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Conserved domains on  [gi|32451662|gb|AAH54598|]
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Rfc4 protein [Danio rerio]

Protein Classification

replication factor C small subunit( domain architecture ID 1001945)

replication factor C small subunit is part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rfc super family cl35099
replication factor C small subunit; Reviewed
 34-180 1.01e-76

replication factor C small subunit; Reviewed


The actual alignment was detected with superfamily member PRK00440:

Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 232.84  E-value: 1.01e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   34 PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELYGpDLYRQRVLELNASDERGIQV 113
Cdd:PRK00440   6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYG-EDWRENFLELNASDERGIDV 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 32451662  114 VREKVKRFAQltvagTRPDGKTcpPFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICNYVSR 180
Cdd:PRK00440  85 IRNKIKEFAR-----TAPVGGA--PFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSK 144
 
Name Accession Description Interval E-value
rfc PRK00440
replication factor C small subunit; Reviewed
 34-180 1.01e-76

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 232.84  E-value: 1.01e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   34 PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELYGpDLYRQRVLELNASDERGIQV 113
Cdd:PRK00440   6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYG-EDWRENFLELNASDERGIDV 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 32451662  114 VREKVKRFAQltvagTRPDGKTcpPFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICNYVSR 180
Cdd:PRK00440  85 IRNKIKEFAR-----TAPVGGA--PFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSK 144
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
50-182 2.75e-31

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 115.07  E-value: 2.75e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  50 QEEVVAVLKKSLEGADLP-NLLFYGPPGTGKTSTILAAARELYG----------------------PDLYrqrvlELNA- 105
Cdd:COG0470   1 QEEAWEQLLAAAESGRLPhALLLHGPPGIGKTTLALALARDLLCenpeggkacgqchsrlmaagnhPDLL-----ELNPe 75

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662 106 --SDERGIQVVREkVKRFAQLTVAGTRpdgktcppFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICNYVSRLS 182
Cdd:COG0470  76 ekSDQIGIDQIRE-LGEFLSLTPLEGG--------RKVVIIDEADAMNEAAANALLKTLEEPPKNTPFILIANDPSRLL 145
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 50-177 2.99e-23

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


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 90.67  E-value: 2.99e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  50 QEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELYGPDLyrqRVLELNASDERGIQVVREKVKRFAQLTVAGT 129
Cdd:cd00009   3 QEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGA---PFLYLNASDLLEGLVVAELFGHFLVRLLFEL 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 32451662 130 RPDGKTCppfkIIILDEADSMTSAAQAALRRTME------KESRTTRFCLICNY 177
Cdd:cd00009  80 AEKAKPG----VLFIDEIDSLSRGAQNALLRVLEtlndlrIDRENVRVIGATNR 129
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 69-181 2.46e-14

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


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 66.46  E-value: 2.46e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    69 LLFYGPPGTGKTSTILAAARELYGPdlyrqrVLELNASDERGIQvVREKVKRFAQ-LTVAgtrpdgKTCPPfKIIILDEA 147
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAP------FIEISGSELVSKY-VGESEKRLRElFEAA------KKLAP-CVIFIDEI 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 32451662   148 DSMTSA-----------AQAALRRTMEKESRTTR---FCLICNYVSRL 181
Cdd:pfam00004  67 DALAGSrgsggdsesrrVVNQLLTELDGFTSSNSkviVIAATNRPDKL 114
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 68-176 1.01e-10

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: 57.38  E-value: 1.01e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662     68 NLLFYGPPGTGKTSTILAAARELYGPDLyrqRVLELNASDERGIQVVREKVKRFAQLTVAGTRPDG--------KTCPPf 139
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGG---GVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRlrlalalaRKLKP- 79

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 32451662    140 KIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICN 176
Cdd:smart00382  80 DVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN 116
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 27-121 1.03e-08

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 54.19  E-value: 1.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    27 EKKQRAVPWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-----LLFYGPPGTGKTSTILAAARELyGPDlYRQRV- 100
Cdd:TIGR00602  66 ENLDGNEPWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENapkriLLITGPSGCGKSTTIKILSKEL-GIQ-VQEWSn 143

                          90       100
                  ....*....|....*....|....
gi 32451662   101 ---LELNASDERGIQVVREKVKRF 121
Cdd:TIGR00602 144 ptlPDFQKNDHKVTLSLESCFSNF 167
 
Name Accession Description Interval E-value
rfc PRK00440
replication factor C small subunit; Reviewed
 34-180 1.01e-76

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 232.84  E-value: 1.01e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   34 PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELYGpDLYRQRVLELNASDERGIQV 113
Cdd:PRK00440   6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYG-EDWRENFLELNASDERGIDV 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 32451662  114 VREKVKRFAQltvagTRPDGKTcpPFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICNYVSR 180
Cdd:PRK00440  85 IRNKIKEFAR-----TAPVGGA--PFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSK 144
PLN03025 PLN03025
replication factor C subunit; Provisional
 33-181 7.29e-63

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 197.64  E-value: 7.29e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   33 VPWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELYGPDlYRQRVLELNASDERGIQ 112
Cdd:PLN03025   1 LPWVEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPN-YKEAVLELNASDDRGID 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662  113 VVREKVKRFAQLTVagTRPDGKTcppfKIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICNYVSRL 181
Cdd:PLN03025  80 VVRNKIKMFAQKKV--TLPPGRH----KIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKI 142
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 35-173 1.46e-38

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 135.12  E-value: 1.46e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   35 WVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELYGpDLYRQRVLELNASD--ERGIQ 112
Cdd:PRK12402   5 WTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYG-DPWENNFTEFNVADffDQGKK 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  113 VVREKvKRFAQLTV--------------------AGTRP-DGktcpPFKIIILDEADSMTSAAQAALRRTMEKESRTTRF 171
Cdd:PRK12402  84 YLVED-PRFAHFLGtdkrirsskidnfkhvlkeyASYRPlSA----DYKTILLDNAEALREDAQQALRRIMEQYSRTCRF 158


                 ..
gi 32451662  172 CL 173
Cdd:PRK12402 159 II 160
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
50-182 2.75e-31

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 115.07  E-value: 2.75e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  50 QEEVVAVLKKSLEGADLP-NLLFYGPPGTGKTSTILAAARELYG----------------------PDLYrqrvlELNA- 105
Cdd:COG0470   1 QEEAWEQLLAAAESGRLPhALLLHGPPGIGKTTLALALARDLLCenpeggkacgqchsrlmaagnhPDLL-----ELNPe 75

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662 106 --SDERGIQVVREkVKRFAQLTVAGTRpdgktcppFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICNYVSRLS 182
Cdd:COG0470  76 ekSDQIGIDQIRE-LGEFLSLTPLEGG--------RKVVIIDEADAMNEAAANALLKTLEEPPKNTPFILIANDPSRLL 145
PRK04132 PRK04132
replication factor C small subunit; Provisional
 63-181 7.36e-31

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 118.40  E-value: 7.36e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   63 GADLPNLLFygppgtgKTSTILAAARELYGPDlYRQRVLELNASDERGIQVVREKVKRFAQltvagTRPDGKTcpPFKII 142
Cdd:PRK04132 570 GGNLPTVLH-------NTTAALALARELFGEN-WRHNFLELNASDERGINVIREKVKEFAR-----TKPIGGA--SFKII 634

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 32451662  143 ILDEADSMTSAAQAALRRTMEKESRTTRFCLICNYVSRL 181
Cdd:PRK04132 635 FLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKI 673
PRK04195 PRK04195
replication factor C large subunit; Provisional
 32-148 7.35e-26

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 103.46  E-value: 7.35e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   32 AVPWVEKYRPKCVDEVAFQEEVVAVLKKSLE----GADLPNLLFYGPPGTGKTSTILAAARElYGPDlyrqrVLELNASD 107
Cdd:PRK04195   1 MMPWVEKYRPKTLSDVVGNEKAKEQLREWIEswlkGKPKKALLLYGPPGVGKTSLAHALAND-YGWE-----VIELNASD 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 32451662  108 ERGiqvvREKVKRFAQltvAGTRPDGKTCPPFKIIILDEAD 148
Cdd:PRK04195  75 QRT----ADVIERVAG---EAATSGSLFGARRKLILLDEVD 108
44 PHA02544
clamp loader, small subunit; Provisional
 35-180 9.01e-26

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 101.22  E-value: 9.01e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   35 WVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGP-PGTGKTSTILAAARELyGPDlyrqrVLELNASDERgIQV 113
Cdd:PHA02544  11 WEQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPsPGTGKTTVAKALCNEV-GAE-----VLFVNGSDCR-IDF 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 32451662  114 VREKVKRFAQlTVAgtrpdgkTCPPFKIIILDEAD-SMTSAAQAALRRTMEKESRTTRFCLICNYVSR 180
Cdd:PHA02544  84 VRNRLTRFAS-TVS-------LTGGGKVIIIDEFDrLGLADAQRHLRSFMEAYSKNCSFIITANNKNG 143
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 50-177 2.99e-23

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


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 90.67  E-value: 2.99e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  50 QEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELYGPDLyrqRVLELNASDERGIQVVREKVKRFAQLTVAGT 129
Cdd:cd00009   3 QEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGA---PFLYLNASDLLEGLVVAELFGHFLVRLLFEL 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 32451662 130 RPDGKTCppfkIIILDEADSMTSAAQAALRRTME------KESRTTRFCLICNY 177
Cdd:cd00009  80 AEKAKPG----VLFIDEIDSLSRGAQNALLRVLEtlndlrIDRENVRVIGATNR 129
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 69-181 2.46e-14

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


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 66.46  E-value: 2.46e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    69 LLFYGPPGTGKTSTILAAARELYGPdlyrqrVLELNASDERGIQvVREKVKRFAQ-LTVAgtrpdgKTCPPfKIIILDEA 147
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAP------FIEISGSELVSKY-VGESEKRLRElFEAA------KKLAP-CVIFIDEI 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 32451662   148 DSMTSA-----------AQAALRRTMEKESRTTR---FCLICNYVSRL 181
Cdd:pfam00004  67 DALAGSrgsggdsesrrVVNQLLTELDGFTSSNSkviVIAATNRPDKL 114
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 37-146 8.25e-14

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 68.96  E-value: 8.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   37 EKYRPKCVDEVAFQEEVVA---VLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELygpdlyRQRVLELNASDErGIQV 113
Cdd:PRK13342   4 ERMRPKTLDEVVGQEHLLGpgkPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT------DAPFEALSAVTS-GVKD 76

                         90       100       110
                 ....*....|....*....|....*....|...
gi 32451662  114 VREKVKRFAQLTVAGTRPdgktcppfkIIILDE 146
Cdd:PRK13342  77 LREVIEEARQRRSAGRRT---------ILFIDE 100
PRK04132 PRK04132
replication factor C small subunit; Provisional
 34-82 4.63e-13

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 67.17  E-value: 4.63e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 32451662   34 PWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPNLLFYGPPGTGKTST 82
Cdd:PRK04132   8 PWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT 56
PRK07133 PRK07133
DNA polymerase III subunits gamma and tau; Validated
 35-163 6.24e-11

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235943 [Multi-domain]  Cd Length: 725  Bit Score: 60.60  E-value: 6.24e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   35 WVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAA------RELYGP------------ 93
Cdd:PRK07133   8 LYRKYRPKTFDDIVGQDHIVQTLKNIIKSNKISHaYLFSGPRGTGKTSVakIFANAlncshkTDLLEPcqecienvnnsl 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 32451662   94 DlyrqrVLELNASDERGIQVVR---EKVKRFAQLTvagtrpdgktcpPFKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK07133  88 D-----IIEMDAASNNGVDEIReliENVKNLPTQS------------KYKIYIIDEVHMLSKSAFNALLKTLE 143
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 68-176 1.01e-10

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: 57.38  E-value: 1.01e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662     68 NLLFYGPPGTGKTSTILAAARELYGPDLyrqRVLELNASDERGIQVVREKVKRFAQLTVAGTRPDG--------KTCPPf 139
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGG---GVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRlrlalalaRKLKP- 79

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 32451662    140 KIIILDEADSMTSAAQAALRRTMEKESRTTRFCLICN 176
Cdd:smart00382  80 DVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN 116
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
41-163 3.25e-10

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 58.28  E-value: 3.25e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  41 PKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAA---------------------RELYGPDly 96
Cdd:COG2812   6 PQTFDDVVGQEHVVRTLKNALASGRLAHaYLFTGPRGVGKTTLarILAKAlncengptgepcgecescraiAAGSHPD-- 83

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662  97 rqrVLEL--NASdERGIQVVREKVKRFAQLTVAGtrpdgktcpPFKIIILDEADSMTSAAQAALRRTME 163
Cdd:COG2812  84 ---VIEIdaEAS-NIGVDDIRELIEKVSYAPVEG---------RYKVYIIDEAHMLTTEAFNALLKTLE 139
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 33-173 3.29e-10

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 58.68  E-value: 3.29e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   33 VPWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAA------------------RELY 91
Cdd:PRK14953   4 IPFARKYRPKFFKEVIGQEIVVRILKNAVKLQRVSHaYIFAGPRGTGKTTIarILAKVlnclnpqegepcgkcencVEID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   92 G---PDLYrqrvlELNASDERGIQVVRekvkrfAQLTVAGTRP-DGKtcppFKIIILDEADSMTSAAQAALRRTMEKESR 167
Cdd:PRK14953  84 KgsfPDLI-----EIDAASNRGIDDIR------ALRDAVSYTPiKGK----YKVYIIDEAHMLTKEAFNALLKTLEEPPP 148


                 ....*.
gi 32451662  168 TTRFCL 173
Cdd:PRK14953 149 RTIFIL 154
PRK14963 PRK14963
DNA polymerase III subunits gamma and tau; Provisional
 37-163 5.54e-10

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184927 [Multi-domain]  Cd Length: 504  Bit Score: 57.93  E-value: 5.54e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   37 EKYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAARELYGPD-----------LYRQ---- 98
Cdd:PRK14963   6 QRARPITFDEVVGQEHVKEVLLAALRQGRLGHaYLFSGPRGVGKTTTarLIAMAVNCSGEDpkpcgecesclAVRRgahp 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 32451662   99 RVLELNASDERGIQVVREKVKRFAQLTVAGTRpdgktcppfKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK14963  86 DVLEIDAASNNSVEDVRDLREKVLLAPLRGGR---------KVYILDEAHMMSKSAFNALLKTLE 141
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 38-173 1.02e-09

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 56.81  E-value: 1.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTSTILAAARELYGPDL------YRQRVLELNASDERG 110
Cdd:PRK14970  10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQaLLFCGPRGVGKTTCARILARKINQPGYddpnedFSFNIFELDAASNNS 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 32451662  111 IQVVREKVK--RFAQLTvagtrpdGKtcppFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCL 173
Cdd:PRK14970  90 VDDIRNLIDqvRIPPQT-------GK----YKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFIL 143
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 38-173 4.50e-09

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 55.16  E-value: 4.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAA-----RELYGP-----------DLYRQ 98
Cdd:PRK14962   7 KYRPKTFSEVVGQDHVKKLIINALKKNSISHaYIFAGPRGTGKTTVarILAKSlncenRKGVEPcnecracrsidEGTFM 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 32451662   99 RVLELNASDERGIQVVReKVKRfaqlTVAGTRPDGKtcppFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCL 173
Cdd:PRK14962  87 DVIELDAASNRGIDEIR-KIRD----AVGYRPMEGK----YKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVL 152
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 40-87 8.02e-09

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 54.29  E-value: 8.02e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 32451662  40 RPKCVDEVAFQEEVVA---VLKKSLEGADLPNLLFYGPPGTGKTS--TILAAA 87
Cdd:COG2256  20 RPRTLDEVVGQEHLLGpgkPLRRAIEAGRLSSMILWGPPGTGKTTlaRLIANA 72
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 27-121 1.03e-08

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 54.19  E-value: 1.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    27 EKKQRAVPWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-----LLFYGPPGTGKTSTILAAARELyGPDlYRQRV- 100
Cdd:TIGR00602  66 ENLDGNEPWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENapkriLLITGPSGCGKSTTIKILSKEL-GIQ-VQEWSn 143

                          90       100
                  ....*....|....*....|....
gi 32451662   101 ---LELNASDERGIQVVREKVKRF 121
Cdd:TIGR00602 144 ptlPDFQKNDHKVTLSLESCFSNF 167
Rad17 pfam03215
Rad17 P-loop domain;
27-90 1.26e-08

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 52.65  E-value: 1.26e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662    27 EKKQRAVPWVEKYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-----LLFYGPPGTGKTSTILAAAREL 90
Cdd:pfam03215   1 INDDGGEQWYEKYKPNCLEQLAVHKRKIKDVQEWLDAMFLENakhriLLISGPSGCGKSTVIKELSKEL 69
PRK13341 PRK13341
AAA family ATPase;
30-158 2.47e-08

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 53.13  E-value: 2.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   30 QRAVPWVEKYRPKCVDEVAFQEEVVA---VLKKSLEGADLPNLLFYGPPGTGKTS--TILAaarelygpDLYRQRVLELN 104
Cdd:PRK13341  13 QSEAPLADRLRPRTLEEFVGQDHILGegrLLRRAIKADRVGSLILYGPPGVGKTTlaRIIA--------NHTRAHFSSLN 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 32451662  105 ASdERGIQVVREKVKRfAQLTVAgtRPDGKTcppfkIIILDEADSMTSAAQAAL 158
Cdd:PRK13341  85 AV-LAGVKDLRAEVDR-AKERLE--RHGKRT-----ILFIDEVHRFNKAQQDAL 129
PRK14948 PRK14948
DNA polymerase III subunit gamma/tau;
38-163 5.49e-08

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237862 [Multi-domain]  Cd Length: 620  Bit Score: 51.89  E-value: 5.49e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADL-PNLLFYGPPGTGKTST--ILaaARELY-----GP--------DLYRQ--- 98
Cdd:PRK14948   9 KYRPQRFDELVGQEAIATTLKNALISNRIaPAYLFTGPRGTGKTSSarIL--AKSLNclnsdKPtpepcgkcELCRAiaa 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662   99 ----RVLELNASDERGIQVVREKVKRfAQLTVAGTRpdgktcppFKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK14948  87 gnalDVIEIDAASNTGVDNIRELIER-AQFAPVQAR--------WKVYVIDECHMLSTAAFNALLKTLE 146
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 67-170 8.07e-08

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


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 49.59  E-value: 8.07e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  67 PNLLFYGPPGTGKTSTILAAARELyGPDLYRqrvleLNASD--ERGIQVVREKVKR-FAQLtvagtrpdgKTCPPfKIII 143
Cdd:cd19481  27 KGILLYGPPGTGKTLLAKALAGEL-GLPLIV-----VKLSSllSKYVGESEKNLRKiFERA---------RRLAP-CILF 90

                        90       100
                ....*....|....*....|....*..
gi 32451662 144 LDEADSMtsaaqaALRRTMEKESRTTR 170
Cdd:cd19481  91 IDEIDAI------GRKRDSSGESGELR 111
PRK14956 PRK14956
DNA polymerase III subunits gamma and tau; Provisional
 38-164 9.31e-08

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184920 [Multi-domain]  Cd Length: 484  Bit Score: 51.49  E-value: 9.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAARELYGPDLYR----------------Q 98
Cdd:PRK14956  11 KYRPQFFRDVIHQDLAIGALQNALKSGKIGHaYIFFGPRGVGKTTIarILAKRLNCENPIGNEpcnectscleitkgisS 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662   99 RVLELNASDERGIQVVRE---KVKrFAQLtvagtrpDGKtcppFKIIILDEADSMTSAAQAALRRTMEK 164
Cdd:PRK14956  91 DVLEIDAASNRGIENIRElrdNVK-FAPM-------GGK----YKVYIIDEVHMLTDQSFNALLKTLEE 147
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
45-165 1.06e-07

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 50.65  E-value: 1.06e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  45 DEVAFQEEVVAVLK---KSLEGADLP---------NLLFYGPPGTGKTSTILAAARELygpdlyRQRVLELNASderGI- 111
Cdd:COG1223   2 DDVVGQEEAKKKLKliiKELRRRENLrkfglwpprKILFYGPPGTGKTMLAEALAGEL------KLPLLTVRLD---SLi 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 32451662 112 -QVVREKVKRFAQL-TVAGTRPdgktCppfkIIILDEADSMtsaaqaALRRTMEKE 165
Cdd:COG1223  73 gSYLGETARNLRKLfDFARRAP----C----VIFFDEFDAI------AKDRGDQND 114
PRK06647 PRK06647
DNA polymerase III subunits gamma and tau; Validated
 38-163 1.08e-07

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235845 [Multi-domain]  Cd Length: 563  Bit Score: 51.31  E-value: 1.08e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTSTILAAAREL---YGPDLY---------------RQ 98
Cdd:PRK06647   9 KRRPRDFNSLEGQDFVVETLKHSIESNKIANaYIFSGPRGVGKTSSARAFARCLncvNGPTPMpcgecsscksidndnSL 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 32451662   99 RVLELNASDERGIQVVREkVKRFAQLTVAGTRpdgktcppFKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK06647  89 DVIEIDGASNTSVQDVRQ-IKEEIMFPPASSR--------YRVYIIDEVHMLSNSAFNALLKTIE 144
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 38-163 1.91e-07

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 50.58  E-value: 1.91e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSL-EGADLPNLLFYGPPGTGKTST--ILAAARELYGPDlYRQR--------------- 99
Cdd:PRK14950   9 KWRSQTFAELVGQEHVVQTLRNAIaEGRVAHAYLFTGPRGVGKTSTarILAKAVNCTTND-PKGRpcgtcemcraiaegs 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 32451662  100 ---VLELNASDERGIQVVREKVKRfAQLTVAGTRpdgktcppFKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK14950  88 avdVIEMDAASHTSVDDAREIIER-VQFRPALAR--------YKVYIIDEVHMLSTAAFNALLKTLE 145
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 40-90 3.20e-07

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 47.88  E-value: 3.20e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 32451662    40 RPKCVDEVAFQEEVVAVLKKSLEGAD-----LPNLLFYGPPGTGKTSTILAAAREL 90
Cdd:pfam05496   2 RPRTLDEYIGQEKVKENLKIFIEAAKqrgeaLDHVLLYGPPGLGKTTLANIIANEM 57
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 50-163 5.60e-07

DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA.


Pssm-ID: 433013 [Multi-domain]  Cd Length: 161  Bit Score: 47.59  E-value: 5.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    50 QEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTSTILAAARELY----GPDLYR------QRVLELN-------ASDERGI 111
Cdd:pfam13177   2 QPEAIQLLQNSLENGRLSHaYLFSGPEGVGKLELALAFAKALFceepGDDLPCgqcrscRRIESGNhpdlviiEPEGQSI 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 32451662   112 QV--VREKVKRFAQLTVAGtrpdgktcpPFKIIILDEADSMTSAAQAALRRTME 163
Cdd:pfam13177  82 KIdqIRELQKEFSKSPYEG---------KKKVYIIEDAEKMTASAANSLLKFLE 126
PRK06305 PRK06305
DNA polymerase III subunits gamma and tau; Validated
 38-173 6.01e-07

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180523 [Multi-domain]  Cd Length: 451  Bit Score: 49.00  E-value: 6.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTS--TILAAA-------------------REL-YGPD 94
Cdd:PRK06305  10 KYRPQTFSEILGQDAVVAVLKNALRFNRAAHaYLFSGIRGTGKTTlaRIFAKAlncqnptedqepcnqcascKEIsSGTS 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662   95 LyrqRVLELNASDERGIQVVREkvkrfAQLTVAGTRPDGKtcppFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCL 173
Cdd:PRK06305  90 L---DVLEIDGASHRGIEDIRQ-----INETVLFTPSKSR----YKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFL 156
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 34-173 6.09e-07

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 48.91  E-value: 6.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   34 PWVEKYRPKCVDEVAFQEEVVAVLKKSL-EGADLPNLLFYGPPGTGKTSTILAAAREL---YGP--------DLYRQ--- 98
Cdd:PRK14959   5 SLTARYRPQTFAEVAGQETVKAILSRAAqENRVAPAYLFSGTRGVGKTTIARIFAKALnceTAPtgepcntcEQCRKvtq 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   99 ----RVLELNASDERGIqvvrEKVKRFAQltVAGTRP-DGKtcppFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCL 173
Cdd:PRK14959  85 gmhvDVVEIDGASNRGI----DDAKRLKE--AIGYAPmEGR----YKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVL 154
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
40-90 1.37e-06

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 47.43  E-value: 1.37e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 32451662   40 RPKCVDEVAFQEEVVAVLKKSLEGAD-----LPNLLFYGPPGTGKTStiLAA--AREL 90
Cdd:PRK00080  20 RPKSLDEFIGQEKVKENLKIFIEAAKkrgeaLDHVLLYGPPGLGKTT--LANiiANEM 75
PRK08451 PRK08451
DNA polymerase III subunits gamma and tau; Validated
 38-163 1.46e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236267 [Multi-domain]  Cd Length: 535  Bit Score: 47.72  E-value: 1.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTSTILAAARELY---GP-----DLYRQRV-------- 100
Cdd:PRK08451   7 KYRPKHFDELIGQESVSKTLSLALDNNRLAHaYLFSGLRGSGKTSSARIFARALVceqGPsstpcDTCIQCQsalenrhi 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 32451662  101 --LELNASDERGIQVVR---EKVK---RFAQltvagtrpdgktcppFKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK08451  87 diIEMDAASNRGIDDIReliEQTKykpSMAR---------------FKIFIIDEVHMLTKEAFNALLKTLE 142
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
51-90 4.27e-06

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 46.38  E-value: 4.27e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 32451662  51 EEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAAREL 90
Cdd:COG1474  36 EELASALRPALRGERPSNVLIYGPTGTGKTAVAKYVLEEL 75
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 51-149 6.35e-06

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 45.67  E-value: 6.35e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  51 EEVVAVLKKSLE-----GADLPN-LLFYGPPGTGKTSTILAAARELYGPdlyrqrVLELNASD---------ERGIqvvR 115
Cdd:COG0464 170 RELVALPLKRPElreeyGLPPPRgLLLYGPPGTGKTLLARALAGELGLP------LIEVDLSDlvskyvgetEKNL---R 240

                        90       100       110
                ....*....|....*....|....*....|....
gi 32451662 116 EKVKRFAQLTVAgtrpdgktcppfkIIILDEADS 149
Cdd:COG0464 241 EVFDKARGLAPC-------------VLFIDEADA 261
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 51-94 7.64e-06

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 45.53  E-value: 7.64e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 32451662  51 EEVVAVLKKSlegadlPNLLFYGPPGTGKTSTILAAARELYGPD 94
Cdd:COG1401 212 EAFLAALKTK------KNVILAGPPGTGKTYLARRLAEALGGED 249
PRK05896 PRK05896
DNA polymerase III subunits gamma and tau; Validated
 37-163 9.54e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235638 [Multi-domain]  Cd Length: 605  Bit Score: 45.22  E-value: 9.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   37 EKYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTS--TILAAARELYGPD--------------LYRQR 99
Cdd:PRK05896   8 RKYRPHNFKQIIGQELIKKILVNAILNNKLTHaYIFSGPRGIGKTSiaKIFAKAINCLNPKdgdccnscsvcesiNTNQS 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 32451662  100 V--LELNASDERGIQVVREKVKRFAQLtvagtrpdgKTCPPFKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK05896  88 VdiVELDAASNNGVDEIRNIIDNINYL---------PTTFKYKVYIIDEAHMLSTSAWNALLKTLE 144
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 40-90 1.02e-05

Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, recombination and repair];


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 45.07  E-value: 1.02e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 32451662  40 RPKCVDEVAFQEEVVAVLKKSLEGAD-----LPNLLFYGPPGTGKT--STILaaAREL 90
Cdd:COG2255  23 RPKRLDEYIGQEKVKENLKIFIEAAKkrgeaLDHVLLYGPPGLGKTtlAHII--ANEM 78
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 45-90 1.58e-05

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 44.61  E-value: 1.58e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662  45 DEVAFQEEVVAVLKKSLE------------GADLPN-LLFYGPPGTGKTSTILAAAREL 90
Cdd:COG1222  78 DDIGGLDEQIEEIREAVElplknpelfrkyGIEPPKgVLLYGPPGTGKTLLAKAVAGEL 136
AAA_22 pfam13401
AAA domain;
69-174 2.13e-05

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 42.33  E-value: 2.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    69 LLFYGPPGTGKTSTILAAARELygpDLYRQRVLELNASDERGIQVVREKVKRFAQLTVAGTRP----------DGKTCPP 138
Cdd:pfam13401   8 LVLTGESGTGKTTLLRRLLEQL---PEVRDSVVFVDLPSGTSPKDLLRALLRALGLPLSGRLSkeellaalqqLLLALAV 84

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 32451662   139 FKIIILDEADSMTSAAQAALRRTMEKESRTTRFCLI 174
Cdd:pfam13401  85 AVVLIIDEAQHLSLEALEELRDLLNLSSKLLQLILV 120
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
 38-163 3.03e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 43.96  E-value: 3.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAA------------------RELY---GP 93
Cdd:PRK14965   9 KYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHaFLFTGARGVGKTSTarILAKAlnceqgltaepcnvcppcVEITegrSV 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 32451662   94 DlyrqrVLELNASDERGIQVVREkvkrfaqltvagTRPDGKTCPP---FKIIILDEADSMTSAAQAALRRTME 163
Cdd:PRK14965  89 D-----VFEIDGASNTGVDDIRE------------LRENVKYLPSrsrYKIFIIDEVHMLSTNAFNALLKTLE 144
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 50-91 6.45e-05

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members 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: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 42.22  E-value: 6.45e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 32451662  50 QEEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAARELY 91
Cdd:cd18038   4 DEQKLAVRNIVTGTSRPPPYIIFGPPGTGKTVTLVEAILQVL 45
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 73-157 7.16e-05

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: 41.78  E-value: 7.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    73 GPPGTGKTsTILAAARELYGPDLYRQRVLelnASDERGIQVVREKVKrFAQLTVA---GTRPDGKTCPPFKIIILDEAdS 149
Cdd:pfam13604  25 GPAGTGKT-TALKALREAWEAAGYRVIGL---APTGRAAKVLGEELG-IPADTIAkllHRLGGRAGLDPGTLLIVDEA-G 98


                  ....*...
gi 32451662   150 MTSAAQAA 157
Cdd:pfam13604  99 MVGTRQMA 106
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 69-167 7.88e-05

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


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 41.51  E-value: 7.88e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  69 LLFYGPPGTGKTSTILAAARE-------LYGPDLYRQRVLElnasDERGIQVVREKVKRFAQltvagtrpdgktcppfKI 141
Cdd:cd19503  37 VLLHGPPGTGKTLLARAVANEaganflsISGPSIVSKYLGE----SEKNLREIFEEARSHAP----------------SI 96

                        90       100
                ....*....|....*....|....*.
gi 32451662 142 IILDEADSMTSAAQAALRrtmEKESR 167
Cdd:cd19503  97 IFIDEIDALAPKREEDQR---EVERR 119
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 38-94 8.92e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 42.39  E-value: 8.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKT--STILAAARELYGPD 94
Cdd:PRK14951   9 KYRPRSFSEMVGQEHVVQALTNALTQQRLHHaYLFTGTRGVGKTtvSRILAKSLNCQGPD 68
TIGR02928 TIGR02928
orc1/cdc6 family replication initiation protein; Members of this protein family are found ...
 51-90 9.13e-05

orc1/cdc6 family replication initiation protein; Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274354 [Multi-domain]  Cd Length: 365  Bit Score: 42.23  E-value: 9.13e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 32451662    51 EEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAAREL 90
Cdd:TIGR02928  25 EELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKEL 64
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 73-174 1.17e-04

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: 40.30  E-value: 1.17e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  73 GPPGTGKTSTILAAARELygpdlyrqrvleLNASDERGIQVVrekvkrfAQLTVAGTRPDgktcppfkIIILDEAdSMTS 152
Cdd:cd17934   6 GPPGTGKTTTIAAIVLQL------------LKGLRGKRVLVT-------AQSNVAVDNVD--------VVIIDEA-SQIT 57

                        90       100
                ....*....|....*....|..
gi 32451662 153 AAQAALRRtmekeSRTTRFCLI 174
Cdd:cd17934  58 EPELLIAL-----IRAKKVVLV 74
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 51-160 1.22e-04

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


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 40.95  E-value: 1.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    51 EEVVAVLKKSLEGaDLPNLLFYGPPGTGKTSTILAAARELYGPDLYrqrVLELNASDERGIQVVREKVKRFAQLTVAGTR 130
Cdd:pfam13191  10 EQLLDALDRVRSG-RPPSVLLTGEAGTGKTTLLRELLRALERDGGY---FLRGKCDENLPYSPLLEALTREGLLRQLLDE 85

                          90       100       110
                  ....*....|....*....|....*....|
gi 32451662   131 PDGKTCPPFKIIILDEADSMTSAAQAALRR 160
Cdd:pfam13191  86 LESSLLEAWRAALLEALAPVPELPGDLAER 115
DUF2075 pfam09848
Schlafen group 3, DNA/RNA helicase domain; This domain is found in at the C terminus of group ...
 69-161 1.35e-04

Schlafen group 3, DNA/RNA helicase domain; This domain is found in at the C terminus of group 3 Schlafen proteins from mammals, and represents the DNA/RNA helicase domain. Schlafen proteins are involved in the control of cell proliferation, induction of immune responses, and in the regulation of viral replication. These proteins inhibit DNA replication and promote cell death in response to DNA damage. They play a role in genome surveillance to kill cells with defective replication. This domain is also found in various uncharacterized prokaryotic proteins fused to a DNA helicase, GIY-YIG or PD-(D/E)XK catalytic domain or HsdR-N(terminal) domain, which are similar to AAA DNA helicase, Type III restriction enzyme ATPase, RecD and RuvB helicase.


Pssm-ID: 430875 [Multi-domain]  Cd Length: 355  Bit Score: 41.88  E-value: 1.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    69 LLFYGPPGTGKTSTILAAARELYGPDLYRQRVLELNASDERgiQVVREKVKR----------FAQLTVAGTRPDgKTCPP 138
Cdd:pfam09848   4 FLVTGGPGTGKTVIGLNLFAELEDSDLGRTAVYLSGNHPLV--LVLYEALAGdlrkkrkksaFQRPTSFINNLH-KTHPH 80

                          90       100
                  ....*....|....*....|...
gi 32451662   139 FKIIILDEADSMTSAAQAALRRT 161
Cdd:pfam09848  81 EDVVIFDEAHRLWDKSDPYNNFS 103
PRK05563 PRK05563
DNA polymerase III subunits gamma and tau; Validated
 38-87 1.55e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235505 [Multi-domain]  Cd Length: 559  Bit Score: 41.78  E-value: 1.55e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEG-----AdlpnLLFYGPPGTGKTST--ILAAA 87
Cdd:PRK05563   9 KWRPQTFEDVVGQEHITKTLKNAIKQgkishA----YLFSGPRGTGKTSAakIFAKA 61
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 70-109 1.94e-04

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


Pssm-ID: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 40.03  E-value: 1.94e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 32451662  70 LFYGPPGTGKTSTILAAARELyGPDLYRQRVLELNASDER 109
Cdd:cd19510  27 LLYGPPGTGKSSFIAALAGEL-DYDICDLNLSEVVLTDDR 65
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
48-147 2.28e-04

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 41.16  E-value: 2.28e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  48 AFQEEVVAVLKKSLEGADlPNLLFYGPPGTGKTSTILAAARELYGPdlyrQRVL------ELN--ASDE-----RGIQVV 114
Cdd:COG1061  83 PYQQEALEALLAALERGG-GRGLVVAPTGTGKTVLALALAAELLRG----KRVLvlvprrELLeqWAEElrrflGDPLAG 157

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 32451662 115 REKVKRFAQLTVA-----GTRPDGKTCPP-FKIIILDEA 147
Cdd:COG1061 158 GGKKDSDAPITVAtyqslARRAHLDELGDrFGLVIIDEA 196
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 48-153 3.11e-04

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


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 39.57  E-value: 3.11e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  48 AFQEEVVAVLKKSLE----GADLPN-LLFYGPPGTGKTSTILAAARE-------LYGPDLYRQRVLElnasDERGiqvVR 115
Cdd:cd19511   4 ELKEAVEWPLKHPDAfkrlGIRPPKgVLLYGPPGCGKTLLAKALASEaglnfisVKGPELFSKYVGE----SERA---VR 76

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 32451662 116 EKVKRFAQLTVAgtrpdgktcppfkIIILDEADSMTSA 153
Cdd:cd19511  77 EIFQKARQAAPC-------------IIFFDEIDSLAPR 101
cdc6 PRK00411
ORC1-type DNA replication protein;
51-90 4.25e-04

ORC1-type DNA replication protein;


Pssm-ID: 234751 [Multi-domain]  Cd Length: 394  Bit Score: 40.22  E-value: 4.25e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 32451662   51 EEVVAVLKKSLEGADLPNLLFYGPPGTGKTSTILAAAREL 90
Cdd:PRK00411  40 EELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEEL 79
PRK14958 PRK14958
DNA polymerase III subunits gamma and tau; Provisional
 38-173 5.04e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184922 [Multi-domain]  Cd Length: 509  Bit Score: 40.10  E-value: 5.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKT--STILAA------------------AREL---YGP 93
Cdd:PRK14958   9 KWRPRCFQEVIGQAPVVRALSNALDQQYLHHaYLFTGTRGVGKTtiSRILAKclncekgvsanpcndcenCREIdegRFP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   94 DLYrqrvlELNASDERGIQVVREKVKRFaqltvagtrPDGKTCPPFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCL 173
Cdd:PRK14958  89 DLF-----EVDAASRTKVEDTRELLDNI---------PYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFIL 154
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
38-173 5.11e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 40.24  E-value: 5.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKT--STILAAARELYGPDL------------------- 95
Cdd:PRK12323   9 KWRPRDFTTLVGQEHVVRALTHALEQQRLHHaYLFTGTRGVGKTtlSRILAKSLNCTGADGeggitaqpcgqcracteid 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   96 ------YrqrvLELNASDERGIQVVREKVKRFAQLTVAGTrpdgktcppFKIIILDEADSMTSAAQAALRRTMEKESRTT 169
Cdd:PRK12323  89 agrfvdY----IEMDAASNRGVDEMAQLLDKAVYAPTAGR---------FKVYMIDEVHMLTNHAFNAMLKTLEEPPEHV 155


                 ....
gi 32451662  170 RFCL 173
Cdd:PRK12323 156 KFIL 159
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 50-90 5.63e-04

N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB, and RXRA. It belongs 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: 350834 [Multi-domain]  Cd Length: 230  Bit Score: 39.49  E-value: 5.63e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 32451662  50 QEEVVA-VLKKSLEGADLPNLLFYGPPGTGKTSTILAAAREL 90
Cdd:cd18076   6 QQLAFNfIAGKPSEARFVPPLLIYGPFGTGKTFTLAMAALEV 47
Lon COG0466
ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, ...
 55-81 6.53e-04

ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440234 [Multi-domain]  Cd Length: 785  Bit Score: 40.00  E-value: 6.53e-04
                        10        20
                ....*....|....*....|....*....
gi 32451662  55 AV--LKKSLEGadlPNLLFYGPPGTGKTS 81
Cdd:COG0466 342 AVrkLKKKLKG---PILCLVGPPGVGKTS 367
ftsH CHL00176
cell division protein; Validated
 51-87 7.66e-04

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 39.65  E-value: 7.66e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 32451662   51 EEVVAVLKKS----LEGADLPN-LLFYGPPGTGKtsTILAAA 87
Cdd:CHL00176 196 EEVVSFLKKPerftAVGAKIPKgVLLVGPPGTGK--TLLAKA 235
COG2842 COG2842
Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons]; ...
 70-160 7.95e-04

Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons];


Pssm-ID: 442090 [Multi-domain]  Cd Length: 254  Bit Score: 39.16  E-value: 7.95e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  70 LFYGPPGTGKTSTILAAARELYG------PDLYRQRVL------ELNASDERG-IQVVREKVKRFAQLTVagtRPdgktc 136
Cdd:COG2842  54 VVYGESGVGKTTAAREYANRNPNviyvtaSPSWTSKELleelaeELGIPAPPGtIADLRDRILERLAGTG---RL----- 125

                        90       100
                ....*....|....*....|....
gi 32451662 137 ppfkiIILDEADSMTSAAQAALRR 160
Cdd:COG2842 126 -----LIIDEADHLKPKALEELRD 144
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 52-90 1.02e-03

lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an evolutionarily conserved ATP-dependent serine protease, present in bacteria and eukaryotic mitochondria and peroxisomes, which mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Lon protease is both an ATP-dependent peptidase and a protein-activated ATPase. This RecA-like Lon domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 38.31  E-value: 1.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 32451662  52 EVVAV--LKKSLEGadlPNLLFYGPPGTGKTSTILAAAREL 90
Cdd:cd19500  24 EYLAVrkLKGSMKG---PILCLVGPPGVGKTSLGKSIARAL 61
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
38-173 1.13e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 38.99  E-value: 1.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLPN-LLFYGPPGTGKTST--ILAAA---RELyGPD------------LYRQR 99
Cdd:PRK14971  10 KYRPSTFESVVGQEALTTTLKNAIATNKLAHaYLFCGPRGVGKTTCarIFAKTincQNL-TADgeacnecescvaFNEQR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  100 ---VLELNASDERGIQVVR---EKVKRFAQLtvagtrpdGKtcppFKIIILDEADSMTSAAQAALRRTMEKESRTTRFCL 173
Cdd:PRK14971  89 synIHELDAASNNSVDDIRnliEQVRIPPQI--------GK----YKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFIL 156
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 51-160 1.33e-03

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 37.18  E-value: 1.33e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  51 EEVVAVLKKSLEGadlPNLLFYGPPGTGKTSTILAAARELygpdLYR-QRVLeLNASDERGIQVVREKVKRFAQLTVAGT 129
Cdd:cd18043   2 SSQEAAIISARNG---KNVVIQGPPGTGKSQTIANIIANA----LARgKRVL-FVSEKKAALDVVRFPCWIMSPLSVSQY 73

                        90       100       110
                ....*....|....*....|....*....|..
gi 32451662 130 RPDGKtcPPFKIIILDEADSM-TSAAQAALRR 160
Cdd:cd18043  74 LPLNR--NLFDLVIFDEASQIpIEEALPALFR 103
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 68-158 1.62e-03

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


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 37.27  E-value: 1.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662    68 NLLFYGPPGTGKTSTILAAARELYG-PDLYRQRVLELNASDERGIQVVREKVKRFAQ--LTVAGTRPDgktcppfkIIIL 144
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSNrPVFYVQLTRDTTEEDLFGRRNIDPGGASWVDgpLVRAAREGE--------IAVL 72

                          90
                  ....*....|....
gi 32451662   145 DEADSMTSAAQAAL 158
Cdd:pfam07728  73 DEINRANPDVLNSL 86
PRK06835 PRK06835
DNA replication protein DnaC; Validated
 51-90 2.06e-03

DNA replication protein DnaC; Validated


Pssm-ID: 235871 [Multi-domain]  Cd Length: 329  Bit Score: 37.96  E-value: 2.06e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 32451662   51 EEVVAVLKKSLEGADLP--NLLFYGPPGTGKTSTILAAAREL 90
Cdd:PRK06835 166 EKILEKCKNFIENFDKNneNLLFYGNTGTGKTFLSNCIAKEL 207
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
70-94 2.33e-03

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 38.03  E-value: 2.33e-03
                        10        20
                ....*....|....*....|....*
gi 32451662  70 LFYGPPGTGKTSTILAAARELyGPD 94
Cdd:COG1224  68 LIVGPPGTGKTALAVAIAREL-GED 91
Kti12 COG4088
tRNA uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein) ...
 73-116 3.59e-03

tRNA uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein) [Translation, ribosomal structure and biogenesis, Defense mechanisms];


Pssm-ID: 443264 [Multi-domain]  Cd Length: 179  Bit Score: 36.63  E-value: 3.59e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 32451662  73 GPPGTGKTSTILAAARELY---------GPDLYRQRVLELNASDERGIQVVRE 116
Cdd:COG4088  11 GPPGSGKTTFAKALAQRLYaegiavallHSDDFRRFLVNESFPKETYEEVVED 63
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 50-90 3.76e-03

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 37.28  E-value: 3.76e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 32451662    50 QEEVVAVLKKSLEGAD-----LPNLLFYGPPGTGKTSTILAAAREL 90
Cdd:TIGR00635   9 QEKVKEQLQLFIEAAKmrqeaLDHLLLYGPPGLGKTTLAHIIANEM 54
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 73-157 3.88e-03

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: 36.38  E-value: 3.88e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  73 GPPGTGKTsTILAAARELYgpdlyrqrvlelnasDERGIQVV------------REKVKRFAQlTVA----------GTR 130
Cdd:cd17933  19 GGAGTGKT-TTLKALLAAL---------------EAEGKRVVlaaptgkaakrlSESTGIEAS-TIHrllginpgggGFY 81

                        90       100
                ....*....|....*....|....*..
gi 32451662 131 PDGKTCPPFKIIILDEAdSMTSAAQAA 157
Cdd:cd17933  82 YNEENPLDADLLIVDEA-SMVDTRLMA 107
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 45-92 4.81e-03

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


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 36.39  E-value: 4.81e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 32451662  45 DEVAFQEE----VVAVLKKSLEGADLPN-----LLFYGPPGTGKTSTILAAARELYG 92
Cdd:cd19499  11 ERVVGQDEavkaVSDAIRRARAGLSDPNrpigsFLFLGPTGVGKTELAKALAELLFG 67
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 70-101 4.90e-03

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.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 36.94  E-value: 4.90e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 32451662    70 LFYGPPGTGKTSTILAAARELYGPDL----YRQRVL 101
Cdd:pfam13086  17 LIQGPPGTGKTTTIVELIRQLLSYPAtsaaAGPRIL 52
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 42-164 5.83e-03

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


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 36.23  E-value: 5.83e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  42 KCVDEVafqEEVVAVLKKSLE-----GADLPN-LLFYGPPGTGKTSTILAAARELYGPdLYRQRVLEL-----NASDERg 110
Cdd:cd19518   7 STLKEL---CELLIHPILPPEyfqhlGVEPPRgVLLHGPPGCGKTMLANAIAGELKVP-FLKISATEIvsgvsGESEEK- 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 32451662 111 IQVVREKVKRFAqltvagtrpdgkTCppfkIIILDEADSMTSAAQAAlRRTMEK 164
Cdd:cd19518  82 IRELFDQAISNA------------PC----IVFIDEIDAITPKRESA-QREMER 118
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 50-156 6.60e-03

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 36.05  E-value: 6.60e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662  50 QEEVVavlKKSLEGADLpnLLFYGPPGTGKTSTILAAARELYGPdlyRQRVLELNASD-------ER----GIQVVR--- 115
Cdd:cd18044   6 QKEAV---KFALSQKDV--ALIHGPPGTGKTTTVVEIILQAVKR---GEKVLACAPSNiavdnlvERlvalKVKVVRigh 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 32451662 116 -----EKVKR------------FAQLTVAGTR-PDGKTcpPFKIIILDEadsmtsAAQA 156
Cdd:cd18044  78 parllESVLDhsldalvaaqvvLATNTGAGSRqLLPNE--LFDVVVIDE------AAQA 128
YifB COG0606
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational ...
 68-102 7.06e-03

Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440371 [Multi-domain]  Cd Length: 502  Bit Score: 36.56  E-value: 7.06e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 32451662  68 NLLFYGPPGTGKT------STILaaarelygPDLYRQRVLE 102
Cdd:COG0606 213 NLLMIGPPGSGKTmlarrlPGIL--------PPLTEEEALE 245
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 73-85 8.55e-03

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 36.04  E-value: 8.55e-03
                        10
                ....*....|...
gi 32451662  73 GPPGTGKTSTILA 85
Cdd:cd18042  24 GPPGTGKTKTIVG 36
Mg_chelatase pfam01078
Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that ...
 68-105 8.69e-03

Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.


Pssm-ID: 426032 [Multi-domain]  Cd Length: 207  Bit Score: 35.97  E-value: 8.69e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 32451662    68 NLLFYGPPGTGKTstiLAAAReLYG--PDLYRQRVLELNA 105
Cdd:pfam01078  24 NLLMIGPPGSGKT---MLAKR-LPGilPPLTEAEALEVTA 59
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 38-158 8.78e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 36.50  E-value: 8.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   38 KYRPKCVDEVAFQEEVVAVLKKSLEGADLpN--LLFYGPPGTGKTST--ILAAA------------------RELY--GP 93
Cdd:PRK07764   8 RYRPATFAEVIGQEHVTEPLSTALDSGRI-NhaYLFSGPRGCGKTSSarILARSlncvegptstpcgecdscVALApgGP 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32451662   94 ---DlyrqrVLELNASDERGIQVVREKVKR--FAQltvAGTRpdgktcppFKIIILDEADSMTSAAQAAL 158
Cdd:PRK07764  87 gslD-----VTEIDAASHGGVDDARELRERafFAP---AESR--------YKIFIIDEAHMVTPQGFNAL 140
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 51-87 8.87e-03

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


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 35.67  E-value: 8.87e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 32451662  51 EEVVAVLKKSLE----GADLPN-LLFYGPPGTGKtsTILAAA 87
Cdd:cd19501  17 KEVVEFLKNPEKftklGAKIPKgVLLVGPPGTGK--TLLAKA 56
 
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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