|
Name |
Accession |
Description |
Interval |
E-value |
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
129-572 |
3.81e-73 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 254.13 E-value: 3.81e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 129 RQYTSRaVIEAERRIVESARHTGGRTISEVRVGIA-IAEAAANELQLNAAQQSLVREMATSGRaVQLALAPAGTGKTTAM 207
Cdd:COG0507 80 RRYLTR-LLEAEQRLARRLRRLARPALDEADVEAAlAALEPRAGITLSDEQREAVALALTTRR-VSVLTGGAGTGKTTTL 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 208 QVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsknllngpwrpgrkkvrADTLAKLVWHAKHGDAPAWM 287
Cdd:COG0507 158 RALLAALEALGLRVALAAPTGKAAKRLSESTGIE--------------------------ARTIHRLLGLRPDSGRFRHN 211
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 288 EK--INSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAGGVLRDI--AHQIGAVTLSEVHRFRNPD 363
Cdd:COG0507 212 RDnpLTPADLLVVDEASMVDTRLMAALLEALPRAGARLILVGDPDQLPSVGAGAVLRDLieSGTVPVVELTEVYRQADDS 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 364 GSLNHAEaaatlALRDGDPSAI--AFYADRGRIHVGDLGACADQAYAAWAADRADGTDSVLIAPTRDLVAELNTRARNDR 441
Cdd:COG0507 292 RIIELAH-----AIREGDAPEAlnARYADVVFVEAEDAEEAAEAIVELYADRPAGGEDIQVLAPTNAGVDALNQAIREAL 366
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 442 lagQPDKEIGRVLTLADGTKVSAGDRIITRENDRRLRisrtnwVKNGDRWHVKNVNTD-GSLTVIHDKlGKTITLPADYV 520
Cdd:COG0507 367 ---NPAGELERELAEDGELELYVGDRVMFTRNDYDLG------VFNGDIGTVLSIDEDeGRLTVRFDG-REIVTYDPSEL 436
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 42558837 521 SKtVQLGYATTVHGAQGITTGTCHVVLTGD----EDRNLLYVALSRGKFANHLYLN 572
Cdd:COG0507 437 DQ-LELAYAITVHKSQGSTFDRVILVLPSEhsplLSRELLYTALTRARELLTLVGD 491
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
173-398 |
1.92e-60 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 205.49 E-value: 1.92e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 173 QLNAAQQSLVREMATSGRAVQLALAPAGTGKTTAMQVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsk 252
Cdd:pfam13604 1 TLNAEQAAAVRALLTSGDRVAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAKVLGEELGIP----------- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 253 nllngpwrpgrkkvrADTLAKLVWhakhgdAPAWMEKINSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQL 332
Cdd:pfam13604 70 ---------------ADTIAKLLH------RLGGRAGLDPGTLLIVDEAGMVGTRQMARLLKLAEDAGARVILVGDPRQL 128
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42558837 333 ASVAAGGVLRDI-AHQIGAVTLSEVHRFRNPdgslnhAEAAATLALRDGDP-SAIAFYADRGRIHVGD 398
Cdd:pfam13604 129 PSVEAGGAFRDLlAAGIGTAELTEIVRQRDP------WQRAASLALRDGDPaEALDALADRGRIHEGD 190
|
|
| DnaG |
COG0358 |
DNA primase (bacterial type) [Replication, recombination and repair]; |
1149-1517 |
4.74e-59 |
|
DNA primase (bacterial type) [Replication, recombination and repair];
Pssm-ID: 440127 [Multi-domain] Cd Length: 465 Bit Score: 211.53 E-value: 4.74e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1149 ERIHELNKQALAYFESCYPRS----WAPGYLRERlGTDLTDYPAYSVGYAPGGGRSLLRHLTDQGATLDELEQAGLISKR 1224
Cdd:COG0358 111 ERLYEALELAAKFYQEQLKNTpegkAARDYLKKR-GLSDETIERFGLGYAPDGWDALLKHLKKKGFSEEELVEAGLVIER 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1225 ERNDgtsyYRDFFRDRLVMPIRDPhdpTGEAIlGFVGRRnptkTDDDyaGPKYLNTRTTPIFTKGEALFGYTEARELLAG 1304
Cdd:COG0358 190 EDGG----YYDRFRGRIMFPIRDL---RGRVI-GFGGRV----LDDG--EPKYLNSPETPLFHKGRVLYGLDLARKAIRK 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1305 GALPVIVEGPMDALAItlgsngAAVGI----APMGTALTVNQIKLLRSHidlvngRDRIAVATDSDPAGWNSAQKAFWHL 1380
Cdd:COG0358 256 EDRVIVVEGYMDVIAL------HQAGIknavATLGTALTEEHIKLLKRY------TDEVILCFDGDAAGQKAALRALELL 323
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1381 TAADLDPTHLDLPDGLDPANLLETQGADAIAAAIENRSPLGDAMIDHLLRTAGhWSDTDVRQKLIHQTARILGSRGAENW 1460
Cdd:COG0358 324 LKDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEFLIERLLEGYD-LDTPEGRAALLREALPLLAKIPDPIL 402
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 42558837 1461 LTGF-ERLRVKLHLAPGILehqtvtESMDRDRNRpaYAQARIEEINDEVRKqtARNDP 1517
Cdd:COG0358 403 RELYlRELAERLGLDEEAL------DALARLKRR--ALEKRIEELKEELKE--ARGDE 450
|
|
| TraA_Ti |
TIGR02768 |
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ... |
131-570 |
1.22e-48 |
|
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Pssm-ID: 274289 [Multi-domain] Cd Length: 744 Bit Score: 186.94 E-value: 1.22e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 131 YTSRAVIEAERRIVESAR---HTGGRTISEVRVGIAIAEAAanelQLNAAQQSLVREMATSGRaVQLALAPAGTGKTTAM 207
Cdd:TIGR02768 311 FSTREMIRLEAQMARSAEalsQSQGHGVSPPIVDAAIDQHY----RLSEEQYEAVRHVTGSGD-IAVVVGRAGTGKSTML 385
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 208 QVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsknllngpwrpgrkkvrADTLAKLVWHAKHGdapawM 287
Cdd:TIGR02768 386 KAAREAWEAAGYRVIGAALSGKAAEGLQAESGIE--------------------------SRTLASLEYAWANG-----R 434
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 288 EKINSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAGGVLRDIAHQIGAVTLSEVHRFRnpdgsln 367
Cdd:TIGR02768 435 DLLSDKDVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQPIEAGAAFRAIAERIGYAELETIRRQR------- 507
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 368 HAEA-AATLALRDGD-PSAIAFYADRGRIHVGDLGACADQA-----YAAWAADRADGTdSVLIAPTRDLVAELNTRARND 440
Cdd:TIGR02768 508 EAWArQASLELARGDvEKALAAYRDHGHITIHDTREEAIEQvvadwKQDLREANPAGS-QIMLAHTRKDVRALNEAAREA 586
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 441 RLAGQPDKEIGRVLTLADGTKVSAGDRIITRENDRRLRisrtnwVKNGDRWHVKNVNtDGSLTVIHDKlGKTITLPADYV 520
Cdd:TIGR02768 587 LIERGELGESILFQTARGERKFAAGDRIVFLENNRDLG------VKNGMLGTVEEIE-DGRLVVQLDS-GELVIIPQAEY 658
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|
gi 42558837 521 sKTVQLGYATTVHGAQGITTGTCHVVLTGDEDRNLLYVALSRGKFANHLY 570
Cdd:TIGR02768 659 -DALDHGYATTIHKSQGVTVDRAFVLASKSMDRHLAYVAMTRHRESVQLY 707
|
|
| dnaG |
TIGR01391 |
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria ... |
1143-1452 |
4.33e-45 |
|
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (pfam01807) and a Toprim domain (pfam01751). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273595 [Multi-domain] Cd Length: 415 Bit Score: 169.32 E-value: 4.33e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1143 PNQIPAERIHELNKQALAYFESCY----PRSWAPGYLRERlGTDLTDYPAYSVGYAPGGGRSLLRHLTDQ-GATLDELEQ 1217
Cdd:TIGR01391 105 EQKSKRKKLYELLELAAKFFKNQLkhtpENRAALDYLQSR-GLSDETIDRFELGYAPNNWDFLFDFLQNKkGFDLELLAE 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1218 AGLISKRERNdgtSYYrDFFRDRLVMPIRDPHDptgeAILGFVGRrnptKTDDdyAGPKYLNTRTTPIFTKGEALFGYTE 1297
Cdd:TIGR01391 184 AGLLVKKENG---KYY-DRFRNRIMFPIHDPKG----RVVGFGGR----ALGD--EKPKYLNSPETPLFKKSELLYGLHK 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1298 ARELLAGGALPVIVEGPMDALAIT-LGSNGAavgIAPMGTALTVNQIKLLRSHIdlvngrDRIAVATDSDPAGWNSAQKA 1376
Cdd:TIGR01391 250 ARKEIRKEKELILVEGYMDVIALHqAGIKNA---VASLGTALTEEHIKLLKRYA------DEIILCFDGDKAGRKAALRA 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1377 FWHLTAADLDPTHLDLPDGLDPANLLETQGADAIAAAIENRSPLGDAMIDHLLRT-------------------AGHWSD 1437
Cdd:TIGR01391 321 IELLLPLGINVKVIKLPGGKDPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSNynldtpeekaklveellplIKKIPD 400
|
330
....*....|....*
gi 42558837 1438 TDVRQKLIHQTARIL 1452
Cdd:TIGR01391 401 PILRDYYLQKLAQLL 415
|
|
| DEXSc_RecD-like |
cd17933 |
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
173-357 |
1.35e-32 |
|
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350691 [Multi-domain] Cd Length: 155 Bit Score: 124.20 E-value: 1.35e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 173 QLNAAQQSLvrematsGRAVQLALAPAGTGKTTAMQVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsk 252
Cdd:cd17933 2 QKAAVRLVL-------RNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIE----------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 253 nllngpwrpgrkkvrADTLAKLVWHAKHGDAPA-WMEKINSKTLVLIDEAGMAATTDLAAAIDYItSRGGQVRLVGDDRQ 331
Cdd:cd17933 64 ---------------ASTIHRLLGINPGGGGFYyNEENPLDADLLIVDEASMVDTRLMAALLSAI-PAGARLILVGDPDQ 127
|
170 180
....*....|....*....|....*...
gi 42558837 332 LASVAAGGVLRDIA--HQIGAVTLSEVH 357
Cdd:cd17933 128 LPSVGAGNVLRDLIasKGVPTVELTEVF 155
|
|
| PRK13889 |
PRK13889 |
conjugal transfer relaxase TraA; Provisional |
127-562 |
1.07e-28 |
|
conjugal transfer relaxase TraA; Provisional
Pssm-ID: 237546 [Multi-domain] Cd Length: 988 Bit Score: 125.57 E-value: 1.07e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 127 GARQYTSRAVIEAERRIVESARHTGGRTISEVRVGIAI---AEAAANELQLNAAQQSLVREMaTSGRAVQLALAPAGTGK 203
Cdd:PRK13889 297 GEDRFTTRAMIETEQRLHRAAELMAERERHAVSDADREaalARAEARGLVLSGEQADALAHV-TDGRDLGVVVGYAGTGK 375
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 204 TTAMQVLTRAWQDSGGTVIGLAPSAVAAQelgasiNLENPDTNTAGTSKNLLNGpWRPGRkkvraDTLaklvwhakhgda 283
Cdd:PRK13889 376 SAMLGVAREAWEAAGYEVRGAALSGIAAE------NLEGGSGIASRTIASLEHG-WGQGR-----DLL------------ 431
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 284 pawmekiNSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAGGVLRDIAHQIGAVTLSEVHRFRnpd 363
Cdd:PRK13889 432 -------TSRDVLVIDEAGMVGTRQLERVLSHAADAGAKVVLVGDPQQLQAIEAGAAFRSIHERHGGAEIGEVRRQR--- 501
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 364 gslNHAEAAATLAL---RDGDpsAIAFYADRGRIHVGDlgacadqAYAAWAADRADGTD----------SVLIAPTRDLV 430
Cdd:PRK13889 502 ---EDWQRDATRDLatgRTGE--ALDAYEAHGMVHAAA-------TREQARADLIDRWDrdrqaapdrsRIILTHTNDEV 569
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 431 AELNTRARND-RLAGQPDKEIGrvLTLADGTKVSA-GDRIITRENDRRLRisrtnwVKNGDRWHVKNVNTDgSLTVIHDK 508
Cdd:PRK13889 570 RALNEAARERmRAAGDLGDDVR--VTVERGERSFAsGDRVMFLQNERGLG------VKNGTLGTIEQVSAQ-SMSVRLDD 640
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 42558837 509 lGKTITLP-ADYvsKTVQLGYATTVHGAQGITTGTCHVVLTGDEDRNLLYVALSR 562
Cdd:PRK13889 641 -GRSVAFDlKDY--DRIDHGYAATIHKAQGMTVDRTHVLATPGMDAHSSYVALSR 692
|
|
| Toprim_N |
pfam08275 |
DNA primase catalytic core, N-terminal domain; |
1174-1299 |
8.18e-28 |
|
DNA primase catalytic core, N-terminal domain;
Pssm-ID: 429892 [Multi-domain] Cd Length: 128 Bit Score: 109.53 E-value: 8.18e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1174 YLRERlGTDLTDYPAYSVGYAPGGGRSLLRHLTDQGATLDELEQAGLISKRERNDgtsyYRDFFRDRLVMPIRDPHdptG 1253
Cdd:pfam08275 17 YLKSR-GLSDETIERFQIGYAPDGWDNLLKFLKKKGFSEEELLEAGLLSKNEDGR----YYDRFRNRIMFPIKDAR---G 88
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 42558837 1254 EaILGFVGRRnptkTDDDyAGPKYLNTRTTPIFTKGEALFGYTEAR 1299
Cdd:pfam08275 89 R-VVGFGGRA----LDDD-KPPKYLNSPETPLFKKSKLLYGLDEAK 128
|
|
| TOPRIM_DnaG_primases |
cd03364 |
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ... |
1309-1392 |
4.26e-18 |
|
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Pssm-ID: 173784 [Multi-domain] Cd Length: 79 Bit Score: 80.25 E-value: 4.26e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1309 VIVEGPMDALAitLGSNGAAVGIAPMGTALTVNQIKLLRSHIdlvngrDRIAVATDSDPAGWNSAQKAFWHLTAADLDPT 1388
Cdd:cd03364 4 ILVEGYMDVIA--LHQAGIKNVVASLGTALTEEQAELLKRLA------KEVILAFDGDEAGQKAALRALELLLKLGLNVR 75
|
....
gi 42558837 1389 HLDL 1392
Cdd:cd03364 76 VLTL 79
|
|
| TOPRIM |
smart00493 |
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins; |
1309-1380 |
2.98e-08 |
|
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
Pssm-ID: 214695 [Multi-domain] Cd Length: 75 Bit Score: 52.26 E-value: 2.98e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42558837 1309 VIVEGPMDALAIT-LGSNGAAVgIAPMGTALTVNQIKLLRSHIDlvngRDRIAVATDSDPAGWNSAQKAFWHL 1380
Cdd:smart00493 4 IIVEGPADAIALEkAGGKRGNV-VALGGHLLSKEQIKLLKKLAK----KAEVILATDPDREGEAIAWELAELL 71
|
|
| PRK14712 |
PRK14712 |
conjugal transfer nickase/helicase TraI; Provisional |
431-878 |
7.72e-06 |
|
conjugal transfer nickase/helicase TraI; Provisional
Pssm-ID: 237796 [Multi-domain] Cd Length: 1623 Bit Score: 51.02 E-value: 7.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 431 AELNTRARNDRLAGQPdkeiGRVLTLADGTKVSAGDRIITRENDRRlrisrTNWVKNgDRWHVKNVNTDgSLTVIHDKLG 510
Cdd:PRK14712 1179 AEGNTRLISPREAVAE----GVTLYTPDTIRVGTGDRIRFTKSDRE-----RGYVAN-SVWTVTAVSGD-SVTLSDGQQT 1247
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 511 KTITLPADYVSKTVQLGYATTVHGAQGiTTGTCHVVLTGDE-DRNLL------YVALSRGKFANHLYL-----------N 572
Cdd:PRK14712 1248 RVIRPGQERAEQHIDLAYAITAHGAQG-ASETFAIALEGTEgNRKLMagfesaYVALSRMKQHVQVYTdnrqgwtdainN 1326
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 573 VASDGDPHNLIRPEALIPPTALDRITEMLRRDGSPVSATTALRDQTNPHqllGDMAARYHDAVTAGAENLIGPVGMDKID 652
Cdd:PRK14712 1327 AVQKGTAHDVFEPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAG---GDSPARFIAPGRKYPQPYVALPAFDRNG 1403
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 653 AHAEALLTGLTEapawptlrshlalialDDHSPLKLLTAAVGVGSLADARDPAAVLDARIDDLVADLNA----ARPHDPD 728
Cdd:PRK14712 1404 KSAGIWLNPLTT----------------DDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQdgvrIARDNPD 1467
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 729 TPPATDAPLPWLPGIPARLADAHDWGPFAGayhqlvreqiDAVRDAARNWTGATAPAWAQPFLED---EDTELRADLAVW 805
Cdd:PRK14712 1468 SGVVVRIAGEGRPWNPGAITGGRVWGDIPD----------NSVQPGAGNGEPVTAEVLAQRQAEEairRETERRADEIVR 1537
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42558837 806 RAVAGTDDndlrPTGDRTIGAPG--AYQAKLNRAVREARPSYPFSQRTWYQVLPETVRADPWITPLCQRLARLER 878
Cdd:PRK14712 1538 KMAENKPD----LPDGKTEQAVReiAGQERDRAAITEREAALPESVLREPQRVREAVREVARENLLQERLQQMER 1608
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
129-572 |
3.81e-73 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 254.13 E-value: 3.81e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 129 RQYTSRaVIEAERRIVESARHTGGRTISEVRVGIA-IAEAAANELQLNAAQQSLVREMATSGRaVQLALAPAGTGKTTAM 207
Cdd:COG0507 80 RRYLTR-LLEAEQRLARRLRRLARPALDEADVEAAlAALEPRAGITLSDEQREAVALALTTRR-VSVLTGGAGTGKTTTL 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 208 QVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsknllngpwrpgrkkvrADTLAKLVWHAKHGDAPAWM 287
Cdd:COG0507 158 RALLAALEALGLRVALAAPTGKAAKRLSESTGIE--------------------------ARTIHRLLGLRPDSGRFRHN 211
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 288 EK--INSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAGGVLRDI--AHQIGAVTLSEVHRFRNPD 363
Cdd:COG0507 212 RDnpLTPADLLVVDEASMVDTRLMAALLEALPRAGARLILVGDPDQLPSVGAGAVLRDLieSGTVPVVELTEVYRQADDS 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 364 GSLNHAEaaatlALRDGDPSAI--AFYADRGRIHVGDLGACADQAYAAWAADRADGTDSVLIAPTRDLVAELNTRARNDR 441
Cdd:COG0507 292 RIIELAH-----AIREGDAPEAlnARYADVVFVEAEDAEEAAEAIVELYADRPAGGEDIQVLAPTNAGVDALNQAIREAL 366
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 442 lagQPDKEIGRVLTLADGTKVSAGDRIITRENDRRLRisrtnwVKNGDRWHVKNVNTD-GSLTVIHDKlGKTITLPADYV 520
Cdd:COG0507 367 ---NPAGELERELAEDGELELYVGDRVMFTRNDYDLG------VFNGDIGTVLSIDEDeGRLTVRFDG-REIVTYDPSEL 436
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 42558837 521 SKtVQLGYATTVHGAQGITTGTCHVVLTGD----EDRNLLYVALSRGKFANHLYLN 572
Cdd:COG0507 437 DQ-LELAYAITVHKSQGSTFDRVILVLPSEhsplLSRELLYTALTRARELLTLVGD 491
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
173-398 |
1.92e-60 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 205.49 E-value: 1.92e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 173 QLNAAQQSLVREMATSGRAVQLALAPAGTGKTTAMQVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsk 252
Cdd:pfam13604 1 TLNAEQAAAVRALLTSGDRVAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAKVLGEELGIP----------- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 253 nllngpwrpgrkkvrADTLAKLVWhakhgdAPAWMEKINSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQL 332
Cdd:pfam13604 70 ---------------ADTIAKLLH------RLGGRAGLDPGTLLIVDEAGMVGTRQMARLLKLAEDAGARVILVGDPRQL 128
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42558837 333 ASVAAGGVLRDI-AHQIGAVTLSEVHRFRNPdgslnhAEAAATLALRDGDP-SAIAFYADRGRIHVGD 398
Cdd:pfam13604 129 PSVEAGGAFRDLlAAGIGTAELTEIVRQRDP------WQRAASLALRDGDPaEALDALADRGRIHEGD 190
|
|
| DnaG |
COG0358 |
DNA primase (bacterial type) [Replication, recombination and repair]; |
1149-1517 |
4.74e-59 |
|
DNA primase (bacterial type) [Replication, recombination and repair];
Pssm-ID: 440127 [Multi-domain] Cd Length: 465 Bit Score: 211.53 E-value: 4.74e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1149 ERIHELNKQALAYFESCYPRS----WAPGYLRERlGTDLTDYPAYSVGYAPGGGRSLLRHLTDQGATLDELEQAGLISKR 1224
Cdd:COG0358 111 ERLYEALELAAKFYQEQLKNTpegkAARDYLKKR-GLSDETIERFGLGYAPDGWDALLKHLKKKGFSEEELVEAGLVIER 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1225 ERNDgtsyYRDFFRDRLVMPIRDPhdpTGEAIlGFVGRRnptkTDDDyaGPKYLNTRTTPIFTKGEALFGYTEARELLAG 1304
Cdd:COG0358 190 EDGG----YYDRFRGRIMFPIRDL---RGRVI-GFGGRV----LDDG--EPKYLNSPETPLFHKGRVLYGLDLARKAIRK 255
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1305 GALPVIVEGPMDALAItlgsngAAVGI----APMGTALTVNQIKLLRSHidlvngRDRIAVATDSDPAGWNSAQKAFWHL 1380
Cdd:COG0358 256 EDRVIVVEGYMDVIAL------HQAGIknavATLGTALTEEHIKLLKRY------TDEVILCFDGDAAGQKAALRALELL 323
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1381 TAADLDPTHLDLPDGLDPANLLETQGADAIAAAIENRSPLGDAMIDHLLRTAGhWSDTDVRQKLIHQTARILGSRGAENW 1460
Cdd:COG0358 324 LKDGLQVRVLFLPDGEDPDELIRKEGAEAFRELLENAKPLIEFLIERLLEGYD-LDTPEGRAALLREALPLLAKIPDPIL 402
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 42558837 1461 LTGF-ERLRVKLHLAPGILehqtvtESMDRDRNRpaYAQARIEEINDEVRKqtARNDP 1517
Cdd:COG0358 403 RELYlRELAERLGLDEEAL------DALARLKRR--ALEKRIEELKEELKE--ARGDE 450
|
|
| TraA_Ti |
TIGR02768 |
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ... |
131-570 |
1.22e-48 |
|
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Pssm-ID: 274289 [Multi-domain] Cd Length: 744 Bit Score: 186.94 E-value: 1.22e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 131 YTSRAVIEAERRIVESAR---HTGGRTISEVRVGIAIAEAAanelQLNAAQQSLVREMATSGRaVQLALAPAGTGKTTAM 207
Cdd:TIGR02768 311 FSTREMIRLEAQMARSAEalsQSQGHGVSPPIVDAAIDQHY----RLSEEQYEAVRHVTGSGD-IAVVVGRAGTGKSTML 385
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 208 QVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsknllngpwrpgrkkvrADTLAKLVWHAKHGdapawM 287
Cdd:TIGR02768 386 KAAREAWEAAGYRVIGAALSGKAAEGLQAESGIE--------------------------SRTLASLEYAWANG-----R 434
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 288 EKINSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAGGVLRDIAHQIGAVTLSEVHRFRnpdgsln 367
Cdd:TIGR02768 435 DLLSDKDVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQPIEAGAAFRAIAERIGYAELETIRRQR------- 507
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 368 HAEA-AATLALRDGD-PSAIAFYADRGRIHVGDLGACADQA-----YAAWAADRADGTdSVLIAPTRDLVAELNTRARND 440
Cdd:TIGR02768 508 EAWArQASLELARGDvEKALAAYRDHGHITIHDTREEAIEQvvadwKQDLREANPAGS-QIMLAHTRKDVRALNEAAREA 586
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 441 RLAGQPDKEIGRVLTLADGTKVSAGDRIITRENDRRLRisrtnwVKNGDRWHVKNVNtDGSLTVIHDKlGKTITLPADYV 520
Cdd:TIGR02768 587 LIERGELGESILFQTARGERKFAAGDRIVFLENNRDLG------VKNGMLGTVEEIE-DGRLVVQLDS-GELVIIPQAEY 658
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|
gi 42558837 521 sKTVQLGYATTVHGAQGITTGTCHVVLTGDEDRNLLYVALSRGKFANHLY 570
Cdd:TIGR02768 659 -DALDHGYATTIHKSQGVTVDRAFVLASKSMDRHLAYVAMTRHRESVQLY 707
|
|
| dnaG |
TIGR01391 |
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria ... |
1143-1452 |
4.33e-45 |
|
DNA primase, catalytic core; Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (pfam01807) and a Toprim domain (pfam01751). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273595 [Multi-domain] Cd Length: 415 Bit Score: 169.32 E-value: 4.33e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1143 PNQIPAERIHELNKQALAYFESCY----PRSWAPGYLRERlGTDLTDYPAYSVGYAPGGGRSLLRHLTDQ-GATLDELEQ 1217
Cdd:TIGR01391 105 EQKSKRKKLYELLELAAKFFKNQLkhtpENRAALDYLQSR-GLSDETIDRFELGYAPNNWDFLFDFLQNKkGFDLELLAE 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1218 AGLISKRERNdgtSYYrDFFRDRLVMPIRDPHDptgeAILGFVGRrnptKTDDdyAGPKYLNTRTTPIFTKGEALFGYTE 1297
Cdd:TIGR01391 184 AGLLVKKENG---KYY-DRFRNRIMFPIHDPKG----RVVGFGGR----ALGD--EKPKYLNSPETPLFKKSELLYGLHK 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1298 ARELLAGGALPVIVEGPMDALAIT-LGSNGAavgIAPMGTALTVNQIKLLRSHIdlvngrDRIAVATDSDPAGWNSAQKA 1376
Cdd:TIGR01391 250 ARKEIRKEKELILVEGYMDVIALHqAGIKNA---VASLGTALTEEHIKLLKRYA------DEIILCFDGDKAGRKAALRA 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1377 FWHLTAADLDPTHLDLPDGLDPANLLETQGADAIAAAIENRSPLGDAMIDHLLRT-------------------AGHWSD 1437
Cdd:TIGR01391 321 IELLLPLGINVKVIKLPGGKDPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSNynldtpeekaklveellplIKKIPD 400
|
330
....*....|....*
gi 42558837 1438 TDVRQKLIHQTARIL 1452
Cdd:TIGR01391 401 PILRDYYLQKLAQLL 415
|
|
| DEXSc_RecD-like |
cd17933 |
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
173-357 |
1.35e-32 |
|
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350691 [Multi-domain] Cd Length: 155 Bit Score: 124.20 E-value: 1.35e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 173 QLNAAQQSLvrematsGRAVQLALAPAGTGKTTAMQVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpdtntagtsk 252
Cdd:cd17933 2 QKAAVRLVL-------RNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSESTGIE----------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 253 nllngpwrpgrkkvrADTLAKLVWHAKHGDAPA-WMEKINSKTLVLIDEAGMAATTDLAAAIDYItSRGGQVRLVGDDRQ 331
Cdd:cd17933 64 ---------------ASTIHRLLGINPGGGGFYyNEENPLDADLLIVDEASMVDTRLMAALLSAI-PAGARLILVGDPDQ 127
|
170 180
....*....|....*....|....*...
gi 42558837 332 LASVAAGGVLRDIA--HQIGAVTLSEVH 357
Cdd:cd17933 128 LPSVGAGNVLRDLIasKGVPTVELTEVF 155
|
|
| PRK13889 |
PRK13889 |
conjugal transfer relaxase TraA; Provisional |
127-562 |
1.07e-28 |
|
conjugal transfer relaxase TraA; Provisional
Pssm-ID: 237546 [Multi-domain] Cd Length: 988 Bit Score: 125.57 E-value: 1.07e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 127 GARQYTSRAVIEAERRIVESARHTGGRTISEVRVGIAI---AEAAANELQLNAAQQSLVREMaTSGRAVQLALAPAGTGK 203
Cdd:PRK13889 297 GEDRFTTRAMIETEQRLHRAAELMAERERHAVSDADREaalARAEARGLVLSGEQADALAHV-TDGRDLGVVVGYAGTGK 375
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 204 TTAMQVLTRAWQDSGGTVIGLAPSAVAAQelgasiNLENPDTNTAGTSKNLLNGpWRPGRkkvraDTLaklvwhakhgda 283
Cdd:PRK13889 376 SAMLGVAREAWEAAGYEVRGAALSGIAAE------NLEGGSGIASRTIASLEHG-WGQGR-----DLL------------ 431
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 284 pawmekiNSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAGGVLRDIAHQIGAVTLSEVHRFRnpd 363
Cdd:PRK13889 432 -------TSRDVLVIDEAGMVGTRQLERVLSHAADAGAKVVLVGDPQQLQAIEAGAAFRSIHERHGGAEIGEVRRQR--- 501
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 364 gslNHAEAAATLAL---RDGDpsAIAFYADRGRIHVGDlgacadqAYAAWAADRADGTD----------SVLIAPTRDLV 430
Cdd:PRK13889 502 ---EDWQRDATRDLatgRTGE--ALDAYEAHGMVHAAA-------TREQARADLIDRWDrdrqaapdrsRIILTHTNDEV 569
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 431 AELNTRARND-RLAGQPDKEIGrvLTLADGTKVSA-GDRIITRENDRRLRisrtnwVKNGDRWHVKNVNTDgSLTVIHDK 508
Cdd:PRK13889 570 RALNEAARERmRAAGDLGDDVR--VTVERGERSFAsGDRVMFLQNERGLG------VKNGTLGTIEQVSAQ-SMSVRLDD 640
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 42558837 509 lGKTITLP-ADYvsKTVQLGYATTVHGAQGITTGTCHVVLTGDEDRNLLYVALSR 562
Cdd:PRK13889 641 -GRSVAFDlKDY--DRIDHGYAATIHKAQGMTVDRTHVLATPGMDAHSSYVALSR 692
|
|
| Toprim_N |
pfam08275 |
DNA primase catalytic core, N-terminal domain; |
1174-1299 |
8.18e-28 |
|
DNA primase catalytic core, N-terminal domain;
Pssm-ID: 429892 [Multi-domain] Cd Length: 128 Bit Score: 109.53 E-value: 8.18e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1174 YLRERlGTDLTDYPAYSVGYAPGGGRSLLRHLTDQGATLDELEQAGLISKRERNDgtsyYRDFFRDRLVMPIRDPHdptG 1253
Cdd:pfam08275 17 YLKSR-GLSDETIERFQIGYAPDGWDNLLKFLKKKGFSEEELLEAGLLSKNEDGR----YYDRFRNRIMFPIKDAR---G 88
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 42558837 1254 EaILGFVGRRnptkTDDDyAGPKYLNTRTTPIFTKGEALFGYTEAR 1299
Cdd:pfam08275 89 R-VVGFGGRA----LDDD-KPPKYLNSPETPLFKKSKLLYGLDEAK 128
|
|
| PRK13826 |
PRK13826 |
Dtr system oriT relaxase; Provisional |
130-562 |
3.36e-23 |
|
Dtr system oriT relaxase; Provisional
Pssm-ID: 237524 [Multi-domain] Cd Length: 1102 Bit Score: 107.56 E-value: 3.36e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 130 QYTSRAVIEAERRIVESARHTGGRTISEVRVGIAIAEAAANElQLNAAQQSLVREMATSGRAVQLaLAPAGTGKTTAMQV 209
Cdd:PRK13826 339 RYTTRAMIRLEAEMARRAIWLSGRSSHGVREAVLAATFARHA-RLSDEQKTAIEHVAGPARIAAV-VGRAGAGKTTMMKA 416
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 210 LTRAWQDSGGTVIGLAPSAVAAQELgasinlenpdTNTAGTSKNLLNG---PWRPGRKKvradtlaklvwhakhgdapaw 286
Cdd:PRK13826 417 AREAWEAAGYRVVGGALAGKAAEGL----------EKEAGIQSRTLSSwelRWNQGRDQ--------------------- 465
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 287 mekINSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAGGVLRDIAHQIGAVTLSEVHRFRNP---D 363
Cdd:PRK13826 466 ---LDNKTVFVLDEAGMVASRQMALFVEAVTRAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQwmrD 542
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 364 GSLNHAeaaatlalRDGDPSAIAFYADRGRIHVGDLGACADQAYAAWAADRADGTDSVLI-APTRDLVAELNTRARnDRL 442
Cdd:PRK13826 543 ASLDLA--------RGNVGKALDAYRANGRVIGSRLKAEAVESLIADWNRDYDPTKTTLIlAHLRRDVRMLNEMAR-AKL 613
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 443 AGQPDKEIGRVLTLADGTK-VSAGDRIITRENDRRLRisrtnwVKNGDRWHVKNVNTDGSLTVIHDKLGKTITLPADYVS 521
Cdd:PRK13826 614 VERGIVGEGHAFRTADGERrFAAGDQIVFLKNEGSLG------VKNGMIGKVVEAAPNRIVAEIGEGEHRRQVTVEQRFY 687
|
410 420 430 440
....*....|....*....|....*....|....*....|.
gi 42558837 522 KTVQLGYATTVHGAQGITTGTCHVVLTGDEDRNLLYVALSR 562
Cdd:PRK13826 688 NNLDHGYATTIHKSQGATVDRVKVLASLSLDRHLTYVAMTR 728
|
|
| TOPRIM_DnaG_primases |
cd03364 |
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ... |
1309-1392 |
4.26e-18 |
|
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Pssm-ID: 173784 [Multi-domain] Cd Length: 79 Bit Score: 80.25 E-value: 4.26e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1309 VIVEGPMDALAitLGSNGAAVGIAPMGTALTVNQIKLLRSHIdlvngrDRIAVATDSDPAGWNSAQKAFWHLTAADLDPT 1388
Cdd:cd03364 4 ILVEGYMDVIA--LHQAGIKNVVASLGTALTEEQAELLKRLA------KEVILAFDGDEAGQKAALRALELLLKLGLNVR 75
|
....
gi 42558837 1389 HLDL 1392
Cdd:cd03364 76 VLTL 79
|
|
| Toprim_2 |
pfam13155 |
Toprim-like; This is a family or Toprim-like proteins. |
1309-1398 |
2.94e-12 |
|
Toprim-like; This is a family or Toprim-like proteins.
Pssm-ID: 463793 [Multi-domain] Cd Length: 88 Bit Score: 63.73 E-value: 2.94e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1309 VIVEGPMDALA-ITLGSNGAAVgIAPMGTALTVNQIKLLRSHIDlvngrdRIAVATDSDPAGWNSAQKAFWHLTAADLDP 1387
Cdd:pfam13155 1 VVFEGYIDALSlAQAGIKNVLY-VATLGTALTEAQIKLLKRYPK------EVILAFDNDEAGRKAAKRLAELLKEAGVDV 73
|
90
....*....|.
gi 42558837 1388 THLDLPDGLDP 1398
Cdd:pfam13155 74 KIRLLPDGKDW 84
|
|
| SF1_C_RecD |
cd18809 |
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
526-570 |
1.09e-11 |
|
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350196 [Multi-domain] Cd Length: 80 Bit Score: 61.81 E-value: 1.09e-11
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 42558837 526 LGYATTVHGAQGITTGTCHVVLTGD---EDRNLLYVALSRGKFANHLY 570
Cdd:cd18809 32 QAYAMTIHKSQGSEFDRVIVVLPTShpmLSRGLLYTALTRARKLLTLV 79
|
|
| TOPRIM_primases |
cd01029 |
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
1309-1384 |
1.35e-10 |
|
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Pssm-ID: 173779 [Multi-domain] Cd Length: 79 Bit Score: 58.82 E-value: 1.35e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 42558837 1309 VIVEGPMDALAITlgSNGAAVGIAPMGTALTVNQIKLLRSHidlvngRDRIAVATDSDPAGWNSAQKAFWHLTAAD 1384
Cdd:cd01029 4 IIVEGYMDVLALH--QAGIKNVVAALGTANTEEQLRLLKRF------ARTVILAFDNDEAGKKAAARALELLLALG 71
|
|
| TraI_TIGR |
TIGR02760 |
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ... |
48-385 |
3.48e-10 |
|
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Pssm-ID: 274285 [Multi-domain] Cd Length: 1960 Bit Score: 65.31 E-value: 3.48e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 48 QRQARAHGIRLTELDDAVDRVVATAIREHSIAFNDPDP-----------LTRETTAAEQDVTIPA---PLQRTDRPAEGG 113
Cdd:TIGR02760 873 QKQHLPDAVTTNNTDKSLEMDISDTLHALEAKAKDGKNsialqyalekvSEKEAAFKQKELVTEAyvfAFEETGFAIKAA 952
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 114 VDAEEVVSA---YSLAGAR-----QYTSRAVIEAERRIVE-SARHTGGRTISEVRVGIAIAEAAANELQ-LNAAQQSLVR 183
Cdd:TIGR02760 953 EIAAALKNRpklYRLLSAEygdgtRWTTRAALRTETSILLhILPGKETVTPLATRAQVFLNLELLERLThGQKQAIHLII 1032
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 184 EMATSGRAVQlalAPAGTGKTTAMQVLTRAWQDSGG----TVIGLAPSAVAAQELGAsinlenpdtntagtsknllngpw 259
Cdd:TIGR02760 1033 STKDRFVAVQ---GLAGVGKTTMLESRYKPVLQAFEseqlQVIGLAPTHEAVGELKS----------------------- 1086
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 260 rpgrKKVRADTLAKLVWHAKHGDAPAWMEKinsKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAG- 338
Cdd:TIGR02760 1087 ----AGVQAQTLDSFLTDISLYRNSGGDFR---NTLFILDESSMVSNFQLTHATELVQKSGSRAVSLGDIAQLQSLAAGk 1159
|
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 42558837 339 -GVLRDIAHQIGAVTLSEVHRfRNPDGSLnhaEAAATLALRDGDPSAI 385
Cdd:TIGR02760 1160 pFELAITFDIIDTAIMKEIVR-QNNSAEL---KAAHNSLDKRSNPKAL 1203
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
200-570 |
5.39e-10 |
|
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 64.01 E-value: 5.39e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 200 GTGKTTAMQVLTRAWQD----SGGTVIGL-APSAVAAQELGASINLENpdtntagtsKNLLNGPWRPGRKKVRADTLAKL 274
Cdd:TIGR01447 169 GTGKTTTVARLLLALVKqspkQGKLRIALaAPTGKAAARLAESLRKAV---------KNLAAAEALIAALPSEAVTIHRL 239
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 275 VwHAKHGDAPAWMEKINSKTL--VLIDEAGMAATTDLAAAIDYItSRGGQVRLVGDDRQLASVAAGGVLRDI-------- 344
Cdd:TIGR01447 240 L-GIKPDTKRFRHHERNPLPLdvLVVDEASMVDLPLMAKLLKAL-PPNTKLILLGDKNQLPSVEAGAVLGDLcelasigk 317
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 345 ------AHQIGAVT----------LSEVHRFRNPDG------SLNHAEAAATL-ALRDGDPSAIAFYADRGRIHVGDLGA 401
Cdd:TIGR01447 318 silyalCKKINSKTrnplsdnvcfLKTSHRFGKDSGigqlakAINSGDIEAVLnNLRSGQLIEFEFLNSKEDAIERLKNL 397
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 402 CADQAYAAWAADRADGTDSVLIA--------PTRD---LVAELNTRARNdRLAGQPDKEigrvltlaDGTKVSAGDRIIT 470
Cdd:TIGR01447 398 YVKYRTFLQKLAALSDAKEILETfdrlrlltALRDgpfGVLGLNRRIEQ-ELQEKYFDP--------DEEGWYIGRPIMV 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 471 RENDRRLRISrtnwvkNGDRwHVKNVNTDGSLTV-IHDKLGKTITLPADYVSktVQLGYATTVHGAQGITTGTCHVVLTG 549
Cdd:TIGR01447 469 TENDYTLGLF------NGDI-GVLLRDPDGILTVwFHFADGSKAVLPSRLPN--YETAFAMTVHKSQGSEFDHVILILPN 539
|
410 420
....*....|....*....|....*
gi 42558837 550 DE----DRNLLYVALSRGKFANHLY 570
Cdd:TIGR01447 540 GNspvlTRELLYTGITRAKDQLSVW 564
|
|
| PRK13709 |
PRK13709 |
conjugal transfer nickase/helicase TraI; Provisional |
199-631 |
5.48e-10 |
|
conjugal transfer nickase/helicase TraI; Provisional
Pssm-ID: 237478 [Multi-domain] Cd Length: 1747 Bit Score: 64.43 E-value: 5.48e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 199 AGTGKTTAMQVLTRAW----QDSGGTVIGLAPSAVAAQELgasinlenpdtNTAGtsknllngpwrpgrkkVRADTLAKL 274
Cdd:PRK13709 993 AGVGKTTQFRAVMSAVntlpESERPRVVGLGPTHRAVGEM-----------RSAG----------------VDAQTLASF 1045
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 275 VwhAKHGDAPAWMEKIN-SKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASVAAG--------------G 339
Cdd:PRK13709 1046 L--HDTQLQQRSGETPDfSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVSSGDTDQLQAIAPGqpfrlmqtrsaadvA 1123
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 340 VLRDIAHQ----------------------IGAVTL-------------SEVHRFRNP-DGSLNHAEAAATLALRDGDPS 383
Cdd:PRK13709 1124 IMKEIVRQtpelreavyslinrdveralsgIESVKPsqvprqegawapeSSVTEFSHPqEAKLAEAQQKAMLAFPDVPMT 1203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 384 AIAF----YADRGR----------------------IH-----VGDLGACADQAYAAWAADRADGTDSVLIA--PTRDLV 430
Cdd:PRK13709 1204 LYEAivrdYTGRTPeareqtliithlnedrrvlnsmIHdarekAGELGKEQVTVPVLDTANIRDGELRRLSTweAHRGAL 1283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 431 AELNTR-------ARNDRLAGQPDKEiGRVLTL------ADGTKVSAGDRIITRENDRrLRISRTN----WVKNgDRWHV 493
Cdd:PRK13709 1284 ALVDNVyhriagiDKDDGLITLRDAE-GNTRLIspreavAEGVTLYTPDTIRVGTGDR-MRFTKSDrergYVAN-SVWTV 1360
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 494 KNVNTDGslTVIHDKLG-KTITLPADYVSKTVQLGYATTVHGAQGiTTGTCHVVLTGDED-RNLL------YVALSRGKF 565
Cdd:PRK13709 1361 TAVSGDS--VTLSDGQQtRVIRPGQERAEQHIDLAYAITAHGAQG-ASETYAIALEGTEGgRKQMagfesaYVALSRMKQ 1437
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42558837 566 ANHLYL-----------NVASDGDPHNLIRPEALIPPTALDRITEMlrrdGSPVSATTALRDQTNPHQL-LGDMAARY 631
Cdd:PRK13709 1438 HVQVYTdnrqgwtdainNAVQKGTAHDVLEPKPDREVMNAERLFST----ARELRDTAAGRAVLRQAGLaGGDSPARF 1511
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
1309-1386 |
1.17e-08 |
|
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173773 [Multi-domain] Cd Length: 83 Bit Score: 53.58 E-value: 1.17e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42558837 1309 VIVEGPMDALAI-TLGSNGAAVgIAPMGTALtVNQIKLLRShidLVNGRDRIAVATDSDPAGWNSAQKAFWHLTAADLD 1386
Cdd:cd00188 4 IIVEGPSDALALaQAGGYGGAV-VALGGHAL-NKTRELLKR---LLGEAKEVIIATDADREGEAIALRLLELLKSLGKK 77
|
|
| Toprim_4 |
pfam13662 |
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ... |
1309-1390 |
1.84e-08 |
|
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.
Pssm-ID: 433387 [Multi-domain] Cd Length: 85 Bit Score: 53.06 E-value: 1.84e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1309 VIVEGPMDALAITlgSNGAAVGIAPMGTAL-TVNQIKLLRSHIDLVNGRDRIAVATDSDPAGWNSAQKAFWHLTAADLDP 1387
Cdd:pfam13662 4 IVVEGYADVIALE--KAGYKGAVAVLGGALsPLDGIGPEDLNIDSLGGIKEVILALDGDVAGEKTALYLAEALLEEGVKV 81
|
...
gi 42558837 1388 THL 1390
Cdd:pfam13662 82 SRL 84
|
|
| TOPRIM |
smart00493 |
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins; |
1309-1380 |
2.98e-08 |
|
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
Pssm-ID: 214695 [Multi-domain] Cd Length: 75 Bit Score: 52.26 E-value: 2.98e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42558837 1309 VIVEGPMDALAIT-LGSNGAAVgIAPMGTALTVNQIKLLRSHIDlvngRDRIAVATDSDPAGWNSAQKAFWHL 1380
Cdd:smart00493 4 IIVEGPADAIALEkAGGKRGNV-VALGGHLLSKEQIKLLKKLAK----KAEVILATDPDREGEAIAWELAELL 71
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
525-570 |
2.74e-06 |
|
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350173 [Multi-domain] Cd Length: 89 Bit Score: 47.05 E-value: 2.74e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 42558837 525 QLGYATTVHGAQGITTGTCHVVL--TGDEDRNLLYVALSRGKFANHLY 570
Cdd:cd18786 41 QLVGAITIDSSQGLTFDVVTLYLptANSLTPRRLYVALTRARKRLVIY 88
|
|
| TraI_TIGR |
TIGR02760 |
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ... |
174-639 |
5.11e-06 |
|
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Pssm-ID: 274285 [Multi-domain] Cd Length: 1960 Bit Score: 51.44 E-value: 5.11e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 174 LNAAQQSLVREMATSGRAVQLALAPAGTGKTTAMQVLTRAWQDSGGTVIGLAPSAVAAQELGASINLEnpDTNTAGTSKN 253
Cdd:TIGR02760 430 LSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIAQLLLHLASEQGYEIQIITAGSLSAQELRQKIPRL--ASTFITWVKN 507
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 254 LLNgpwrpgrkkvraDTLAKLVWHAKHGDAPawmekINSKTLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLA 333
Cdd:TIGR02760 508 LFN------------DDQDHTVQGLLDKSSP-----FSNKDIFVVDEANKLSNNELLKLIDKAEQHNSKLILLNDSAQRQ 570
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 334 SVAAGGVLRDIAHQigavtlsEVHRFRnpdgSLNHAEAAATLALRDGDpsaiafyaDRGRIHvgdlgacadQAYAAWAAD 413
Cdd:TIGR02760 571 GMSAGSAIDLLKEG-------GVTTYA----WVDTKQQKASVEISEAV--------DKLRVD---------YIASAWLDL 622
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 414 RADGTDSVLIAPTRDLVAELNTRARND-----RLAGQ--------------PDKEI------GRVLTLADGTKVSAGDRI 468
Cdd:TIGR02760 623 TPDRQNSQVLATTHREQQDLTQIIRNAlkqegQLSRQevtvptlkpvnltgIQRRNaahykqGMVIRFWQKGKIPHDDYV 702
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 469 ITREN--------------------------DRRLRISRT-------------------NWVKNGDRWHVKNVNTDGsLT 503
Cdd:TIGR02760 703 VTNVNkhnntltlkdaqgktqkfkpsslkdlERPFSVYRPeqlevaagerlqvtgnhfhSRVRNGELLTVSSINNEG-IT 781
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 504 VIHDKlGKTITLPADYVS-KTVQLGYATTVHGAQGITTGTCHVVLTGDEDRNLLYvalSRGKFANHLyLNVASDGDPHNL 582
Cdd:TIGR02760 782 LITED-GQTLHLPHGALEdAHLDYGYVLTPYHTQPDDAKVFLGVKQYALSKALLN---SLNRSASRV-DLFTDLDEKAQR 856
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 42558837 583 IRPEALIPPTALDRITEMLRRDGSPVSATTALRDQTNPHQLLGDMAARYHDAVTAGA 639
Cdd:TIGR02760 857 YLEKTRGIPSAIVVVDQKQHLPDAVTTNNTDKSLEMDISDTLHALEAKAKDGKNSIA 913
|
|
| PRK14712 |
PRK14712 |
conjugal transfer nickase/helicase TraI; Provisional |
431-878 |
7.72e-06 |
|
conjugal transfer nickase/helicase TraI; Provisional
Pssm-ID: 237796 [Multi-domain] Cd Length: 1623 Bit Score: 51.02 E-value: 7.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 431 AELNTRARNDRLAGQPdkeiGRVLTLADGTKVSAGDRIITRENDRRlrisrTNWVKNgDRWHVKNVNTDgSLTVIHDKLG 510
Cdd:PRK14712 1179 AEGNTRLISPREAVAE----GVTLYTPDTIRVGTGDRIRFTKSDRE-----RGYVAN-SVWTVTAVSGD-SVTLSDGQQT 1247
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 511 KTITLPADYVSKTVQLGYATTVHGAQGiTTGTCHVVLTGDE-DRNLL------YVALSRGKFANHLYL-----------N 572
Cdd:PRK14712 1248 RVIRPGQERAEQHIDLAYAITAHGAQG-ASETFAIALEGTEgNRKLMagfesaYVALSRMKQHVQVYTdnrqgwtdainN 1326
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 573 VASDGDPHNLIRPEALIPPTALDRITEMLRRDGSPVSATTALRDQTNPHqllGDMAARYHDAVTAGAENLIGPVGMDKID 652
Cdd:PRK14712 1327 AVQKGTAHDVFEPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAG---GDSPARFIAPGRKYPQPYVALPAFDRNG 1403
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 653 AHAEALLTGLTEapawptlrshlalialDDHSPLKLLTAAVGVGSLADARDPAAVLDARIDDLVADLNA----ARPHDPD 728
Cdd:PRK14712 1404 KSAGIWLNPLTT----------------DDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQdgvrIARDNPD 1467
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 729 TPPATDAPLPWLPGIPARLADAHDWGPFAGayhqlvreqiDAVRDAARNWTGATAPAWAQPFLED---EDTELRADLAVW 805
Cdd:PRK14712 1468 SGVVVRIAGEGRPWNPGAITGGRVWGDIPD----------NSVQPGAGNGEPVTAEVLAQRQAEEairRETERRADEIVR 1537
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 42558837 806 RAVAGTDDndlrPTGDRTIGAPG--AYQAKLNRAVREARPSYPFSQRTWYQVLPETVRADPWITPLCQRLARLER 878
Cdd:PRK14712 1538 KMAENKPD----LPDGKTEQAVReiAGQERDRAAITEREAALPESVLREPQRVREAVREVARENLLQERLQQMER 1608
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
1309-1380 |
1.86e-05 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 44.65 E-value: 1.86e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 42558837 1309 VIVEGPMDALAI--TLGSNGAAVgIAPMGTALTV--NQIKLLRSHID-LVNGRDRIAVATDSDPAGwnsaQKAFWHL 1380
Cdd:pfam01751 3 IIVEGPSDAIALekALGGGFQAV-VAVLGHLLSLekGPKKKALKALKeLALKAKEVILATDPDREG----EAIALKL 74
|
|
| Viral_helicase1 |
pfam01443 |
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
475-562 |
2.52e-05 |
|
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.
Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 47.37 E-value: 2.52e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 475 RRLRISRTNwvKNGDRWHVKNvntDGSLTVIHDKLGKTITLPADYVSKTV-QLGY-ATTVHGAQGITTGTCHVVLTGD-- 550
Cdd:pfam01443 127 PSLRAPILS--AKGFEVVVER---SGEYKVDYDPNGVLVLVYLTFTQALKeSLGVrVTTVHEVQGLTFDSVTLVLDTDtd 201
|
90
....*....|....*..
gi 42558837 551 -----EDRNLLYVALSR 562
Cdd:pfam01443 202 lliisDSPEHLYVALTR 218
|
|
| Toprim_3 |
pfam13362 |
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ... |
1309-1408 |
1.80e-04 |
|
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.
Pssm-ID: 433146 [Multi-domain] Cd Length: 97 Bit Score: 42.00 E-value: 1.80e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 1309 VIVEGPMDALAITLGSN-GAAVGIAPMGTALTVNqikllrshIDLVNGRDRIAVATDSDPAgwNSAQKAFW----HLTAA 1383
Cdd:pfam13362 3 IIGEGIETALSLTQRLNpPGTPVIALLSAANLKA--------VAWPERVKRVYIAADNDAA--NDGQAAAEklaeRLEAA 72
|
90 100
....*....|....*....|....*
gi 42558837 1384 DLDPTHLDLPDGLDPANLLETQGAD 1408
Cdd:pfam13362 73 GIEAVLLEPEAGEDWNDDLQQTGAA 97
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
6-332 |
1.85e-04 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 46.27 E-value: 1.85e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 6 LGHRPDAQDVTDQWVAETAQQVVARVAEDRATWQVWHLRAEAQRQARAHGIRLTELDDAVDRVVATAIREHSIAFNDPDP 85
Cdd:COG1112 260 ALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAALLALLALLALLAARLAAALAALLLLLLL 339
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 86 LTRETTAAEQDVTIPAPLQRTDRPAEGGVDAEEVVSAYSLAGARQYTSRAVIEAERRIVESARHTGGRTISEVRVGIAIA 165
Cdd:COG1112 340 EELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAA 419
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 166 EAAANELQLNAAQQSLVREMATSGRAVQLALAPAGTGKTTAMQVLTRAWQDSGGTVIGLAPSAVAAQELGASINLENPDT 245
Cdd:COG1112 420 AAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKL 499
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 246 NTAGTSKNLLNGPWRpgRKKVRADTLAKLVWHAKHGDAPAWM-------EKINSKT----LVLIDEAGMAATTDLAAAId 314
Cdd:COG1112 500 IAELREAARLRRALR--RELKKRRELRKLLWDALLELAPVVGmtpasvaRLLPLGEgsfdLVIIDEASQATLAEALGAL- 576
|
330
....*....|....*...
gi 42558837 315 yitSRGGQVRLVGDDRQL 332
Cdd:COG1112 577 ---ARAKRVVLVGDPKQL 591
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
178-337 |
2.24e-04 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 42.98 E-value: 2.24e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 178 QQSLVREMATSGraVQLALAPAGTGKTTAMQVLTRAWQDSGG---TVIGLAPSAVAAQELGASINLEnpdtntagtsknl 254
Cdd:pfam13245 1 QREAVRTALPSK--VVLLTGGPGTGKTTTIRHIVALLVALGGvsfPILLAAPTGRAAKRLSERTGLP------------- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42558837 255 lngpwrpgrkkvrADTLAKLVwhAKHGDAPAWMEKINSK----TLVLIDEAGMaATTDLAAAIDYITSRGGQVRLVGDDR 330
Cdd:pfam13245 66 -------------ASTIHRLL--GFDDLEAGGFLRDEEEpldgDLLIVDEFSM-VDLPLAYRLLKALPDGAQLLLVGDPD 129
|
....*..
gi 42558837 331 QLASVAA 337
Cdd:pfam13245 130 QLPSVGP 136
|
|
| DEXXQc_Mov10L1 |
cd18078 |
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
294-335 |
4.15e-04 |
|
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350836 [Multi-domain] Cd Length: 230 Bit Score: 43.51 E-value: 4.15e-04
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 42558837 294 TLVLIDEAGMAATTDLAAAIDYITSRGGQVRLVGDDRQLASV 335
Cdd:cd18078 138 THVFVDEAGQATEPESLIPLGLISSRDGQIILAGDPMQLGPV 179
|
|
| DEXXQc_Upf1-like |
cd17934 |
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
296-332 |
3.43e-03 |
|
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438708 [Multi-domain] Cd Length: 121 Bit Score: 39.14 E-value: 3.43e-03
10 20 30
....*....|....*....|....*....|....*..
gi 42558837 296 VLIDEAGMAATTDLAAAIdyitSRGGQVRLVGDDRQL 332
Cdd:cd17934 48 VIIDEASQITEPELLIAL----IRAKKVVLVGDPKQL 80
|
|
| UvrD_C_2 |
pfam13538 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
526-571 |
3.50e-03 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 463913 [Multi-domain] Cd Length: 52 Bit Score: 37.17 E-value: 3.50e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 42558837 526 LGYATTVHGAQGITTGtcHVVLTG---------DEDRNLLYVALSRGKfaNHLYL 571
Cdd:pfam13538 1 LAYALTVHKAQGSEFP--AVFLVDpdltahyhsMLRRRLLYTAVTRAR--KKLVL 51
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
296-358 |
9.24e-03 |
|
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438706 [Multi-domain] Cd Length: 121 Bit Score: 37.85 E-value: 9.24e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42558837 296 VLIDEAGMAATTDLAAAIDYItSRGGQVRLVGDDRQLASVAAGGVLRDIAHQIGAVTLSEVHR 358
Cdd:cd17914 50 ILVDEAAQILEPETSRLIDLA-LDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLVRLG 111
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