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Conserved domains on  [gi|255304946|ref|NP_001157284|]
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twinkle mtDNA helicase isoform B [Homo sapiens]

Protein Classification

bifunctional DNA primase/helicase( domain architecture ID 10099140)

bifunctional DNA primase/helicase similar to mitochondrial Twinkle protein, chloroplastic Twinkle homolog, and bacteriophage T7 gp4, which have both DNA primase and helicase activities

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 366-580 6.03e-147

C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid localization, also known as C10orf2, PEO1, SCA8, ATXN8, IOSCA, PEOA3 or SANDO) is a homohexameric DNA helicases which unwinds short stretches of double-stranded DNA in the 5' to 3' direction and, along with mitochondrial single-stranded DNA binding protein and mtDNA polymerase gamma, is thought to play a key role in mtDNA replication. Mutations in the human gene cause infantile onset spinocerebellar ataxia (IOSCA) and progressive external ophthalmoplegia (PEO) and are also associated with several mitochondrial depletion syndromes. This group also contains viral GP4-like and related bacterial helicases.


:

Pssm-ID: 410867  Cd Length: 266  Bit Score: 424.34  E-value: 6.03e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 366 SIVSFRQLREEVLGELSNVEQAAGLRWSRFPDLNRILKGHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFE 445
Cdd:cd01122    1 SITTFDDLRELVYEELLNSEQVAGVQWKRFPSLNKLLKGHRRGELTIFTGPTGSGKTTFLSEYSLDLCMQGVNTLWGSFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 446 ISNVRLARVMLTQFAEGRLEDQLDKYDHWADRFEDLPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHE 525
Cdd:cd01122   81 IKNVRLAKTMLTQFAGKNLEDNLREFDEWADKFELLPMYFMKFHGSTDIDEVLDAMEHAVYVYDIQHIVIDNLQFMMGTQ 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 255304946 526 QLSTDRIAAQDYIIGVFRKFATDNNCHVTLVIHPRKEDDDKELQTASIFGSAKVS 580
Cdd:cd01122  161 ASGSDRFELQDLIIGKFRRFATNNNVHITLVIHPRKEDDDNELTTSSIFGSAKAT 215
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 259-335 5.20e-06

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: 44.57  E-value: 5.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 259 EVVLTSRELDSLALNQSTGLPTlTLPRGTtCLPPALLPYLEQF-RRIVFWLGDDLRSWEAA-KLFARKLN-PKRCFLVRP 335
Cdd:cd01029    2 EVIIVEGYMDVLALHQAGIKNV-VAALGT-ANTEEQLRLLKRFaRTVILAFDNDEAGKKAAaRALELLLAlGGRVRVPPL 79
 
Name Accession Description Interval E-value
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 366-580 6.03e-147

C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid localization, also known as C10orf2, PEO1, SCA8, ATXN8, IOSCA, PEOA3 or SANDO) is a homohexameric DNA helicases which unwinds short stretches of double-stranded DNA in the 5' to 3' direction and, along with mitochondrial single-stranded DNA binding protein and mtDNA polymerase gamma, is thought to play a key role in mtDNA replication. Mutations in the human gene cause infantile onset spinocerebellar ataxia (IOSCA) and progressive external ophthalmoplegia (PEO) and are also associated with several mitochondrial depletion syndromes. This group also contains viral GP4-like and related bacterial helicases.


Pssm-ID: 410867  Cd Length: 266  Bit Score: 424.34  E-value: 6.03e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 366 SIVSFRQLREEVLGELSNVEQAAGLRWSRFPDLNRILKGHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFE 445
Cdd:cd01122    1 SITTFDDLRELVYEELLNSEQVAGVQWKRFPSLNKLLKGHRRGELTIFTGPTGSGKTTFLSEYSLDLCMQGVNTLWGSFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 446 ISNVRLARVMLTQFAEGRLEDQLDKYDHWADRFEDLPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHE 525
Cdd:cd01122   81 IKNVRLAKTMLTQFAGKNLEDNLREFDEWADKFELLPMYFMKFHGSTDIDEVLDAMEHAVYVYDIQHIVIDNLQFMMGTQ 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 255304946 526 QLSTDRIAAQDYIIGVFRKFATDNNCHVTLVIHPRKEDDDKELQTASIFGSAKVS 580
Cdd:cd01122  161 ASGSDRFELQDLIIGKFRRFATNNNVHITLVIHPRKEDDDNELTTSSIFGSAKAT 215
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 393-564 1.95e-23

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 97.84  E-value: 1.95e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946  393 SRFPDLNRILKGHR-KGELTVFTGPTGSGKTTFISEYALDLCS-----------QGVNTLWGSFEISNVRLARvmltqfa 460
Cdd:pfam13481  17 APPPPRRWLIKGLLpAGGLGLLAGAPGTGKTTLALDLAAAVATgkpwlggprvpEQGKVLYVSAEGPADELRR------- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946  461 egRLEDQLDKYDHWA-----DRFEDLPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHEQLSTDRIAAq 535
Cdd:pfam13481  90 --RLRAAGADLDLPArllflSLVESLPLFFLDRGGPLLDADVDALEAALEEVEDPDLVVIDPLARALGGDENSNSDVGR- 166

                         170       180
                  ....*....|....*....|....*....
gi 255304946  536 dyIIGVFRKFATDNNCHVTLVIHPRKEDD 564
Cdd:pfam13481 167 --LVKALDRLARRTGATVLLVHHVGKDGA 193
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
401-576 1.00e-11

RecA-family ATPase [Replication, recombination and repair];


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 66.08  E-value: 1.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 401 ILKGH-RKGELTVFTGPTGSGKTTFiseyALDL--------------CSQGvNTLWGSFEISNVRLARvmltqfaegRLE 465
Cdd:COG3598    5 LVPGLlPEGGVTLLAGPPGTGKSFL----ALQLaaavaaggpwlgrrVPPG-KVLYLAAEDDRGELRR---------RLK 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 466 DQLDKYDHWADRFEDlPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHEQLSTDRIAAqdyIIGVFRKF 545
Cdd:COG3598   71 ALGADLGLPFADLDG-RLRLLSLAGDLDDTDDLEALERAIEEEGPDLVVIDPLARVFGGDENDAEEMRA---FLNPLDRL 146

                        170       180       190
                 ....*....|....*....|....*....|.
gi 255304946 546 ATDNNCHVTLVIHPRKeDDDKELQTASIFGS 576
Cdd:COG3598  147 AERTGAAVLLVHHTGK-GGAGKDSGDRARGS 176
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 259-335 5.20e-06

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: 44.57  E-value: 5.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 259 EVVLTSRELDSLALNQSTGLPTlTLPRGTtCLPPALLPYLEQF-RRIVFWLGDDLRSWEAA-KLFARKLN-PKRCFLVRP 335
Cdd:cd01029    2 EVIIVEGYMDVLALHQAGIKNV-VAALGT-ANTEEQLRLLKRFaRTVILAFDNDEAGKKAAaRALELLLAlGGRVRVPPL 79
PRK08506 PRK08506
replicative DNA helicase; Provisional
 395-528 2.47e-04

replicative DNA helicase; Provisional


Pssm-ID: 236278 [Multi-domain]  Cd Length: 472  Bit Score: 43.85  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 395 FPDLNRILKGHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFEISNVRLARVMLTQFAE--------GRLED 466
Cdd:PRK08506 179 FVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFSLEMPAEQLMLRMLSAKTSiplqnlrtGDLDD 258

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 255304946 467 qlDKYDHWADRFEDL---PLYFMTfHGQQSIRTVIDTM-----QHAvyvyDICHVIIDNLQFMMG-------HEQLS 528
Cdd:PRK08506 259 --DEWERLSDACDELskkKLFVYD-SGYVNIHQVRAQLrklksQHP----EIGLAVIDYLQLMSGsgnfkdrHLQIS 328
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 407-568 7.79e-03

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: 37.35  E-value: 7.79e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946   407 KGELTVFTGPTGSGKTTFISEYAldlcsqgvntlwGSFEISNVRLARVMLTQFAEGRLEDQLDKYDHwadrfedlpLYFM 486
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALA------------RELGPPGGGVIYIDGEDILEEVLDQLLLIIVG---------GKKA 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946   487 TFHGQQSIRTVIDTMQHavYVYDIchVIIDNLQFMMGHEQLSTDRIAAQDYIIGVFRKfatDNNCHVTLVIHPRKEDDDK 566
Cdd:smart00382  60 SGSGELRLRLALALARK--LKPDV--LILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNLTVILTTNDEKDLGPA 132


                   ..
gi 255304946   567 EL 568
Cdd:smart00382 133 LL 134
ATPase_ComGA NF041000
competence type IV pilus ATPase ComGA;
395-430 8.32e-03

competence type IV pilus ATPase ComGA;


Pssm-ID: 468930 [Multi-domain]  Cd Length: 265  Bit Score: 38.20  E-value: 8.32e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 255304946 395 FPDLNRILKG---HRKGeLTVFTGPTGSGKTTFIseYAL 430
Cdd:NF041000 113 FPEQFQLLKQllqRRSG-LILFSGPTGSGKTTTM--YSL 148
 
Name Accession Description Interval E-value
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 366-580 6.03e-147

C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid localization, also known as C10orf2, PEO1, SCA8, ATXN8, IOSCA, PEOA3 or SANDO) is a homohexameric DNA helicases which unwinds short stretches of double-stranded DNA in the 5' to 3' direction and, along with mitochondrial single-stranded DNA binding protein and mtDNA polymerase gamma, is thought to play a key role in mtDNA replication. Mutations in the human gene cause infantile onset spinocerebellar ataxia (IOSCA) and progressive external ophthalmoplegia (PEO) and are also associated with several mitochondrial depletion syndromes. This group also contains viral GP4-like and related bacterial helicases.


Pssm-ID: 410867  Cd Length: 266  Bit Score: 424.34  E-value: 6.03e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 366 SIVSFRQLREEVLGELSNVEQAAGLRWSRFPDLNRILKGHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFE 445
Cdd:cd01122    1 SITTFDDLRELVYEELLNSEQVAGVQWKRFPSLNKLLKGHRRGELTIFTGPTGSGKTTFLSEYSLDLCMQGVNTLWGSFE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 446 ISNVRLARVMLTQFAEGRLEDQLDKYDHWADRFEDLPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHE 525
Cdd:cd01122   81 IKNVRLAKTMLTQFAGKNLEDNLREFDEWADKFELLPMYFMKFHGSTDIDEVLDAMEHAVYVYDIQHIVIDNLQFMMGTQ 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 255304946 526 QLSTDRIAAQDYIIGVFRKFATDNNCHVTLVIHPRKEDDDKELQTASIFGSAKVS 580
Cdd:cd01122  161 ASGSDRFELQDLIIGKFRRFATNNNVHITLVIHPRKEDDDNELTTSSIFGSAKAT 215
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 393-564 1.95e-23

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 97.84  E-value: 1.95e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946  393 SRFPDLNRILKGHR-KGELTVFTGPTGSGKTTFISEYALDLCS-----------QGVNTLWGSFEISNVRLARvmltqfa 460
Cdd:pfam13481  17 APPPPRRWLIKGLLpAGGLGLLAGAPGTGKTTLALDLAAAVATgkpwlggprvpEQGKVLYVSAEGPADELRR------- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946  461 egRLEDQLDKYDHWA-----DRFEDLPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHEQLSTDRIAAq 535
Cdd:pfam13481  90 --RLRAAGADLDLPArllflSLVESLPLFFLDRGGPLLDADVDALEAALEEVEDPDLVVIDPLARALGGDENSNSDVGR- 166

                         170       180
                  ....*....|....*....|....*....
gi 255304946  536 dyIIGVFRKFATDNNCHVTLVIHPRKEDD 564
Cdd:pfam13481 167 --LVKALDRLARRTGATVLLVHHVGKDGA 193
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 411-579 7.60e-16

RecA-like_NTPases; RecA-like NTPases. This superfamily 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: 410865 [Multi-domain]  Cd Length: 119  Bit Score: 74.08  E-value: 7.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 411 TVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFEISNVRLARVMLTQFAegrledqldkydhwadrfedlplyfmtfhg 490
Cdd:cd01120    1 ILITGPPGSGKTTLLLQFAEQALLSDEPVIFISFLDTILEAIEDLIEEKK------------------------------ 50

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 491 qqsirtvidtmqhavyvydICHVIIDNLQFMMGHEQlsTDRIAAQDYIIGVFRKFATDNNCHVTLVIHPRKEDDDKELQT 570
Cdd:cd01120   51 -------------------LDIIIIDSLSSLARASQ--GDRSSELLEDLAKLLRAARNTGITVIATIHSDKFDIDRGGSS 109


                 ....*....
gi 255304946 571 ASIFGSAKV 579
Cdd:cd01120  110 NDERLLKSL 118
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
401-576 1.00e-11

RecA-family ATPase [Replication, recombination and repair];


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 66.08  E-value: 1.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 401 ILKGH-RKGELTVFTGPTGSGKTTFiseyALDL--------------CSQGvNTLWGSFEISNVRLARvmltqfaegRLE 465
Cdd:COG3598    5 LVPGLlPEGGVTLLAGPPGTGKSFL----ALQLaaavaaggpwlgrrVPPG-KVLYLAAEDDRGELRR---------RLK 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 466 DQLDKYDHWADRFEDlPLYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHEQLSTDRIAAqdyIIGVFRKF 545
Cdd:COG3598   71 ALGADLGLPFADLDG-RLRLLSLAGDLDDTDDLEALERAIEEEGPDLVVIDPLARVFGGDENDAEEMRA---FLNPLDRL 146

                        170       180       190
                 ....*....|....*....|....*....|.
gi 255304946 546 ATDNNCHVTLVIHPRKeDDDKELQTASIFGS 576
Cdd:COG3598  147 AERTGAAVLLVHHTGK-GGAGKDSGDRARGS 176
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 411-566 5.15e-10

RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily 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: 410891 [Multi-domain]  Cd Length: 231  Bit Score: 59.89  E-value: 5.15e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 411 TVFTGPTGSGKTTFISEYALDLC-SQGVNTLWGSFEISNVRLARVMLTQFA-------EGRLEDQLDKYDHWADRFEDLP 482
Cdd:cd19483    1 VTIGAGSGIGKSTIVRELAYHLItEHGEKVGIISLEESVEETAKGLAGKHLgkpepleLPRDDITEEEEDDAFDNELGSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 483 -LYFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQfMMGHEQLSTDRIAAQDYIIGVFRKFATDNNCHVTLVIHPRK 561
Cdd:cd19483   81 rFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLT-ILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLRR 159


                 ....*
gi 255304946 562 EDDDK 566
Cdd:cd19483  160 PGGGK 164
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 389-521 4.57e-07

C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.


Pssm-ID: 410864 [Multi-domain]  Cd Length: 256  Bit Score: 51.36  E-value: 4.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 389 GLRWSrFPDLNRILKGHRKGELTVFTGPTGSGKTTF---ISEYAldLCSQGVNTLWGSFEISNVRL--------ARVMLT 457
Cdd:cd00984    1 GLPTG-FTDLDKLTGGLQPGDLIIIAARPSMGKTAFalnIAENI--ALDEGLPVLFFSLEMSAEQLaerllsseSGVSLS 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 255304946 458 QFAEGRL-EDQLDKYDHWADRFEDLPLYF-----MTFHgqqSIRTVIDTM--QHAvyvyDICHVIIDNLQFM 521
Cdd:cd00984   78 KLRTGRLdDEDWERLTAAMGELSELPLYIddtpgLTVD---EIRAKARRLkrEHG----GLGLIVIDYLQLI 142
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
396-557 1.80e-06

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 49.14  E-value: 1.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 396 PDLNRILK-GHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFEISNVRL---ARVMLTQFAEGRLEDQLdky 471
Cdd:COG0467    7 PGLDELLGgGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrrAESLGLDLEEYIESGLL--- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 472 dhwadRFEDLPLYFMtfhgQQSIRTVIDTMQHAVYVYDICHVIIDNLqfmMGHEQLSTDRIAAQDYIIGVFRkFATDNNC 551
Cdd:COG0467   84 -----RIIDLSPEEL----GLDLEELLARLREAVEEFGAKRVVIDSL---SGLLLALPDPERLREFLHRLLR-YLKKRGV 150


                 ....*.
gi 255304946 552 hVTLVI 557
Cdd:COG0467  151 -TTLLT 155
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 259-335 5.20e-06

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: 44.57  E-value: 5.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 259 EVVLTSRELDSLALNQSTGLPTlTLPRGTtCLPPALLPYLEQF-RRIVFWLGDDLRSWEAA-KLFARKLN-PKRCFLVRP 335
Cdd:cd01029    2 EVIIVEGYMDVLALHQAGIKNV-VAALGT-ANTEEQLRLLKRFaRTVILAFDNDEAGKKAAaRALELLLAlGGRVRVPPL 79
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 395-521 3.03e-05

DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.


Pssm-ID: 427509 [Multi-domain]  Cd Length: 254  Bit Score: 45.87  E-value: 3.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946  395 FPDLNRILKGHRKGELTVFTGPTGSGKTTFiseyALDLC-----SQGVNTLWGSFEISNVRLARVMLTQFAE-------- 461
Cdd:pfam03796   6 FTDLDRLTGGLQPGDLIIIAARPSMGKTAF----ALNIArnaavKHKKPVAIFSLEMSAEQLVMRLLASEAGvdsqklrt 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 255304946  462 GRL-EDQLDKYDHWADRFEDLPLYF-----MTFhgqQSIRTVIDTMQHAvyvYDICHVIIDNLQFM 521
Cdd:pfam03796  82 GQLtDEDWEKLAKAAGRLSEAPLYIddtpgLSI---AEIRAKARRLKRE---HGLGLIVIDYLQLM 141
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 396-518 5.31e-05

Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.


Pssm-ID: 410869 [Multi-domain]  Cd Length: 222  Bit Score: 44.95  E-value: 5.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 396 PDLNRILK-GHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFEISNVRL---ARVMLTQFAEGRLEDQLDky 471
Cdd:cd01124    6 PGLDELLGgGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLlrnAKSFGWDFDEMEDEGKLI-- 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 255304946 472 dhwadrFEDLPlyfMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNL 518
Cdd:cd01124   84 ------IVDAP---PTEAGRFSLDELLSRILSIIKSFKAKRVVIDSL 121
PRK08506 PRK08506
replicative DNA helicase; Provisional
 395-528 2.47e-04

replicative DNA helicase; Provisional


Pssm-ID: 236278 [Multi-domain]  Cd Length: 472  Bit Score: 43.85  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 395 FPDLNRILKGHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFEISNVRLARVMLTQFAE--------GRLED 466
Cdd:PRK08506 179 FVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFSLEMPAEQLMLRMLSAKTSiplqnlrtGDLDD 258

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 255304946 467 qlDKYDHWADRFEDL---PLYFMTfHGQQSIRTVIDTM-----QHAvyvyDICHVIIDNLQFMMG-------HEQLS 528
Cdd:PRK08506 259 --DEWERLSDACDELskkKLFVYD-SGYVNIHQVRAQLrklksQHP----EIGLAVIDYLQLMSGsgnfkdrHLQIS 328
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 408-556 4.29e-04

RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs RadA and RadB.


Pssm-ID: 410881 [Multi-domain]  Cd Length: 185  Bit Score: 41.57  E-value: 4.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 408 GELTVFTGPTGSGKTTFISEYALDLCSQGVNTLW----GSFEISnvRLarVMLTQFAEGRLEDQLDKydhwADRFedlpL 483
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWidteGAFPPS--RL--VQILEASPSSELELAEA----LSRL----L 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 484 YFMTFHGQQSIRTVIDTMQHAVYVYDICHVIIDNLQFMMGHE--------QLSTDRIAAQDYIIGVFRKFATDNNCHVTL 555
Cdd:cd01393   69 YFRPPDTLAHLLALDSLPESLFPPPNTSLVVVDSVSALFRKAfprggdgdSSSSLRARLLSQLARALQKLAAQFNLAVVV 148


                 .
gi 255304946 556 V 556
Cdd:cd01393  149 T 149
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
365-485 4.47e-04

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 42.76  E-value: 4.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 365 KSIVSFRQLREEVLGEL----SNVEQAAGLRwSRFPDLNRILKGHRKGELTVFTGPTGSGKTTFiseyALDLC-----SQ 435
Cdd:COG0305  145 KGFVSISDILKEALERIeelyKNGGGITGVP-TGFTDLDKLTGGLQPGDLIILAARPSMGKTAF----ALNIArnaaiKE 219

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 255304946 436 GVNTLWGSFEISNVRLARVMLTQFAE--------GRLED-QLDKYDHWADRFEDLPLYF 485
Cdd:COG0305  220 GKPVAIFSLEMSAEQLVMRLLSSEARidssklrtGKLSDeDWERLSSAAGELSEAPIYI 278
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 393-455 7.91e-04

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 42.17  E-value: 7.91e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 255304946 393 SRFPDLNRIL-KGHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFEISNVRLARVM 455
Cdd:PRK09302 257 SGVPDLDEMLgGGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIRNA 320
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 396-478 2.15e-03

C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.


Pssm-ID: 410892 [Multi-domain]  Cd Length: 218  Bit Score: 40.00  E-value: 2.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 396 PDLNRIL--KGHRKGELTVFTGPTGSGKTTFISEYALDLCSQGVNTLWGSFEISNVRLARVM--------------LTQF 459
Cdd:cd19484    6 PRLDAMLggGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIRNAksigidleqmerkgLLKI 85

                         90       100
                 ....*....|....*....|....
gi 255304946 460 AEGR-----LEDQLDKYDHWADRF 478
Cdd:cd19484   86 ICARpelygLEDHLIIIKSEINEF 109
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 408-576 6.91e-03

Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family includes the homo-hexameric replicative helicase RepA encoded by plasmid RSF1010. RSF1010 is found in most Gram-negative bacteria and some Gram-positive bacteria . The RepA protein of Plasmid RSF1010 is a 5'-3' DNA helicase which can utilize ATP, dATP, GTP and dGTP (and CTP and dCTP to a lesser extent).


Pssm-ID: 410870  Cd Length: 238  Bit Score: 38.52  E-value: 6.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 408 GELTVFTGPTGSGKTTFiseyALDLC---SQGVnTLWGSfeiSNVRLARV-MLTqfAEG-------RLEDQLDKYDHWAD 476
Cdd:cd01125    1 GTLGMLVGPPGSGKSFL----ALDLAvavATGR-DWLGE---RRVKQGRVvYLA--AEDprdglrrRLKAIGAHLGDEDA 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946 477 RFEDLPLYFMTFHGQQSIRTVIDTMQHAV-YVYDICHVIIDNLQfMMGHEQLSTDriAAQDY-IIGVFRKFATDNNCHVT 554
Cdd:cd01125   71 ALAENLVIENLRGKPVSIDAEAPELERIIeELEGVRLIIIDTLA-RVLHGGDEND--AADMGaFVAGLDRIARETGAAVL 147

                        170       180
                 ....*....|....*....|..
gi 255304946 555 LVIHPRKEDDDKELQTASifGS 576
Cdd:cd01125  148 LVHHTGKDAAGDSQQAAR--GS 167
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 407-568 7.79e-03

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: 37.35  E-value: 7.79e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946   407 KGELTVFTGPTGSGKTTFISEYAldlcsqgvntlwGSFEISNVRLARVMLTQFAEGRLEDQLDKYDHwadrfedlpLYFM 486
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALA------------RELGPPGGGVIYIDGEDILEEVLDQLLLIIVG---------GKKA 59

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255304946   487 TFHGQQSIRTVIDTMQHavYVYDIchVIIDNLQFMMGHEQLSTDRIAAQDYIIGVFRKfatDNNCHVTLVIHPRKEDDDK 566
Cdd:smart00382  60 SGSGELRLRLALALARK--LKPDV--LILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNLTVILTTNDEKDLGPA 132


                   ..
gi 255304946   567 EL 568
Cdd:smart00382 133 LL 134
ABCC_MRP_domain1 cd03250
ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C; This ...
 406-426 8.30e-03

ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C; This subfamily is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.


Pssm-ID: 213217 [Multi-domain]  Cd Length: 204  Bit Score: 37.83  E-value: 8.30e-03
                         10        20
                 ....*....|....*....|.
gi 255304946 406 RKGELTVFTGPTGSGKTTFIS 426
Cdd:cd03250   29 PKGELVAIVGPVGSGKSSLLS 49
ATPase_ComGA NF041000
competence type IV pilus ATPase ComGA;
395-430 8.32e-03

competence type IV pilus ATPase ComGA;


Pssm-ID: 468930 [Multi-domain]  Cd Length: 265  Bit Score: 38.20  E-value: 8.32e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 255304946 395 FPDLNRILKG---HRKGeLTVFTGPTGSGKTTFIseYAL 430
Cdd:NF041000 113 FPEQFQLLKQllqRRSG-LILFSGPTGSGKTTTM--YSL 148
 
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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