFMRKGADCLSKWVG 479
Cdd:cd19524     2 IAGQDLAKQALQEMVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAES-----NATFFNISAASLTSKYVG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  480 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIHSSIVSTLLALMDGLDNRGE--IVVIGATNRLDSIDPA-L 556
Cdd:cd19524    76 EGEKLVRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAvL 155


                  ..
gi 568977806  557 RR 558
Cdd:cd19524   156 RR 157
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 428-570 1.60e-26

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 106.85  E-value: 1.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  428 KIQPPRGCLFYGPPGTGKTLVARALANECSqgDKKVAFFMRKGADCLSKWVGESERQ---LRLLFDQAYLMRPSIIFFDE 504
Cdd:cd00009    15 ELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGhflVRLLFELAEKAKPGVLFIDE 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  505 IDGLAPvrssrqdQIHSSIVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNL 570
Cdd:cd00009    93 IDSLSR-------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 400-567 3.89e-26

ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410931 [Multi-domain]  Cd Length: 163  Bit Score: 106.12  E-value: 3.89e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  400 IGGLSHHIHALKEMVVFPLLYPEIFEKFkIQPPRGCLFYGPPGTGKTLVARALANECSqgdkkVAFFMRKGADCLSKWVG 479
Cdd:cd19523     2 IAGLGALKAAIKEEVLWPLLRPDAFSGL-LRLPRSILLFGPRGTGKTLLGRCLASQLG-----ATFLRLRGSTLVAKWAG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  480 ESERQLRLLFDQAYLMRPSIIFFDEIDGLAPVRSSRQDQIhSSIVSTLLALMDGLDNRGE--IVVIGATNRLDSIDPALR 557
Cdd:cd19523    76 EGEKILQASFLAARCRQPSVLFISDLDALLSSQDDEASPV-GRLQVELLAQLDGVLGSGEdgVLVVCTTSKPEEIDESLR 154

                         170
                  ....*....|
gi 568977806  558 RpgRFDREFL 567
Cdd:cd19523   155 R--YFSKRLL 162
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 958-1061 7.88e-22

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 91.28  E-value: 7.88e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  958 LRELRLFLRDVTKRLATDkRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:cd04369     1 LKKKLRSLLDALKKLKRD-LSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNG 79

                          90       100
                  ....*....|....*....|....
gi 568977806 1038 DkdpgDKIIRHRACTLKDTAHAII 1061
Cdd:cd04369    80 P----GSPIYKDAKKLEKLFEKLL 99
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 961-1061 4.50e-20

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 86.30  E-value: 4.50e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  961 LRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNpDKD 1040
Cdd:cd05512     2 LEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN-AKD 80

                          90       100
                  ....*....|....*....|..
gi 568977806 1041 pgdkIIRHRACT-LKDTAHAII 1061
Cdd:cd05512    81 ----TIFYRAAVrLRDQGGAIL 98
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 981-1076 7.58e-19

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 82.99  E-value: 7.58e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPdkdpgdkiirhractlKDTAHAI 1060
Cdd:cd05509    22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNG----------------PDTEYYK 85

                          90
                  ....*....|....*.
gi 568977806 1061 IAAELDPEFNKLCEEI 1076
Cdd:cd05509    86 CANKLEKFFWKKLKEL 101
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 431-572 8.74e-19

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 84.73  E-value: 8.74e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806    431 PPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFF------------MRKGADCLSKWVGESERQLRLLFDQAYLMRPS 498
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIdgedileevldqLLLIIVGGKKASGSGELRLRLALALARKLKPD 80

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568977806    499 IIFFDEIDGLAPVRSSRQDQihssiVSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPgRFDREFLFNLPD 572
Cdd:smart00382   81 VLILDEITSLLDAEQEALLL-----LLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
BROMO smart00297
bromo domain;
958-1056 1.20e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 82.71  E-value: 1.20e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806    958 LRELRLFLRDVTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:smart00297    5 QKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90
                    ....*....|....*....
gi 568977806   1038 DkdpgDKIIRHRACTLKDT 1056
Cdd:smart00297   85 P----DSEVYKDAKKLEKF 99
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 964-1041 1.03e-17

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 80.01  E-value: 1.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  964 FLRDVTKRLATDKRFNI---FSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPD 1038
Cdd:cd05498     4 FCSGILKELFSKKHKAYawpFYKPVDPEalGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPP 83


                  ...
gi 568977806 1039 KDP 1041
Cdd:cd05498    84 DHP 86
ycf46 CHL00195
Ycf46; Provisional
 432-663 1.81e-16

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 84.30  E-value: 1.81e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  432 PRGCLFYGPPGTGKTLVARALANECSQGDKKVAFfmrkgADCLSKWVGESERQLRLLFDQAYLMRPSIIFFDEIDGLAPV 511
Cdd:CHL00195  259 PRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDV-----GKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSN 333

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  512 RSSRQDQIHSSIV-STLLALMDglDNRGEIVVIGATNRLDSIDPALRRPGRFDREFLFNLPDQRARKHILQIHTRDWNPK 590
Cdd:CHL00195  334 SESKGDSGTTNRVlATFITWLS--EKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPK 411

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  591 LSDAF-LGELAEKCVGYCGADIKALCTEAALTAL--RRRYpqiyasshklqldvtsivlSAHDFYHAMQNIVPASQ 663
Cdd:CHL00195  412 SWKKYdIKKLSKLSNKFSGAEIEQSIIEAMYIAFyeKREF-------------------TTDDILLALKQFIPLAQ 468
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 425-566 2.91e-16

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 77.79  E-value: 2.91e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  425 EKFKIQPPRGCLFYGPPGTGKTLVARALANECSQGDKKV---AFFmrkgadclSKWVGESERQLRLLFDQAYLMRPSIIF 501
Cdd:cd19507    24 SAYGLPTPKGLLLVGIQGTGKSLTAKAIAGVWQLPLLRLdmgRLF--------GGLVGESESRLRQMIQTAEAIAPCVLW 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  502 FDEIDGLAPVRSSRQDQ-IHSSIVSTLLALMDglDNRGEIVVIGATNRLDSIDPALRRPGRFDREF 566
Cdd:cd19507    96 IDEIEKGFSNADSKGDSgTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRFDEIF 159
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 980-1037 7.21e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 73.89  E-value: 7.21e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806   980 IFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:pfam00439   16 PFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNG 73
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 981-1036 7.29e-15

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 71.91  E-value: 7.29e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05511    21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 970-1041 1.45e-14

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 70.82  E-value: 1.45e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568977806  970 KRLATDKRFNIFSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPDKDP 1041
Cdd:cd05506    10 RKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGND 83
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 950-1040 1.99e-13

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 67.85  E-value: 1.99e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  950 MEDQEENTLRELRLFLRDVTKrlatdkrfniFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLIC 1029
Cdd:cd05510     8 FYESLDKVLNELKTYTEHSTP----------FLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIW 77

                          90
                  ....*....|.
gi 568977806 1030 SNALEYNPDKD 1040
Cdd:cd05510    78 KNCLLYNSDPS 88
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 960-1041 1.94e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 64.61  E-value: 1.94e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  960 ELRlFLRDVTKRLATDKRFNI---FSKPVDieEVSD----YLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNA 1032
Cdd:cd05499     1 ELK-FCEEVLKELMKPKHSAYnwpFLDPVD--PVALnipnYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNC 77


                  ....*....
gi 568977806 1033 LEYNPDKDP 1041
Cdd:cd05499    78 YTFNPEGTD 86
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 433-564 1.32e-11

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 63.91  E-value: 1.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  433 RGCLFYGPPGTGKTLVARALANECsqgDKKVaffmrkgadC---LSKwVGESERQLRLLFDQAylMRPSIIFFDEID--- 506
Cdd:cd19510    24 RGYLLYGPPGTGKSSFIAALAGEL---DYDI---------CdlnLSE-VVLTDDRLNHLLNTA--PKQSIILLEDIDaaf 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568977806  507 --GLAPVRSSRQDQIHSSI-VSTLLALMDGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 564
Cdd:cd19510    89 esREHNKKNPSAYGGLSRVtFSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 981-1039 1.70e-11

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 62.86  E-value: 1.70e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPDK 1039
Cdd:cd05496    26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNK 84
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 981-1040 2.95e-11

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 62.03  E-value: 2.95e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPDKD 1040
Cdd:cd05504    33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHT 92
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 436-568 4.97e-11

type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 188437 [Multi-domain]  Cd Length: 557  Bit Score: 67.18  E-value: 4.97e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   436 LFYGPPGTGKTLVARALANE-CSQG---DKKVAFFMRkgADCLSKWVGESERQLRLLFDQAYlmrPSIIFFDEIDGLAPV 511
Cdd:TIGR03922  316 LFAGPPGTGKTTIARVVAKIyCGLGvlrKPLVREVSR--ADLIGQYIGESEAKTNEIIDSAL---GGVLFLDEAYTLVET 390

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568977806   512 RSSRQDQIHSSIVSTLLALMDglDNRGEIVVIGATNRLD-----SIDPALRRpgRFDREFLF 568
Cdd:TIGR03922  391 GYGQKDPFGLEAIDTLLARME--NDRDRLVVIGAGYRKDldkflEVNEGLRS--RFTRVIEF 448
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 981-1036 8.63e-11

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 60.12  E-value: 8.63e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05513    22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 981-1036 2.04e-10

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 59.09  E-value: 2.04e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05505    21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYY 76
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 969-1036 2.99e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 58.48  E-value: 2.99e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  969 TKRLaTDKRFniFSKPVDIEE--VSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05500    16 LKRL-KDARP--FLVPVDPVKlnIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFN 82
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 960-1037 4.56e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 58.22  E-value: 4.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  960 ELRLFLRDVTKRLATDKRFNI-FSKPVD--IEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05495     3 ELRQALMPTLEKLYKQDPESLpFRQPVDpkLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYN 82


                  .
gi 568977806 1037 P 1037
Cdd:cd05495    83 R 83
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 436-556 6.73e-10

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion


Pssm-ID: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 60.15  E-value: 6.73e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  436 LFYGPPGTGKTLVARALANECSqgdKKVAFFMRKG-------ADCLSKWVGESERQLRLLFDQAYLM---RPSIIF--FD 503
Cdd:cd19508    56 LLHGPPGTGKTSLCKALAQKLS---IRLSSRYRYGqlieinsHSLFSKWFSESGKLVTKMFQKIQELiddKDALVFvlID 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568977806  504 EIDGLAPVRSSRQDQIHSS----IVSTLLALMDGLDNRGEIVVIGATNRLDSIDPAL 556
Cdd:cd19508   133 EVESLAAARSASSSGTEPSdairVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 960-1046 7.12e-10

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 57.82  E-value: 7.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  960 ELRLFLRDVTKRLATDKRFNIFSKPVDIE--EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:cd05497     5 QLQYLLKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84


                  ....*....
gi 568977806 1038 dkdPGDKII 1046
Cdd:cd05497    85 ---PGDDVV 90
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 593-633 1.11e-09

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 55.24  E-value: 1.11e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 568977806   593 DAFLGELAEKCVGYCGADIKALCTEAALTALRRRYPQIYAS 633
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALRRGLEAVTQE 41
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 981-1041 1.40e-09

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 56.61  E-value: 1.40e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPDKDP 1041
Cdd:cd05503    21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 839-1084 2.32e-08

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 57.89  E-value: 2.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  839 DAVSDTVRATFLTLLQDIPSFS--PIFLLSTSETMYSELPEEVKcIFRIQYEEV-LYIQRPIEEDRRKFF-QELILHQAS 914
Cdd:COG5076    31 NDSSPFPNAPEEEGSKNLFQKQlkRMPKEYITSIVDDREPGSMA-NVNDDLENVgGITYSPFEKNRPESLrFDEIVFLAI 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  915 MAPPRRKHTALRAMEVLPLalPSPPRQLSESEKNRMEDQEENTLRELR-LFLRDVTKRlatdkrFNIFSKPVDIEEVSDY 993
Cdd:COG5076   110 ESVTPESGLGSLLMAHLKT--SVKKRKTPKIEDELLYADNKAIAKFKKqLFLRDGRFL------SSIFLGLPSKREYPDY 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  994 LEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNpdkDPGDKIIRHrACTLKDTahaiiaaeLDPEFNKLC 1073
Cdd:COG5076   182 YEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYN---GPDSSVYVD-AKELEKY--------FLKLIEEIP 249

                         250
                  ....*....|.
gi 568977806 1074 EEIKEARIKRG 1084
Cdd:COG5076   250 EEMLELSIKPG 260
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 968-1040 2.58e-08

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 53.14  E-value: 2.58e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568977806  968 VTKRLATDKRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN-PDKD 1040
Cdd:cd05507    11 VYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNsSDHD 84
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 981-1039 3.03e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 53.06  E-value: 3.03e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568977806  981 FSKPVDiEEVSDYLEVIKEPMDLSTVITKIDKHN---YLTAKDFLQDIDLICSNALEYNPDK 1039
Cdd:cd05502    25 FHEPVS-PSVPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEED 85
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 958-1038 6.76e-08

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 51.92  E-value: 6.76e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  958 LRELRLFLRDVT----KRLATdkrfnIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNAL 1033
Cdd:cd05515     5 LWELYNAVKNYTdgrgRRLSL-----IFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNAC 79


                  ....*.
gi 568977806 1034 EYN-PD 1038
Cdd:cd05515    80 KYNePD 85
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 436-578 7.13e-08

AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400187 [Multi-domain]  Cd Length: 168  Bit Score: 53.74  E-value: 7.13e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   436 LFYGPPGTGKTLVARALANEcsQGDKKVAF-------FMRKGAdcLSKWVGESERQLR-----LLFDQAYLMRPSIIFFD 503
Cdd:pfam07724    7 LFLGPTGVGKTELAKALAEL--LFGDERALiridmseYMEEHS--VSRLIGAPPGYVGyeeggQLTEAVRRKPYSIVLID 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   504 EIdglapvrssrqDQIHSSIVSTLLALMDG---LDNRGE------IVVIGATNrLDSIDP--ALRRPGRFDREFLFNLPD 572
Cdd:pfam07724   83 EI-----------EKAHPGVQNDLLQILEGgtlTDKQGRtvdfknTLFIMTGN-FGSEKIsdASRLGDSPDYELLKEEVM 150


                   ....*.
gi 568977806   573 QRARKH 578
Cdd:pfam07724  151 DLLKKG 156
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 433-563 3.22e-07

ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 51.37  E-value: 3.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  433 RGCLFYGPPGTGKTLVARALANEC-------SQGDkkVAFFMRKGADCLSK---WVGESERQLrllfdqaylmrpsIIFF 502
Cdd:cd19512    23 RNILFYGPPGTGKTLFAKKLALHSgmdyaimTGGD--VAPMGREGVTAIHKvfdWANTSRRGL-------------LLFV 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568977806  503 DEIDGLAPVRSSrqDQIHSSIVSTLLALM--DGLDNRgEIVVIGATNRLDSIDPALRrpGRFD 563
Cdd:cd19512    88 DEADAFLRKRST--EKISEDLRAALNAFLyrTGEQSN-KFMLVLASNQPEQFDWAIN--DRID 145
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 981-1036 5.27e-07

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 49.30  E-value: 5.27e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  981 FSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05508    23 FLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYN 78
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
 431-564 5.75e-07

ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; however, its function remains unclear. The gene encoding YCF2 is the largest known plastid gene in angiosperms and has been used to predict phylogenetic relationships. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410913 [Multi-domain]  Cd Length: 161  Bit Score: 50.84  E-value: 5.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  431 PPRGCLFYGPPGTGKTLVARALA------------NECSqgDKKVAFFMRKGADCLSKWvGESERQLRLLFDQAYLMRPS 498
Cdd:cd19505    11 PSKGILLIGSIETGRSYLIKSLAansyvplirislNKLL--YNKPDFGNDDWIDGMLIL-KESLHRLNLQFELAKAMSPC 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568977806  499 IIFFDEIDGLApVRSSRQDQIHSSivSTLLALM-------DGLDNRGEIVVIGATNRLDSIDPALRRPGRFDR 564
Cdd:cd19505    88 IIWIPNIHELN-VNRSTQNLEEDP--KLLLGLLlnylsrdFEKSSTRNILVIASTHIPQKVDPALIAPNRLDT 157
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 950-1061 5.80e-07

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 49.16  E-value: 5.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  950 MEDQEENTLRELRLFlRDVTKRLatdkRFNIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLIC 1029
Cdd:cd05522     2 YEARIKNILKGLRKE-RDENGRL----LTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMF 76

                          90       100       110
                  ....*....|....*....|....*....|..
gi 568977806 1030 SNALEYNpdkDPGDKIIRhRACTLKDTAHAII 1061
Cdd:cd05522    77 ENAKLYN---ENDSQEYK-DAVLLEKEARLLA 104
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 992-1059 1.60e-06

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 47.82  E-value: 1.60e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  992 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNpdkDPGDKiIRHRACTLKDTAHA 1059
Cdd:cd05517    38 DYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN---EPGSQ-VYKDANAIKKIFTA 101
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 980-1056 2.99e-06

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 48.10  E-value: 2.99e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  980 IFSKPVDI-EEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPDKDPGDKIIRHRACTLKDT 1056
Cdd:cd05529    47 YFEYPVDLrAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRI 124
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 435-557 4.13e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 50.85  E-value: 4.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  435 CLFYGPPGTGKTLVARALANECsqgdkKVAFFMrkgadcLSKwVGESERQLRLLFDQAYLMRPS----IIFFDEIDGLAp 510
Cdd:PRK13342   39 MILWGPPGTGKTTLARIIAGAT-----DAPFEA------LSA-VTSGVKDLREVIEEARQRRSAgrrtILFIDEIHRFN- 105

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 568977806  511 vrSSRQDqihssivsTLLALMDgldnRGEIVVIGAT--NRLDSIDPALR 557
Cdd:PRK13342  106 --KAQQD--------ALLPHVE----DGTITLIGATteNPSFEVNPALL 140
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 989-1036 4.27e-06

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 47.04  E-value: 4.27e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568977806  989 EVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05516    36 ELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 959-1036 6.17e-06

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 46.28  E-value: 6.17e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568977806  959 RELRLFLRDVTKRLATDKRF-NIFSKPVDIEEVSDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYN 1036
Cdd:cd05518     4 RMLALFLYVLEYREGSGRRLcDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 982-1047 2.84e-05

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 44.34  E-value: 2.84e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568977806  982 SKPVDIEevsDYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPDKDPGDKIIR 1047
Cdd:cd05501    25 SKPYYIR---DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDDDFGQVGIT 87
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 992-1037 4.43e-05

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 43.87  E-value: 4.43e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568977806  992 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNP 1037
Cdd:cd05520    38 DYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
 960-1077 6.32e-05

Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99926 [Multi-domain]  Cd Length: 114  Bit Score: 43.59  E-value: 6.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  960 ELRLFLRdVTKRLATDKRFNIFSKPVD--IEEVSDYLEVIKEPMDLST---VITKIDKHNYLTAkdflqdidlicsnale 1034
Cdd:cd05494     4 ALERVLR-ELKRHRRNEDAWPFLEPVNppRRGAPDYRDVIKRPMSFGTkvnNIVETGARDLEDL---------------- 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 568977806 1035 YNPDKDPGDKIIRHRACTLKDTAHAIIAAELDPEFNKLCEEIK 1077
Cdd:cd05494    67 QIVQEDPADKQIDDEGRRSPSNIYAVEALEQLIVFQCKQVKGL 109
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 992-1079 8.75e-05

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 43.48  E-value: 8.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  992 DYLEVIKEPMDLSTVITKIDKHNYLTAKDFLQDIDLICSNALEYNPDKDPgdkiiRHRActlkdtahaiiAAELDPEFNK 1071
Cdd:cd05524    40 EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSP-----EHKD-----------ACKLWELFLS 103


                  ....*...
gi 568977806 1072 LCEEIKEA 1079
Cdd:cd05524   104 ARNEVLSG 111
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 436-546 1.07e-04

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 46.59  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  436 LFYGPPGTGKTLVARALANECsqgdkKVAFFMrkgadcLSKwVGESERQLRLLFDQAYLMR----PSIIFFDEIDglapv 511
Cdd:COG2256    53 ILWGPPGTGKTTLARLIANAT-----DAEFVA------LSA-VTSGVKDIREVIEEARERRaygrRTILFVDEIH----- 115

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 568977806  512 R--SSRQDqihssivsTLLALMDgldnRGEIVVIGAT 546
Cdd:COG2256   116 RfnKAQQD--------ALLPHVE----DGTITLIGAT 140
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
429-511 1.10e-04

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 45.54  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  429 IQPPRGCLFYGPPGTGKTLVARALANECSQGDKKVAFFmrkgadCLSKWVGE-----SERQLRLLFDQayLMRPSIIFFD 503
Cdd:COG1484    96 IERGENLILLGPPGTGKTHLAIALGHEACRAGYRVRFT------TAPDLVNElkearADGRLERLLKR--LAKVDLLILD 167


                  ....*...
gi 568977806  504 EIdGLAPV 511
Cdd:COG1484   168 EL-GYLPL 174
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
432-570 2.98e-04

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 43.75  E-value: 2.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  432 PRGC--LFYGPPGTGKTLVARALANE-CSQGDkKVAFFMrkgadclskwVGESERQLR-----LLFD-QAYLMRPSIIFF 502
Cdd:COG0467    18 PRGSstLLSGPPGTGKTTLALQFLAEgLRRGE-KGLYVS----------FEESPEQLLrraesLGLDlEEYIESGLLRII 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568977806  503 DeidglapVRSSRQDQIHSSIVSTLLALMDGLDNRgeIVVIgatnrlDSIDP---ALRRPGRFdREFLFNL 570
Cdd:COG0467    87 D-------LSPEELGLDLEELLARLREAVEEFGAK--RVVI------DSLSGlllALPDPERL-REFLHRL 141
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 757-893 3.32e-04

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 42.74  E-value: 3.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  757 YHQPTsyrPR-LLLSGERGSGQtSHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI- 834
Cdd:cd19507    26 YGLPT---PKgLLLVGIQGTGK-SLTAKAIAGVW-QLPLLRLDMGRLFGGLVGESESRLRQMIQTAEAIAPCVLWIDEIe 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568977806  835 ---------GDwwDAVSDTVRATFLTLLQDipSFSPIFLLSTSETMYSeLPEEVkcIFRIQYEEVLYI 893
Cdd:cd19507   101 kgfsnadskGD--SGTSSRVLGTFLTWLQE--KKKPVFVVATANNVQS-LPPEL--LRKGRFDEIFFV 161
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 435-511 1.22e-03

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 42.07  E-value: 1.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  435 CLFYGPPGTGKTLVARALANE-CSQGdKKVAFFmrKGADCLSKWvGESERQLRL--LFDQayLMRPSIIFFDEIdGLAPV 511
Cdd:NF038214   93 VLLLGPPGTGKTHLAIALGYAaCRQG-YRVRFT--TAADLVEQL-AQARADGRLgrLLRR--LARYDLLIIDEL-GYLPF 165
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 432-580 1.44e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 40.95  E-value: 1.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806   432 PRGCLFYGPPGTGKTLVARALANecSQGDKKVAFFMRKGADCLSK---WVGESERQLRLLFDQAYLMRPSIIFFDEIDGL 508
Cdd:pfam13191   24 PPSVLLTGEAGTGKTTLLRELLR--ALERDGGYFLRGKCDENLPYsplLEALTREGLLRQLLDELESSLLEAWRAALLEA 101

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568977806   509 APVRSSRQDQIHSSIVSTLLALMDGLDNRGEIVVIgATNRLDSIDPAlrrpgrfDREFLFNLPDQRARKHIL 580
Cdd:pfam13191  102 LAPVPELPGDLAERLLDLLLRLLDLLARGERPLVL-VLDDLQWADEA-------SLQLLAALLRLLESLPLL 165
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 992-1055 2.23e-03

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 39.23  E-value: 2.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568977806  992 DYLEVIKEPMDLSTVITKIDkhNYLTAKDFLQDIDLICSNALEYNPdkdPGDKIIRHrACTLKD 1055
Cdd:cd05521    39 DYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNT---KGSVIYKY-ALILEK 96
PRK04195 PRK04195
replication factor C large subunit; Provisional
 428-455 2.59e-03

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 42.22  E-value: 2.59e-03
                          10        20
                  ....*....|....*....|....*...
gi 568977806  428 KIQPPRGCLFYGPPGTGKTLVARALANE 455
Cdd:PRK04195   35 KGKPKKALLLYGPPGVGKTSLAHALAND 62
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
430-557 2.62e-03

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 41.76  E-value: 2.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  430 QPPRGCLFYGPPGTGKTLVARA----LANECSQGDKKVAF-------------FMRKGADCLSKWVGESERQLRllFDQA 492
Cdd:COG1474    49 ERPSNVLIYGPTGTGKTAVAKYvleeLEEEAEERGVDVRVvyvncrqastryrVLSRILEELGSGEDIPSTGLS--TDEL 126

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568977806  493 YLM---------RPSIIFFDEIDGLapvrssrQDQIHSSIVSTLLALMDGLDNRGeIVVIGATNRL---DSIDPALR 557
Cdd:COG1474   127 FDRlyealderdGVLVVVLDEIDYL-------VDDEGDDLLYQLLRANEELEGAR-VGVIGISNDLeflENLDPRVK 195
PRK08116 PRK08116
hypothetical protein; Validated
 420-465 3.07e-03

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 41.16  E-value: 3.07e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568977806  420 YPEIFEKFKIQPpRGCLFYGPPGTGKTLVARALANECSQGDKKVAF 465
Cdd:PRK08116  103 YVKKFEEMKKEN-VGLLLWGSVGTGKTYLAACIANELIEKGVPVIF 147
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 763-868 3.28e-03

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 39.96  E-value: 3.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  763 YRPRLLLSGERGSGQTsHLAPALLHTLeRFSVHRLDLPALYSVSAKTPEESCAQIFREARRTVPSIVYMPHI-------- 834
Cdd:cd19481    25 LPKGILLYGPPGTGKT-LLAKALAGEL-GLPLIVVKLSSLLSKYVGESEKNLRKIFERARRLAPCILFIDEIdaigrkrd 102

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568977806  835 GDWWDAVSDTVRATFLTLLQDIPSFSPIFLLSTS 868
Cdd:cd19481   103 SSGESGELRRVLNQLLTELDGVNSRSKVLVIAAT 136
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 436-552 3.55e-03

Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 39.85  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568977806  436 LFYGPPGTGKTLVARALANECSQGDKK-VAF----FMRKGADCLSK-----WVGESERQlrLLFDQAYLMRPSIIFFDEI 505
Cdd:cd19499    45 LFLGPTGVGKTELAKALAELLFGDEDNlIRIdmseYMEKHSVSRLIgappgYVGYTEGG--QLTEAVRRKPYSVVLLDEI 122

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568977806  506 dglapvrssrqDQIHSSIVSTLLALMD-G--LDNRGEIVVIGAT--------------NRLDSI 552
Cdd:cd19499   123 -----------EKAHPDVQNLLLQVLDdGrlTDSHGRTVDFKNTiiimtsnhfrpeflNRIDEI 175
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
435-455 8.45e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 40.11  E-value: 8.45e-03
                          10        20
                  ....*....|....*....|.
gi 568977806  435 CLFYGPPGTGKTLVARALANE 455
Cdd:PRK00080   54 VLLYGPPGLGKTTLANIIANE 74
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
436-460 9.19e-03

DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 40.17  E-value: 9.19e-03
                          10        20
                  ....*....|....*....|....*...
gi 568977806  436 LFYGPPGTGKTLVARALA---NeCSQGD 460
Cdd:COG2812    36 LFTGPRGVGKTTLARILAkalN-CENGP 62
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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