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Conserved domains on  [gi|398364719|ref|NP_009644|]
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replication factor C subunit 5 [Saccharomyces cerevisiae S288C]

Protein Classification

replication factor C small subunit( domain architecture ID 1005402)

replication factor C small subunit is an AAA family ATPase containing an AAA (ATPases Associated with various cellular Activities) domain, similar to replication factor C subunit 3 (RFC3), which forms a heterotetramer with subunits RFC2, RFC4 and RFC5 and is involved in the elongation of primed DNA templates by DNA polymerases delta and epsilon

CATH:  3.40.50.300|1.10.8.60|1.20.272.10
Gene Ontology:  GO:0016887|GO:0003677|GO:0003689|GO:0006281|GO:0006260|GO:0005663
SCOP:  4000283|4001080

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12402 super family cl36124
replication factor C small subunit 2; Reviewed
 3-243 3.14e-42

replication factor C small subunit 2; Reviewed


The actual alignment was detected with superfamily member PRK12402:

Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 149.75  E-value: 3.14e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPrDLPHLLLYGPNGTGKKTRCMALLESI-----------------FGPGV 65
Cdd:PRK12402   4 LWTEKYRPALLEDILGQDEVVERLSRAVDSP-NLPHLLVQGPPGSGKTAAVRALARELygdpwennftefnvadfFDQGK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  66 YRLKIDVR--QFVTaSNRKLELNVVSspyhleitpsdmgnndriVIQELLKEVAQMEQVDFQdskdglahrYKCVIINEA 143
Cdd:PRK12402  83 KYLVEDPRfaHFLG-TDKRIRSSKID------------------NFKHVLKEYASYRPLSAD---------YKTILLDNA 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 144 NSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLeTKDILKRIA 223
Cdd:PRK12402 135 EALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDY-DDDGLELIA 213

                        250       260
                 ....*....|....*....|
gi 398364719 224 QASNGNLRVSLLMLESMALN 243
Cdd:PRK12402 214 YYAGGDLRKAILTLQTAALA 233
 
Name Accession Description Interval E-value
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 3-243 3.14e-42

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 149.75  E-value: 3.14e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPrDLPHLLLYGPNGTGKKTRCMALLESI-----------------FGPGV 65
Cdd:PRK12402   4 LWTEKYRPALLEDILGQDEVVERLSRAVDSP-NLPHLLVQGPPGSGKTAAVRALARELygdpwennftefnvadfFDQGK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  66 YRLKIDVR--QFVTaSNRKLELNVVSspyhleitpsdmgnndriVIQELLKEVAQMEQVDFQdskdglahrYKCVIINEA 143
Cdd:PRK12402  83 KYLVEDPRfaHFLG-TDKRIRSSKID------------------NFKHVLKEYASYRPLSAD---------YKTILLDNA 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 144 NSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLeTKDILKRIA 223
Cdd:PRK12402 135 EALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDY-DDDGLELIA 213

                        250       260
                 ....*....|....*....|
gi 398364719 224 QASNGNLRVSLLMLESMALN 243
Cdd:PRK12402 214 YYAGGDLRKAILTLQTAALA 233
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
19-301 2.91e-28

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 111.22  E-value: 2.91e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  19 NEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGvyrlKIDVRQFVTASNRKLELNvvSSPYHLEITP 98
Cdd:COG0470    1 QEEAWEQLLAAAESGRLPHALLLHGPPGIGKTTLALALARDLLCEN----PEGGKACGQCHSRLMAAG--NHPDLLELNP 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  99 SDMGNNDRI-VIQELLKEVAQMeqvdfqdskdGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPI 177
Cdd:COG0470   75 EEKSDQIGIdQIRELGEFLSLT----------PLEGGRKVVIIDEADAMNEAAANALLKTLEEPPKNTPFILIANDPSRL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 178 IAPIKSRCLLIRCPAPSDSEISTILSDvvtneriQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKP 257
Cdd:COG0470  145 LPTIRSRCQVIRFRPPSEEEALAWLRE-------EGVDEDALEAILRLAGGDPRAAINLLQALAGRKELLEDLAALLSRD 217

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 398364719 258 DWIIVIHKLTRKIVKERsVNSLIEcraVLYDLLAHCIPANIILK 301
Cdd:COG0470  218 RALELLDALLKAEALEL-LDWLLK---WLLDNLPLEYAGEDLAR 257
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 19-193 2.40e-11

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: 61.01  E-value: 2.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  19 NEELTNFLKSLSDQPRDlPHLLLYGPNGTGKKTRCMALLESIFGPGVyrlkidvrqfvtasnrklelnvvsspYHLEITP 98
Cdd:cd00009    3 QEEAIEALREALELPPP-KNLLLYGPPGTGKTTLARAIANELFRPGA--------------------------PFLYLNA 55

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  99 SDMGNNDRIVIQELLKEVAQMEQVDFQdskdglaHRYKCVIINEANSLTKDAQAALRRTMEKYS------KNIRLIMVC- 171
Cdd:cd00009   56 SDLLEGLVVAELFGHFLVRLLFELAEK-------AKPGVLFIDEIDSLSRGAQNALLRVLETLNdlridrENVRVIGATn 128

                        170       180
                 ....*....|....*....|...
gi 398364719 172 -DSMSPIIAPIKSRCLLIRCPAP 193
Cdd:cd00009  129 rPLLGDLDRALYDRLDIRIVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 38-181 2.50e-05

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: 43.90  E-value: 2.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719    38 HLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFvtasnrkleLNVVSSPYHLEITPSDMGNNDRIVIQELLKEVA 117
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDI---------LEEVLDQLLLIIVGGKKASGSGELRLRLALALA 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398364719   118 QmeqvdfqdskdglAHRYKCVIINEANSLTKDAQAALRR--------TMEKYSKNIRLIMVCDSMSPIIAPI 181
Cdd:smart00382  75 R-------------KLKPDVLILDEITSLLDAEQEALLLlleelrllLLLKSEKNLTVILTTNDEKDLGPAL 133
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 19-194 1.48e-04

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: 41.81  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   19 NEELTNFLKSLSDQPRdLPH-LLLYGPNGTGKKTRCMALLESIF----GPGVYRLKIDvrqfvtaSNRKLELNvvSSPYH 93
Cdd:pfam13177   2 QPEAIQLLQNSLENGR-LSHaYLFSGPEGVGKLELALAFAKALFceepGDDLPCGQCR-------SCRRIESG--NHPDL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   94 LEITPSD--MGNNDrivIQELLKEVAQMeqvdfqdskdGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVC 171
Cdd:pfam13177  72 VIIEPEGqsIKIDQ---IRELQKEFSKS----------PYEGKKKVYIIEDAEKMTASAANSLLKFLEEPPGNTVIILLT 138

                         170       180
                  ....*....|....*....|...
gi 398364719  172 DSMSPIIAPIKSRCLLIRCPAPS 194
Cdd:pfam13177 139 ENPSRLLPTIRSRCQIIRFKPLS 161
 
Name Accession Description Interval E-value
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 3-243 3.14e-42

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 149.75  E-value: 3.14e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPrDLPHLLLYGPNGTGKKTRCMALLESI-----------------FGPGV 65
Cdd:PRK12402   4 LWTEKYRPALLEDILGQDEVVERLSRAVDSP-NLPHLLVQGPPGSGKTAAVRALARELygdpwennftefnvadfFDQGK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  66 YRLKIDVR--QFVTaSNRKLELNVVSspyhleitpsdmgnndriVIQELLKEVAQMEQVDFQdskdglahrYKCVIINEA 143
Cdd:PRK12402  83 KYLVEDPRfaHFLG-TDKRIRSSKID------------------NFKHVLKEYASYRPLSAD---------YKTILLDNA 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 144 NSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLeTKDILKRIA 223
Cdd:PRK12402 135 EALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDY-DDDGLELIA 213

                        250       260
                 ....*....|....*....|
gi 398364719 224 QASNGNLRVSLLMLESMALN 243
Cdd:PRK12402 214 YYAGGDLRKAILTLQTAALA 233
rfc PRK00440
replication factor C small subunit; Reviewed
 3-349 1.89e-38

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 139.24  E-value: 1.89e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQpRDLPHLLLYGPNGTGKKTRCMALLESIFGPgvyrlkiDVRQFVtasnrk 82
Cdd:PRK00440   6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKE-KNMPHLLFAGPPGTGKTTAALALARELYGE-------DWRENF------ 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  83 LELNVvsspyhleitpSDMGNNDriVIQELLKEVAQMEQVdfqdskdGLAhRYKCVIINEANSLTKDAQAALRRTMEKYS 162
Cdd:PRK00440  72 LELNA-----------SDERGID--VIRNKIKEFARTAPV-------GGA-PFKIIFLDEADNLTSDAQQALRRTMEMYS 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 163 KNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLeTKDILKRIAQASNGNLRVSLLMLESMAl 242
Cdd:PRK00440 131 QNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEI-TDDALEAIYYVSEGDMRKAINALQAAA- 208

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 243 nnelalkSSSPIIKPDwiiVIHKLT--------RKIVKERSVNSLIECRAVLYDLLA-HCIPANIILKELTFSLLDVEtL 313
Cdd:PRK00440 209 -------ATGKEVTEE---AVYKITgtarpeeiREMIELALNGDFTEAREKLRDLMIdYGLSGEDIIKQIHREVWSLD-I 277

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 398364719 314 NTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKV 349
Cdd:PRK00440 278 PEELKVELIDAIGEADFRITEGANERIQLEALLAKL 313
PLN03025 PLN03025
replication factor C subunit; Provisional
 4-244 2.37e-28

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 112.13  E-value: 2.37e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   4 WVDKYRPKSLNALSHNEELTNFLKSLSdQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPgvyrlkidvrqfvTASNRKL 83
Cdd:PLN03025   3 WVEKYRPTKLDDIVGNEDAVSRLQVIA-RDGNMPNLILSGPPGTGKTTSILALAHELLGP-------------NYKEAVL 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  84 ELNVvsspyhleitpSDMGNNDriVIQELLKEVAQmEQVDFQDSkdglahRYKCVIINEANSLTKDAQAALRRTMEKYSK 163
Cdd:PLN03025  69 ELNA-----------SDDRGID--VVRNKIKMFAQ-KKVTLPPG------RHKIVILDEADSMTSGAQQALRRTMEIYSN 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 164 NIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLeTKDILKRIAQASNGNLRvsllmlesMALN 243
Cdd:PLN03025 129 TTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPY-VPEGLEAIIFTADGDMR--------QALN 199


                 .
gi 398364719 244 N 244
Cdd:PLN03025 200 N 200
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
19-301 2.91e-28

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 111.22  E-value: 2.91e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  19 NEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGvyrlKIDVRQFVTASNRKLELNvvSSPYHLEITP 98
Cdd:COG0470    1 QEEAWEQLLAAAESGRLPHALLLHGPPGIGKTTLALALARDLLCEN----PEGGKACGQCHSRLMAAG--NHPDLLELNP 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  99 SDMGNNDRI-VIQELLKEVAQMeqvdfqdskdGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPI 177
Cdd:COG0470   75 EEKSDQIGIdQIRELGEFLSLT----------PLEGGRKVVIIDEADAMNEAAANALLKTLEEPPKNTPFILIANDPSRL 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 178 IAPIKSRCLLIRCPAPSDSEISTILSDvvtneriQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKP 257
Cdd:COG0470  145 LPTIRSRCQVIRFRPPSEEEALAWLRE-------EGVDEDALEAILRLAGGDPRAAINLLQALAGRKELLEDLAALLSRD 217

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 398364719 258 DWIIVIHKLTRKIVKERsVNSLIEcraVLYDLLAHCIPANIILK 301
Cdd:COG0470  218 RALELLDALLKAEALEL-LDWLLK---WLLDNLPLEYAGEDLAR 257
PRK04132 PRK04132
replication factor C small subunit; Provisional
 94-241 1.30e-18

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 87.20  E-value: 1.30e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  94 LEITPSDMGNNDriVIQELLKEVAQMEQVdfqdskdGLAhRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDS 173
Cdd:PRK04132 600 LELNASDERGIN--VIREKVKEFARTKPI-------GGA-SFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNY 669

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398364719 174 MSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLeTKDILKRIAQASNGNLRVSLLMLESMA 241
Cdd:PRK04132 670 SSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLEL-TEEGLQAILYIAEGDMRRAINILQAAA 736
44 PHA02544
clamp loader, small subunit; Provisional
 3-197 1.48e-16

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 79.26  E-value: 1.48e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPRdLPHLLLYGPN-GTGKKTRCMALLESIfGPGVYrlkidvrqFVTASNR 81
Cdd:PHA02544  10 MWEQKYRPSTIDECILPAADKETFKSIVKKGR-IPNMLLHSPSpGTGKTTVAKALCNEV-GAEVL--------FVNGSDC 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  82 KLElnvvsspyhleitpsdmgnndriVIQELLKEVAqmeqvdfqdSKDGLAHRYKCVIINEA-NSLTKDAQAALRRTMEK 160
Cdd:PHA02544  80 RID-----------------------FVRNRLTRFA---------STVSLTGGGKVIIIDEFdRLGLADAQRHLRSFMEA 127

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 398364719 161 YSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSE 197
Cdd:PHA02544 128 YSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEE 164
PRK04195 PRK04195
replication factor C large subunit; Provisional
 1-241 2.13e-12

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 68.02  E-value: 2.13e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   1 MSLWVDKYRPKSLNALSHNEE----LTNFLKS-LSDQPRdlPHLLLYGPNGTGKKTRCMALlesifgpgvyrlkidvrqf 75
Cdd:PRK04195   1 MMPWVEKYRPKTLSDVVGNEKakeqLREWIESwLKGKPK--KALLLYGPPGVGKTSLAHAL------------------- 59

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  76 vtASNRKLELnvvsspyhLEITPSDMGNNDRIviqellKEVAQMEQVdfqdSKDGLAHRYKCVIINEANSL--TKDA--Q 151
Cdd:PRK04195  60 --ANDYGWEV--------IELNASDQRTADVI------ERVAGEAAT----SGSLFGARRKLILLDEVDGIhgNEDRggA 119

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 152 AALRRTMEKySKN-IRLIMvCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLEtKDILKRIAQASNGNL 230
Cdd:PRK04195 120 RAILELIKK-AKQpIILTA-NDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECD-DEALKEIAERSGGDL 196

                        250
                 ....*....|.
gi 398364719 231 RVSLLMLESMA 241
Cdd:PRK04195 197 RSAINDLQAIA 207
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 19-193 2.40e-11

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: 61.01  E-value: 2.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  19 NEELTNFLKSLSDQPRDlPHLLLYGPNGTGKKTRCMALLESIFGPGVyrlkidvrqfvtasnrklelnvvsspYHLEITP 98
Cdd:cd00009    3 QEEAIEALREALELPPP-KNLLLYGPPGTGKTTLARAIANELFRPGA--------------------------PFLYLNA 55

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  99 SDMGNNDRIVIQELLKEVAQMEQVDFQdskdglaHRYKCVIINEANSLTKDAQAALRRTMEKYS------KNIRLIMVC- 171
Cdd:cd00009   56 SDLLEGLVVAELFGHFLVRLLFELAEK-------AKPGVLFIDEIDSLSRGAQNALLRVLETLNdlridrENVRVIGATn 128

                        170       180
                 ....*....|....*....|...
gi 398364719 172 -DSMSPIIAPIKSRCLLIRCPAP 193
Cdd:cd00009  129 rPLLGDLDRALYDRLDIRIVIPL 151
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 7-238 1.10e-09

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 59.12  E-value: 1.10e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVyrlkidvrqfvTASNRKLELN 86
Cdd:PRK14970  10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGY-----------DDPNEDFSFN 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  87 VvsspYHLEITpsdmGNNDRIVIQELLKEVAQMEQVDfqdskdglahRYKCVIINEANSLTKDAQAALRRTMEKYSKNIR 166
Cdd:PRK14970  79 I----FELDAA----SNNSVDDIRNLIDQVRIPPQTG----------KYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAI 140

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398364719 167 LIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLEtKDILKRIAQASNGNLRVSLLMLE 238
Cdd:PRK14970 141 FILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFE-DDALHIIAQKADGALRDALSIFD 211
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
134-238 1.24e-09

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 58.66  E-value: 1.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 134 RYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQL 213
Cdd:COG2812  114 RYKVYIIDEAHMLTTEAFNALLKTLEEPPPHVVFILATTEPQKLLPTILSRCQRFDFRRLPPEEIAEHLAKIAEREGIEI 193

                         90       100
                 ....*....|....*....|....*
gi 398364719 214 EtKDILKRIAQASNGNLRVSLLMLE 238
Cdd:COG2812  194 E-PEALALIARAADGSMRDALSLLD 217
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 7-241 1.58e-09

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 59.01  E-value: 1.58e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEEL-TNFLKSLsdQPRDLPHLLLY-GPNGTGKKTRCMALLESifgpgvyrLKIDVRQFVTASNRKLE 84
Cdd:PRK14962   7 KYRPKTFSEVVGQDHVkKLIINAL--KKNSISHAYIFaGPRGTGKTTVARILAKS--------LNCENRKGVEPCNECRA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  85 LNVVSSPYHLEITPSDMGNNDRIviqellKEVAQM-EQVDFQDSKDglahRYKCVIINEANSLTKDAQAALRRTMEKYSK 163
Cdd:PRK14962  77 CRSIDEGTFMDVIELDAASNRGI------DEIRKIrDAVGYRPMEG----KYKVYIIDEVHMLTKEAFNALLKTLEEPPS 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398364719 164 NIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLeTKDILKRIAQASNGNLRVSLLMLESMA 241
Cdd:PRK14962 147 HVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEI-DREALSFIAKRASGGLRDALTMLEQVW 223
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 134-235 2.95e-09

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 58.30  E-value: 2.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 134 RYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQL 213
Cdd:PRK14953 119 KYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEY 198

                         90       100
                 ....*....|....*....|....
gi 398364719 214 EtKDILKRIAQASNGNLR--VSLL 235
Cdd:PRK14953 199 E-EKALDLLAQASEGGMRdaASLL 221
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 7-303 2.40e-08

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 55.46  E-value: 2.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTrcmalLESIFGPGvyrLKIDVRQFVTASNRKLELN 86
Cdd:PRK14959   9 RYRPQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTT-----IARIFAKA---LNCETAPTGEPCNTCEQCR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  87 VVSSPYHLEITPSDMGNNDRIVIQELLKEV---AQMEQvdfqdskdglahRYKCVIINEANSLTKDAQAALRRTMEKYSK 163
Cdd:PRK14959  81 KVTQGMHVDVVEIDGASNRGIDDAKRLKEAigyAPMEG------------RYKVFIIDEAHMLTREAFNALLKTLEEPPA 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 164 NIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDIlKRIAQASNGNLRVSLLML-ESMAL 242
Cdd:PRK14959 149 RVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAV-RLIARRAAGSVRDSMSLLgQVLAL 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398364719 243 -NNELALKSSSPIIKpdwiIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILKEL 303
Cdd:PRK14959 228 gESRLTIDGARGVLG----LAGQELFLRLMEALAAQDCLGVANVVRELLDRGVDMGFFLREL 285
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
 7-238 6.62e-08

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 54.33  E-value: 6.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRdLPH-LLLYGPNGTGKKTRCMALLESI-FGPGVYRLKIDVRQFVTA--SNRK 82
Cdd:PRK08691   9 KWRPKTFADLVGQEHVVKALQNALDEGR-LHHaYLLTGTRGVGKTTIARILAKSLnCENAQHGEPCGVCQSCTQidAGRY 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  83 LELnvvsspyhLEItpsDMGNNDRI-VIQELLkEVAQMEQVdfqdskdglAHRYKCVIINEANSLTKDAQAALRRTMEKY 161
Cdd:PRK08691  88 VDL--------LEI---DAASNTGIdNIREVL-ENAQYAPT---------AGKYKVYIIDEVHMLSKSAFNAMLKTLEEP 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398364719 162 SKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKdILKRIAQASNGNLRVSLLMLE 238
Cdd:PRK08691 147 PEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPP-ALQLLGRAAAGSMRDALSLLD 222
PRK14969 PRK14969
DNA polymerase III subunits gamma and tau; Provisional
 7-238 1.99e-07

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237873 [Multi-domain]  Cd Length: 527  Bit Score: 52.44  E-value: 1.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEE----LTNFLkslsDQPRdLPHLLLY-GPNGTGKKTRCMALLESI----------FGPGVYRLKID 71
Cdd:PRK14969   9 KWRPKSFSELVGQEHvvraLTNAL----EQQR-LHHAYLFtGTRGVGKTTLARILAKSLncetgvtatpCGVCSACLEID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  72 VRQFV------TASNRKLElnvvsspyhleitpsDMgnndriviQELLkEVAQMEQVdfqdskdglAHRYKCVIINEANS 145
Cdd:PRK14969  84 SGRFVdlievdAASNTQVD---------------AM--------RELL-DNAQYAPT---------RGRFKVYIIDEVHM 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 146 LTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCL---LIRCPAPSdseISTILSDVVTNERIQLETKDiLKRI 222
Cdd:PRK14969 131 LSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLqfnLKQMPPPL---IVSHLQHILEQENIPFDATA-LQLL 206

                        250
                 ....*....|....*.
gi 398364719 223 AQASNGNLRVSLLMLE 238
Cdd:PRK14969 207 ARAAAGSMRDALSLLD 222
PRK05707 PRK05707
DNA polymerase III subunit delta'; Validated
 28-215 4.69e-07

DNA polymerase III subunit delta'; Validated


Pssm-ID: 180215 [Multi-domain]  Cd Length: 328  Bit Score: 50.86  E-value: 4.69e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  28 SLSDQPRdLPH-LLLYGPNGTGKK---TRCMALL--ESIFGPGVY------RLkidvrqfvtasnrkleLNVVSSPYHLE 95
Cdd:PRK05707  14 QLAGRGR-HPHaYLLHGPAGIGKRalaERLAAALlcEAPQGGGACgsckgcQL----------------LRAGSHPDNFV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  96 ITPSDMGNNDRI-VIQELLKEVAQMEQVDfqdskdglahRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSM 174
Cdd:PRK05707  77 LEPEEADKTIKVdQVRELVSFVVQTAQLG----------GRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQP 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 398364719 175 SPIIAPIKSRCLLIRCPAPSDSE----ISTILSDVVTNERIQLET 215
Cdd:PRK05707 147 SRLLPTIKSRCQQQACPLPSNEEslqwLQQALPESDERERIELLT 191
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 6-288 1.00e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 50.08  E-value: 1.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   6 DKYRPKSLN-------ALSHNEELTNFLKSlsdqpRDLPHLLLYGPNGTGKKT--RCMAllesifgpgvyrlkidvrqfv 76
Cdd:PRK13342   4 ERMRPKTLDevvgqehLLGPGKPLRRMIEA-----GRLSSMILWGPPGTGKTTlaRIIA--------------------- 57

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  77 TASNRKLE-LNVVSSpyhleitpsdmGnndriviqellkeVAQMEQVdFQDSKDGLAHRYKCV-IINEANSLTKDAQAAL 154
Cdd:PRK13342  58 GATDAPFEaLSAVTS-----------G-------------VKDLREV-IEEARQRRSAGRRTIlFIDEIHRFNKAQQDAL 112

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 155 RRTMEKYskNIRLImv---cdSMSpIIAPIKSRCLLIRCPAPSDSEISTILSDVVTN-ERIQLE-TKDILKRIAQASNGN 229
Cdd:PRK13342 113 LPHVEDG--TITLIgattenpSFE-VNPALLSRAQVFELKPLSEEDIEQLLKRALEDkERGLVElDDEALDALARLANGD 189

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 398364719 230 LRVSLLMLESMALNNElalkssspiikpdwiivihKLTRKIVKErsvnsLIECRAVLYD 288
Cdd:PRK13342 190 ARRALNLLELAALGVD-------------------SITLELLEE-----ALQKRAARYD 224
PRK14960 PRK14960
DNA polymerase III subunit gamma/tau;
7-234 2.03e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237868 [Multi-domain]  Cd Length: 702  Bit Score: 49.66  E-value: 2.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRdLPHLLLY-GPNGTGKKTRCMALLESIfgpgvyrlkidvrqfvtasnrKLEL 85
Cdd:PRK14960   8 KYRPRNFNELVGQNHVSRALSSALERGR-LHHAYLFtGTRGVGKTTIARILAKCL---------------------NCET 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  86 NVVSSPyhLEITPSDMGNNDRIVIQelLKEVAQMEQVDFQDSKDGLAH--------RYKCVIINEANSLTKDAQAALRRT 157
Cdd:PRK14960  66 GVTSTP--CEVCATCKAVNEGRFID--LIEIDAASRTKVEDTRELLDNvpyaptqgRFKVYLIDEVHMLSTHSFNALLKT 141

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398364719 158 MEKYSKNIRLIMVcdSMSPIIAPIK--SRCLLIRCPAPSDSEISTILSDVVTNERIQLEtKDILKRIAQASNGNLRVSL 234
Cdd:PRK14960 142 LEEPPEHVKFLFA--TTDPQKLPITviSRCLQFTLRPLAVDEITKHLGAILEKEQIAAD-QDAIWQIAESAQGSLRDAL 217
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
7-234 3.61e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 48.72  E-value: 3.61e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRdLPHLLLY-GPNGTGKKT--RCMALLESIFGP-----------GVYR--LKI 70
Cdd:PRK12323   9 KWRPRDFTTLVGQEHVVRALTHALEQQR-LHHAYLFtGTRGVGKTTlsRILAKSLNCTGAdgeggitaqpcGQCRacTEI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  71 DVRQFV------TASNRKLElnvvsspyhleitpsdmgnndriviqellkEVAQM-EQVDFQDSkdglAHRYKCVIINEA 143
Cdd:PRK12323  88 DAGRFVdyiemdAASNRGVD------------------------------EMAQLlDKAVYAPT----AGRFKVYMIDEV 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 144 NSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCL---LIRCPAPSdseISTILSDVVTNERIQLETkDILK 220
Cdd:PRK12323 134 HMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLqfnLKQMPPGH---IVSHLDAILGEEGIAHEV-NALR 209

                        250
                 ....*....|....
gi 398364719 221 RIAQASNGNLRVSL 234
Cdd:PRK12323 210 LLAQAAQGSMRDAL 223
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 134-250 6.46e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 47.86  E-value: 6.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 134 RYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQL 213
Cdd:PRK14964 116 KFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEH 195

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 398364719 214 EtKDILKRIAQASNGNLRVSLLMLESMAL--NNELALKS 250
Cdd:PRK14964 196 D-EESLKLIAENSSGSMRNALFLLEQAAIysNNKISEKS 233
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 7-238 7.79e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 47.77  E-value: 7.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIfgpgvyrlkiDVRQFVTASNRKLELN 86
Cdd:PRK14957   9 KYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCL----------NCKTGVTAEPCNKCEN 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  87 VVSSPYHLEITPSDMGNNDRIVIQELlKEVaqMEQVDFQDSKDglahRYKCVIINEANSLTKDAQAALRRTMEKYSKNIR 166
Cdd:PRK14957  79 CVAINNNSFIDLIEIDAASRTGVEET-KEI--LDNIQYMPSQG----RYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVK 151

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398364719 167 LIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDiLKRIAQASNGNLRVSLLMLE 238
Cdd:PRK14957 152 FILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINSDEQS-LEYIAYHAKGSLRDALSLLD 222
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 7-241 1.12e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 47.11  E-value: 1.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKT-------------------------RCMALLEsif 61
Cdd:PRK14950   9 KWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTStarilakavncttndpkgrpcgtceMCRAIAE--- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  62 GPGVyrlkiDVRQFVTASNRKLElnvvsspyhleitpsdmgnnDrivIQELLkevaqmEQVDFQDSkdgLAhRYKCVIIN 141
Cdd:PRK14950  86 GSAV-----DVIEMDAASHTSVD--------------------D---AREII------ERVQFRPA---LA-RYKVYIID 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 142 EANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLEtKDILKR 221
Cdd:PRK14950 128 EVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLE-PGALEA 206

                        250       260
                 ....*....|....*....|
gi 398364719 222 IAQASNGNLRVSLLMLESMA 241
Cdd:PRK14950 207 IARAATGSMRDAENLLQQLA 226
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 38-181 2.50e-05

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: 43.90  E-value: 2.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719    38 HLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFvtasnrkleLNVVSSPYHLEITPSDMGNNDRIVIQELLKEVA 117
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDI---------LEEVLDQLLLIIVGGKKASGSGELRLRLALALA 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 398364719   118 QmeqvdfqdskdglAHRYKCVIINEANSLTKDAQAALRR--------TMEKYSKNIRLIMVCDSMSPIIAPI 181
Cdd:smart00382  75 R-------------KLKPDVLILDEITSLLDAEQEALLLlleelrllLLLKSEKNLTVILTTNDEKDLGPAL 133
PRK05564 PRK05564
DNA polymerase III subunit delta'; Validated
 136-203 2.64e-05

DNA polymerase III subunit delta'; Validated


Pssm-ID: 180132 [Multi-domain]  Cd Length: 313  Bit Score: 45.41  E-value: 2.64e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398364719 136 KCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILS 203
Cdd:PRK05564  95 KVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFIS 162
PRK06305 PRK06305
DNA polymerase III subunits gamma and tau; Validated
 120-231 8.66e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180523 [Multi-domain]  Cd Length: 451  Bit Score: 43.99  E-value: 8.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 120 EQVDFQDSKDglahRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRC---LLIRCPapsDS 196
Cdd:PRK06305 111 ETVLFTPSKS----RYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCqkmHLKRIP---EE 183

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 398364719 197 EISTILSDVVTNERIQLEtKDILKRIAQASNGNLR 231
Cdd:PRK06305 184 TIIDKLALIAKQEGIETS-REALLPIARAAQGSLR 217
PRK07399 PRK07399
DNA polymerase III subunit delta'; Validated
 19-273 9.72e-05

DNA polymerase III subunit delta'; Validated


Pssm-ID: 236011 [Multi-domain]  Cd Length: 314  Bit Score: 43.74  E-value: 9.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  19 NEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIdvrqfvtaSNRKLELNvvsSPYHLEITP 98
Cdd:PRK07399   9 QPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNI--------RRRLEEGN---HPDLLWVEP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  99 SDMGNNDRIVIQELLKEVAQM--------EQVdfQDSKDGLAHR-----YKCVIINEANSLTKDAQAALRRTMEKYSKNI 165
Cdd:PRK07399  78 TYQHQGKLITASEAEEAGLKRkappqirlEQI--REIKRFLSRPpleapRKVVVIEDAETMNEAAANALLKTLEEPGNGT 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 166 rLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKrIAQASNGNLRVSLLMLESmaLNNE 245
Cdd:PRK07399 156 -LILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEILNINFPELLA-LAQGSPGAAIANIEQLQS--IPPE 231

                        250       260
                 ....*....|....*....|....*...
gi 398364719 246 LALKSSSPIIKPdwiIVIHKLTRKIVKE 273
Cdd:PRK07399 232 LLQKLEQPPKSP---LEALELAKDISEE 256
PRK06645 PRK06645
DNA polymerase III subunits gamma and tau; Validated
 131-260 1.12e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180643 [Multi-domain]  Cd Length: 507  Bit Score: 44.08  E-value: 1.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 131 LAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNER 210
Cdd:PRK06645 125 LQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQEN 204

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 398364719 211 IQlETKDILKRIAQASNGNLRVSLLMLESMAlnnELALKSSSpIIKPDWI 260
Cdd:PRK06645 205 LK-TDIEALRIIAYKSEGSARDAVSILDQAA---SMSAKSDN-IISPQVI 249
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 19-194 1.48e-04

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: 41.81  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   19 NEELTNFLKSLSDQPRdLPH-LLLYGPNGTGKKTRCMALLESIF----GPGVYRLKIDvrqfvtaSNRKLELNvvSSPYH 93
Cdd:pfam13177   2 QPEAIQLLQNSLENGR-LSHaYLFSGPEGVGKLELALAFAKALFceepGDDLPCGQCR-------SCRRIESG--NHPDL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   94 LEITPSD--MGNNDrivIQELLKEVAQMeqvdfqdskdGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVC 171
Cdd:pfam13177  72 VIIEPEGqsIKIDQ---IRELQKEFSKS----------PYEGKKKVYIIEDAEKMTASAANSLLKFLEEPPGNTVIILLT 138

                         170       180
                  ....*....|....*....|...
gi 398364719  172 DSMSPIIAPIKSRCLLIRCPAPS 194
Cdd:pfam13177 139 ENPSRLLPTIRSRCQIIRFKPLS 161
PRK09112 PRK09112
DNA polymerase III subunit delta'; Validated
 125-238 2.47e-04

DNA polymerase III subunit delta'; Validated


Pssm-ID: 169667 [Multi-domain]  Cd Length: 351  Bit Score: 42.72  E-value: 2.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 125 QDSKDGlahRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSD 204
Cdd:PRK09112 135 QTSGDG---NWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSH 211

                         90       100       110
                 ....*....|....*....|....*....|....
gi 398364719 205 VVTNeriQLETKDILKRIAQASNGNLRVSLLMLE 238
Cdd:PRK09112 212 LGSS---QGSDGEITEALLQRSKGSVRKALLLLN 242
PRK14963 PRK14963
DNA polymerase III subunits gamma and tau; Provisional
 136-250 3.20e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184927 [Multi-domain]  Cd Length: 504  Bit Score: 42.52  E-value: 3.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 136 KCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLEt 215
Cdd:PRK14963 118 KVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAE- 196

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 398364719 216 KDILKRIAQASNGNLRVSLLMLESM-ALNNELALKS 250
Cdd:PRK14963 197 PEALQLVARLADGAMRDAESLLERLlALGTPVTRKQ 232
PRK08451 PRK08451
DNA polymerase III subunits gamma and tau; Validated
 7-238 4.86e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236267 [Multi-domain]  Cd Length: 535  Bit Score: 41.94  E-value: 4.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719   7 KYRPKSLNALSHNEELTNFLKSLSDQPRdLPHLLLY-GPNGTGKKT------------------------RCMALLESif 61
Cdd:PRK08451   7 KYRPKHFDELIGQESVSKTLSLALDNNR-LAHAYLFsGLRGSGKTSsarifaralvceqgpsstpcdtciQCQSALEN-- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  62 gpgvyrLKIDVRQFVTASNRKLElnvvsspyhleitpsdmgnnDrivIQELLkevaqmEQVDFQDSkdglAHRYKCVIIN 141
Cdd:PRK08451  84 ------RHIDIIEMDAASNRGID--------------------D---IRELI------EQTKYKPS----MARFKIFIID 124

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 142 EANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLEtKDILKR 221
Cdd:PRK08451 125 EVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSYE-PEALEI 203

                        250
                 ....*....|....*..
gi 398364719 222 IAQASNGNLRVSLLMLE 238
Cdd:PRK08451 204 LARSGNGSLRDTLTLLD 220
PRK14958 PRK14958
DNA polymerase III subunits gamma and tau; Provisional
 134-244 6.49e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184922 [Multi-domain]  Cd Length: 509  Bit Score: 41.64  E-value: 6.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 134 RYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQL 213
Cdd:PRK14958 119 RFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEF 198

                         90       100       110
                 ....*....|....*....|....*....|..
gi 398364719 214 ETKdILKRIAQASNGNLRVSLLML-ESMALNN 244
Cdd:PRK14958 199 ENA-ALDLLARAANGSVRDALSLLdQSIAYGN 229
PRK04132 PRK04132
replication factor C small subunit; Provisional
 4-49 6.85e-04

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 41.75  E-value: 6.85e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 398364719   4 WVDKYRPKSLNALSHNEELTNFLKSLSdQPRDLPHLLLYGPNGTGK 49
Cdd:PRK04132   9 WVEKYRPQRLDDIVGQEHIVKRLKHYV-KTGSMPHLLFAGPPGVGK 53
PRK08699 PRK08699
DNA polymerase III subunit delta'; Validated
 89-204 1.85e-03

DNA polymerase III subunit delta'; Validated


Pssm-ID: 181538 [Multi-domain]  Cd Length: 325  Bit Score: 39.85  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  89 SSPYHLEITP-SDMGNNDRIVIQelLKEVAQMEQVDFQDSKdglAHR--YKCVIINEANSLTKDAQAALRRTMEKYSKNI 165
Cdd:PRK08699  70 SHPDFYEITPlSDEPENGRKLLQ--IKIDAVREIIDNVYLT---SVRggLRVILIHPAESMNLQAANSLLKVLEEPPPQV 144

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 398364719 166 RLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSD 204
Cdd:PRK08699 145 VFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRE 183
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 193-245 4.08e-03

helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein clamp loader complex that forms a stable ATP-dependent complex with the sliding clamp, PCNA, which binds specifically to primed DNA. RFC subunits belong to the clamp loader clade of the AAA+ superfamily.


Pssm-ID: 350842 [Multi-domain]  Cd Length: 63  Bit Score: 35.20  E-value: 4.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 398364719 193 PSDSEISTILSDVVTNERIQLEtKDILKRIAQASNGNLRVSLLMLESMALNNE 245
Cdd:cd18140    1 LSKEQIVKRLREICKKEGVKID-EEALEAIAEKSEGDMRKAINDLQAAAAGGG 52
PRK06647 PRK06647
DNA polymerase III subunits gamma and tau; Validated
 134-231 5.01e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235845 [Multi-domain]  Cd Length: 563  Bit Score: 38.60  E-value: 5.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719 134 RYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQL 213
Cdd:PRK06647 119 RYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIKY 198

                         90
                 ....*....|....*...
gi 398364719 214 EtKDILKRIAQASNGNLR 231
Cdd:PRK06647 199 E-DEALKWIAYKSTGSVR 215
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 17-175 8.80e-03

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: 37.18  E-value: 8.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  17 SHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKK-TRCMALLESIFGPGVyRLKIDVRqfvTASNRKLELNVVSSPY--- 92
Cdd:cd18076    4 NKQQLAFNFIAGKPSEARFVPPLLIYGPFGTGKTfTLAMAALEVIREPGT-KVLICTH---TNSAADIYIREYFHPYvdk 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364719  93 -HLEITPSDMGNNDRiviqellkEVAQMEQVDFQdskdglahrYKCviineansLTKDAQAALRRTMEKYSKNiRLIMVC 171
Cdd:cd18076   80 gHPEARPLRIKATDR--------PNAITDPDTIT---------YCC--------LTKDRQCFRLPTRDELDFH-NIVITT 133


                 ....
gi 398364719 172 DSMS 175
Cdd:cd18076  134 TAMA 137
 
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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