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Conserved domains on  [gi|4506489|ref|NP_002906|]
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replication factor C subunit 3 isoform 1 [Homo sapiens]

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
 3-339 4.80e-47

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: 162.47  E-value: 4.80e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEKLRIEHQTITTPSKKKI 82
Cdd:PRK12402   4 LWTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQGKK 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    83 EISTIASNYHLEVNPSDAGNSDRVVIQEMLKTVAQSQQLETnsqrDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLI 162
Cdd:PRK12402  84 YLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSA----DYKTILLDNAEALREDAQQALRRIMEQYSRTCRFI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   163 LCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTa 242
Cdd:PRK12402 160 IATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEIT- 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   243 DQEIPETDWEVYLRETANAIVSQQTPQRLLEVRGRLYELLthcippeiIMKGL-----LSELLHNCDGQLKG----EVAQ 313
Cdd:PRK12402 239 MEAAYEALGDVGTDEVIESLLDAAEAGDFTDARKTLDDLL--------IDEGLsggevLEELLRVARSRYRGdnlaRLHR 310

                        330       340
                 ....*....|....*....|....*.
gi 4506489   314 MAAYYEHRLQLGSKAIYHLEAFVAKF 339
Cdd:PRK12402 311 LAADADARLTDGANDRIQLEALLAEL 336
 
Name Accession Description Interval E-value
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 3-339 4.80e-47

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 162.47  E-value: 4.80e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEKLRIEHQTITTPSKKKI 82
Cdd:PRK12402   4 LWTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQGKK 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    83 EISTIASNYHLEVNPSDAGNSDRVVIQEMLKTVAQSQQLETnsqrDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLI 162
Cdd:PRK12402  84 YLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSA----DYKTILLDNAEALREDAQQALRRIMEQYSRTCRFI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   163 LCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTa 242
Cdd:PRK12402 160 IATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEIT- 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   243 DQEIPETDWEVYLRETANAIVSQQTPQRLLEVRGRLYELLthcippeiIMKGL-----LSELLHNCDGQLKG----EVAQ 313
Cdd:PRK12402 239 MEAAYEALGDVGTDEVIESLLDAAEAGDFTDARKTLDDLL--------IDEGLsggevLEELLRVARSRYRGdnlaRLHR 310

                        330       340
                 ....*....|....*....|....*.
gi 4506489   314 MAAYYEHRLQLGSKAIYHLEAFVAKF 339
Cdd:PRK12402 311 LAADADARLTDGANDRIQLEALLAEL 336
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
19-342 3.52e-32

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 122.01  E-value: 3.52e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   19 HKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKTRIMCILRELYGvgveklrieHQTITTPSKKKIEISTIASNYH---LE 94
Cdd:COG0470   1 QEEAWEQLLAAAESGRLPHaLLLHGPPGIGKTTLALALARDLLC---------ENPEGGKACGQCHSRLMAAGNHpdlLE 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   95 VNPSDAGNSDRV-VIQEMLKTVAQSqqletnSQRD-FKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVI 172
Cdd:COG0470  72 LNPEEKSDQIGIdQIRELGEFLSLT------PLEGgRKVVIIDEADAMNEAAANALLKTLEEPPKNTPFILIANDPSRLL 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  173 PPIRSRCLAVRVPAPSIEDICHVLstvcKKEGlnLPSQLAHRLAEKSCRNLRKALLMCEAcrvqqypftadqeipetdWE 252
Cdd:COG0470 146 PTIRSRCQVIRFRPPSEEEALAWL----REEG--VDEDALEAILRLAGGDPRAAINLLQA------------------LA 201

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  253 VY--LRETANAIVSQQTPQRLLEV--RGRLYELLthcippEIIMKGLLSELLHNCDGQLKGEVAQMAAYYEHRLQLGSKA 328
Cdd:COG0470 202 GRkeLLEDLAALLSRDRALELLDAllKAEALELL------DWLLKWLLDNLPLEYAGEDLARAYEALSEADRRLGRYAND 275

                       330
                ....*....|....
gi 4506489  329 IYHLEAFVAKFMAL 342
Cdd:COG0470 276 RLLLEALLAKLGRL 289
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 21-179 1.42e-09

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: 56.00  E-value: 1.42e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   21 EQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEklriehqtittpskkkieistiasnyHLEVNPSDA 100
Cdd:cd00009   5 EAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAP--------------------------FLYLNASDL 58

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  101 GNSDRVVIQEmlKTVAQSQQLETNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMST------CRLILCCNSTS--KVI 172
Cdd:cd00009  59 LEGLVVAELF--GHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLridrenVRVIGATNRPLlgDLD 136


                ....*..
gi 4506489  173 PPIRSRC 179
Cdd:cd00009 137 RALYDRL 143
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 18-188 4.46e-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: 49.13  E-value: 4.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     18 YHKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKTRIMCILRELYGvgvEKLRIEHQTITTPSKKKIEiSTIASNYHLeVN 96
Cdd:pfam13177   1 GQPEAIQLLQNSLENGRLSHaYLFSGPEGVGKLELALAFAKALFC---EEPGDDLPCGQCRSCRRIE-SGNHPDLVI-IE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     97 PSdaGNSDRV-VIQEMLKTVAQSQqLETNsqrdFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPI 175
Cdd:pfam13177  76 PE--GQSIKIdQIRELQKEFSKSP-YEGK----KKVYIIEDAEKMTASAANSLLKFLEEPPGNTVIILLTENPSRLLPTI 148

                         170
                  ....*....|...
gi 4506489    176 RSRCLAVRVPAPS 188
Cdd:pfam13177 149 RSRCQIIRFKPLS 161
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 37-190 4.02e-06

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: 46.21  E-value: 4.02e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489      37 HLLVYGPSGAGKKTRIMCILRELYGVGVEKLRIEHQTITTPSKKKIeistiasnyHLEVNPSDAGNSDRVVIQEMLKTVA 116
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQL---------LLIIVGGKKASGSGELRLRLALALA 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     117 QsqqletnsQRDFKVVLLTEVDKLTKDAQHALRR--------TMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPS 188
Cdd:smart00382  75 R--------KLKPDVLILDEITSLLDAEQEALLLlleelrllLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLL 146


                   ..
gi 4506489     189 IE 190
Cdd:smart00382 147 IL 148
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 3-164 1.06e-03

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: 41.10  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489      3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPH-----LLVYGPSGAGKKTRIMCILRELygvgVEKLR--IEHQTIT 75
Cdd:TIGR00602  73 PWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENapkriLLITGPSGCGKSTTIKILSKEL----GIQVQewSNPTLPD 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     76 TPSKKKIEISTIASNYHLEVnpsdagnSDRVVIQEMLKTVAQS-QQLETNSQRDFKVVLLTEVDK---LTKDAQHALRRT 151
Cdd:TIGR00602 149 FQKNDHKVTLSLESCFSNFQ-------SQIEVFSEFLLRATNKlQMLGDDLMTDKKIILVEDLPNqfyRDTRALHEILRW 221

                         170
                  ....*....|...
gi 4506489    152 MEKYMSTCRLILC 164
Cdd:TIGR00602 222 KYVSIGRCPLVFI 234
 
Name Accession Description Interval E-value
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 3-339 4.80e-47

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 162.47  E-value: 4.80e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEKLRIEHQTITTPSKKKI 82
Cdd:PRK12402   4 LWTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNVADFFDQGKK 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    83 EISTIASNYHLEVNPSDAGNSDRVVIQEMLKTVAQSQQLETnsqrDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLI 162
Cdd:PRK12402  84 YLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSA----DYKTILLDNAEALREDAQQALRRIMEQYSRTCRFI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   163 LCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTa 242
Cdd:PRK12402 160 IATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEIT- 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   243 DQEIPETDWEVYLRETANAIVSQQTPQRLLEVRGRLYELLthcippeiIMKGL-----LSELLHNCDGQLKG----EVAQ 313
Cdd:PRK12402 239 MEAAYEALGDVGTDEVIESLLDAAEAGDFTDARKTLDDLL--------IDEGLsggevLEELLRVARSRYRGdnlaRLHR 310

                        330       340
                 ....*....|....*....|....*.
gi 4506489   314 MAAYYEHRLQLGSKAIYHLEAFVAKF 339
Cdd:PRK12402 311 LAADADARLTDGANDRIQLEALLAEL 336
rfc PRK00440
replication factor C small subunit; Reviewed
 3-345 8.05e-46

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 158.88  E-value: 8.05e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGvgvEKLRiehqtittpskkki 82
Cdd:PRK00440   6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYG---EDWR-------------- 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    83 eistiasNYHLEVNPSDAGNSDrvVIQEMLKTVAQSQQLETnsqRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLI 162
Cdd:PRK00440  69 -------ENFLELNASDERGID--VIRNKIKEFARTAPVGG---APFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFI 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   163 LCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALlmceacRVQQYPFTA 242
Cdd:PRK00440 137 LSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAI------NALQAAAAT 210

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   243 DQEIPEtdwevylrETANAIVSQQTPQ------------RLLEVRGRLYELLT-HCIPPEIIMKGLLSELLH-NCDGQLK 308
Cdd:PRK00440 211 GKEVTE--------EAVYKITGTARPEeiremielalngDFTEAREKLRDLMIdYGLSGEDIIKQIHREVWSlDIPEELK 282

                        330       340       350
                 ....*....|....*....|....*....|....*..
gi 4506489   309 GEVAQMAAYYEHRLQLGSKAIYHLEAFVAKFMALYKK 345
Cdd:PRK00440 283 VELIDAIGEADFRITEGANERIQLEALLAKLALLGKK 319
PLN03025 PLN03025
replication factor C subunit; Provisional
 4-205 1.47e-32

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 123.69  E-value: 1.47e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     4 WVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGvgveklriehqtittPSKKkie 83
Cdd:PLN03025   3 WVEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLG---------------PNYK--- 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    84 istiasNYHLEVNPSDAGNSDrvVIQEMLKTVAQSQQleTNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLIL 163
Cdd:PLN03025  65 ------EAVLELNASDDRGID--VVRNKIKMFAQKKV--TLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFAL 134

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 4506489   164 CCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGL 205
Cdd:PLN03025 135 ACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKV 176
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
19-342 3.52e-32

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 122.01  E-value: 3.52e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   19 HKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKTRIMCILRELYGvgveklrieHQTITTPSKKKIEISTIASNYH---LE 94
Cdd:COG0470   1 QEEAWEQLLAAAESGRLPHaLLLHGPPGIGKTTLALALARDLLC---------ENPEGGKACGQCHSRLMAAGNHpdlLE 71

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   95 VNPSDAGNSDRV-VIQEMLKTVAQSqqletnSQRD-FKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVI 172
Cdd:COG0470  72 LNPEEKSDQIGIdQIRELGEFLSLT------PLEGgRKVVIIDEADAMNEAAANALLKTLEEPPKNTPFILIANDPSRLL 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  173 PPIRSRCLAVRVPAPSIEDICHVLstvcKKEGlnLPSQLAHRLAEKSCRNLRKALLMCEAcrvqqypftadqeipetdWE 252
Cdd:COG0470 146 PTIRSRCQVIRFRPPSEEEALAWL----REEG--VDEDALEAILRLAGGDPRAAINLLQA------------------LA 201

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  253 VY--LRETANAIVSQQTPQRLLEV--RGRLYELLthcippEIIMKGLLSELLHNCDGQLKGEVAQMAAYYEHRLQLGSKA 328
Cdd:COG0470 202 GRkeLLEDLAALLSRDRALELLDAllKAEALELL------DWLLKWLLDNLPLEYAGEDLARAYEALSEADRRLGRYAND 275

                       330
                ....*....|....
gi 4506489  329 IYHLEAFVAKFMAL 342
Cdd:COG0470 276 RLLLEALLAKLGRL 289
PRK04132 PRK04132
replication factor C small subunit; Provisional
 93-339 7.88e-28

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 114.94  E-value: 7.88e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    93 LEVNPSDAGNSDrvVIQEMLKTVAQSQQLETNSqrdFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVI 172
Cdd:PRK04132 600 LELNASDERGIN--VIREKVKEFARTKPIGGAS---FKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKII 674

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   173 PPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALlmceacRVQQYPFTADQEIpeTDWE 252
Cdd:PRK04132 675 EPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAI------NILQAAAALDDKI--TDEN 746

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   253 VYLretanaIVSQQTPQ------------RLLEVRGRLYE-LLTHCIPPEIIMKGLLSELLH-NCDGQLKGEVAQMAAYY 318
Cdd:PRK04132 747 VFL------VASRARPEdiremmllalkgNFLKAREKLREiLLKQGLSGEDVLVQMHREVFNlPIDEPKKVELADKIGEY 820

                        250       260
                 ....*....|....*....|.
gi 4506489   319 EHRLQLGSKAIYHLEAFVAKF 339
Cdd:PRK04132 821 NFRLVEGANEMIQLEALLAQF 841
44 PHA02544
clamp loader, small subunit; Provisional
 3-204 6.56e-18

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 83.12  E-value: 6.56e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPS-GAGKKTRIMCILRElygVGVEklriehqtittpskkk 81
Cdd:PHA02544  10 MWEQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSpGTGKTTVAKALCNE---VGAE---------------- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    82 ieistiasnyHLEVNPSDaGNSDrvVIQEMLKTVAQSQQLETNsqrdFKVVLLTEVDKL-TKDAQHALRRTMEKYMSTCR 160
Cdd:PHA02544  71 ----------VLFVNGSD-CRID--FVRNRLTRFASTVSLTGG----GKVIIIDEFDRLgLADAQRHLRSFMEAYSKNCS 133

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 4506489   161 LILCCNSTSKVIPPIRSRCLAVRVPAPSIED-------ICHVLSTVCKKEG 204
Cdd:PHA02544 134 FIITANNKNGIIEPLRSRCRVIDFGVPTKEEqiemmkqMIVRCKGILEAEG 184
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
19-342 1.27e-14

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 73.69  E-value: 1.27e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   19 HKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKT--RIM-----CilrelygvgveklriEHQTITTP-----SKKKIeis 85
Cdd:COG2812  15 QEHVVRTLKNALASGRLAHaYLFTGPRGVGKTTlaRILakalnC---------------ENGPTGEPcgeceSCRAI--- 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   86 tiASNYHLEVNPSDAGNSDRVV--IQEMLKTVAQSqqletNSQRDFKVVLLTEVDKLTKDAQHALRRTME------Kyms 157
Cdd:COG2812  77 --AAGSHPDVIEIDAEASNIGVddIRELIEKVSYA-----PVEGRYKVYIIDEAHMLTTEAFNALLKTLEeppphvV--- 146

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  158 tcrLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMceacrvqq 237
Cdd:COG2812 147 ---FILATTEPQKLLPTILSRCQRFDFRRLPPEEIAEHLAKIAEREGIEIEPEALALIARAADGSMRDALSL-------- 215

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  238 ypftADQEIP--ETDWEVYLRETANAIVSQQTPQRLLEV-----RGR-----LYELLTHCIppEIIMKGLLSELLHNCDG 305
Cdd:COG2812 216 ----LDQAIAfgLLDRRELLLDLLEALLAGDVAALLALAeelakRGRdlkrfLDDLLSLLR--DLLLLKLGPDAELLVNE 289

                       330       340       350       360
                ....*....|....*....|....*....|....*....|..
gi 4506489  306 QLKGEVAQMAAYY-----EHRLQLGSKAIYHLEAFVAKFMAL 342
Cdd:COG2812 290 DERERLQELARRLsperlLRAIQILLEARRELERNVNPRLAL 331
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 7-231 7.91e-10

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 59.78  E-value: 7.91e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVY-GPSGAGKKT--RIMcilrelygvgVEKLRIEHQTITTPSKKKIE 83
Cdd:PRK14962   7 KYRPKTFSEVVGQDHVKKLIINALKKNSISHAYIFaGPRGTGKTTvaRIL----------AKSLNCENRKGVEPCNECRA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    84 ISTIASNYHLEVNPSDAGnSDRVV--IQEMLKTVAQsqqleTNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRL 161
Cdd:PRK14962  77 CRSIDEGTFMDVIELDAA-SNRGIdeIRKIRDAVGY-----RPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVF 150

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   162 ILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCE 231
Cdd:PRK14962 151 VLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLE 220
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 21-179 1.42e-09

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: 56.00  E-value: 1.42e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   21 EQAAQLRNLVQCGDFPHLLVYGPSGAGKKTRIMCILRELYGVGVEklriehqtittpskkkieistiasnyHLEVNPSDA 100
Cdd:cd00009   5 EAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAP--------------------------FLYLNASDL 58

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489  101 GNSDRVVIQEmlKTVAQSQQLETNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMST------CRLILCCNSTS--KVI 172
Cdd:cd00009  59 LEGLVVAELF--GHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLridrenVRVIGATNRPLlgDLD 136


                ....*..
gi 4506489  173 PPIRSRC 179
Cdd:cd00009 137 RALYDRL 143
PRK14961 PRK14961
DNA polymerase III subunits gamma and tau; Provisional
 7-231 1.76e-09

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184925 [Multi-domain]  Cd Length: 363  Bit Score: 58.67  E-value: 1.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHL-LVYGPSGAGKKTrimcILRELygvgVEKLRIEHQTITTPSKKKIEIS 85
Cdd:PRK14961   9 KWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAwLLSGTRGVGKTT----IARLL----AKSLNCQNGITSNPCRKCIICK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    86 TIASNYHLEVNPSDAgnSDRVVIQEMLKTVAQSQQLETNSQrdFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCC 165
Cdd:PRK14961  81 EIEKGLCLDLIEIDA--ASRTKVEEMREILDNIYYSPSKSR--FKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILAT 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4506489   166 NSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCE 231
Cdd:PRK14961 157 TDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLE 222
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 7-272 1.24e-08

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 56.04  E-value: 1.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVY-GPSGAGKKTrimCIlrelygvgveklRIEHQTITTPSkkkieIS 85
Cdd:PRK14970  10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFcGPRGVGKTT---CA------------RILARKINQPG-----YD 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    86 TIASNYHLEVNPSDAGNSDRVV-IQEMLKTVAQSQQLEtnsqrDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILC 164
Cdd:PRK14970  70 DPNEDFSFNIFELDAASNNSVDdIRNLIDQVRIPPQTG-----KYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILA 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   165 CNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEacRVQQYPFT--- 241
Cdd:PRK14970 145 TTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFD--RVVTFCGKnit 222

                        250       260       270
                 ....*....|....*....|....*....|....
gi 4506489   242 ---ADQEIPETDWEVYLRETaNAIVSQQTPQRLL 272
Cdd:PRK14970 223 rqaVTENLNILDYDTYINVT-DLILENKIPELLL 255
PRK07940 PRK07940
DNA polymerase III subunit delta'; Validated
 108-216 1.47e-08

DNA polymerase III subunit delta'; Validated


Pssm-ID: 236134 [Multi-domain]  Cd Length: 394  Bit Score: 55.69  E-value: 1.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   108 IQEMLKTVAQSQQLETNSQrdFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAP 187
Cdd:PRK07940  99 VDEVRELVTIAARRPSTGR--WRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTP 176

                         90       100
                 ....*....|....*....|....*....
gi 4506489   188 SIEDICHVLStvckkEGLNLPSQLAHRLA 216
Cdd:PRK07940 177 SVEAVAEVLV-----RRDGVDPETARRAA 200
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 7-227 1.86e-07

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 52.78  E-value: 1.86e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVY-GPSGAGKKT--RIMC-ILRELYGVGVEklriehqtittPSKKKI 82
Cdd:PRK14957   9 KYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFtGTRGVGKTTlgRLLAkCLNCKTGVTAE-----------PCNKCE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    83 EISTIASNYHLEVNPSDAgnSDRVVIQEMLKTVAQSQQLEtnSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLI 162
Cdd:PRK14957  78 NCVAINNNSFIDLIEIDA--ASRTGVEETKEILDNIQYMP--SQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFI 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4506489   163 LCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKAL 227
Cdd:PRK14957 154 LATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDAL 218
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
129-272 3.59e-07

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 51.70  E-value: 3.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   129 FKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLP 208
Cdd:PRK14971 122 YKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAE 201

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4506489   209 SQLAHRLAEKSCRNLRKALLMCEacrvQQYPFTAD----QEIPET----DWEVYLRETaNAIVSQQTPQRLL 272
Cdd:PRK14971 202 PEALNVIAQKADGGMRDALSIFD----QVVSFTGGnityKSVIENlnilDYDYYFRLT-DALLAGKVSDSLL 268
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 129-227 3.73e-07

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 51.75  E-value: 3.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   129 FKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLP 208
Cdd:PRK14953 120 YKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYE 199

                         90
                 ....*....|....*....
gi 4506489   209 SQLAHRLAEKSCRNLRKAL 227
Cdd:PRK14953 200 EKALDLLAQASEGGMRDAA 218
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 18-188 4.46e-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: 49.13  E-value: 4.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     18 YHKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKTRIMCILRELYGvgvEKLRIEHQTITTPSKKKIEiSTIASNYHLeVN 96
Cdd:pfam13177   1 GQPEAIQLLQNSLENGRLSHaYLFSGPEGVGKLELALAFAKALFC---EEPGDDLPCGQCRSCRRIE-SGNHPDLVI-IE 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     97 PSdaGNSDRV-VIQEMLKTVAQSQqLETNsqrdFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPI 175
Cdd:pfam13177  76 PE--GQSIKIdQIRELQKEFSKSP-YEGK----KKVYIIEDAEKMTASAANSLLKFLEEPPGNTVIILLTENPSRLLPTI 148

                         170
                  ....*....|...
gi 4506489    176 RSRCLAVRVPAPS 188
Cdd:pfam13177 149 RSRCQIIRFKPLS 161
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 37-190 4.02e-06

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: 46.21  E-value: 4.02e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489      37 HLLVYGPSGAGKKTRIMCILRELYGVGVEKLRIEHQTITTPSKKKIeistiasnyHLEVNPSDAGNSDRVVIQEMLKTVA 116
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQL---------LLIIVGGKKASGSGELRLRLALALA 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     117 QsqqletnsQRDFKVVLLTEVDKLTKDAQHALRR--------TMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPS 188
Cdd:smart00382  75 R--------KLKPDVLILDEITSLLDAEQEALLLlleelrllLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLL 146


                   ..
gi 4506489     189 IE 190
Cdd:smart00382 147 IL 148
PRK14960 PRK14960
DNA polymerase III subunit gamma/tau;
7-227 4.53e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237868 [Multi-domain]  Cd Length: 702  Bit Score: 48.51  E-value: 4.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVY-GPSGAGKKTrimcILRELygvgVEKLRIEHQTITTPSKKKIEIS 85
Cdd:PRK14960   8 KYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFtGTRGVGKTT----IARIL----AKCLNCETGVTSTPCEVCATCK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    86 TIASNYHLEVNPSDAGNSDRVV-IQEMLKTVAQSQqletnSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILC 164
Cdd:PRK14960  80 AVNEGRFIDLIEIDAASRTKVEdTRELLDNVPYAP-----TQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFA 154

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4506489   165 CNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKAL 227
Cdd:PRK14960 155 TTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDAL 217
PRK14956 PRK14956
DNA polymerase III subunits gamma and tau; Provisional
 7-231 5.50e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184920 [Multi-domain]  Cd Length: 484  Bit Score: 48.02  E-value: 5.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVY-GPSGAGKKTrimcILRELygvgVEKLRIEHQTITTPSKKK---I 82
Cdd:PRK14956  11 KYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFfGPRGVGKTT----IARIL----AKRLNCENPIGNEPCNECtscL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    83 EISTIASNYHLEVNPsdAGNSDRVVIQEMLKTVAQSQQletnsQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLI 162
Cdd:PRK14956  83 EITKGISSDVLEIDA--ASNRGIENIRELRDNVKFAPM-----GGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFI 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4506489   163 LCCNSTSKVIPPIRSRC---LAVRVPAPSIEDichVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCE 231
Cdd:PRK14956 156 LATTEFHKIPETILSRCqdfIFKKVPLSVLQD---YSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLSFME 224
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 7-231 1.52e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 46.70  E-value: 1.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKT--RI--MCilrelygvgvekLRIEHQTITTPSKKK 81
Cdd:PRK14964   6 KYRPSSFKDLVGQDVLVRILRNAFTLNKIPQsILLVGASGVGKTTcaRIisLC------------LNCSNGPTSDPCGTC 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    82 IEISTIASNYHLEVNPSDAGNSDRV----VIQEmlktvaQSQQLETNSQrdFKVVLLTEVDKLTKDAQHALRRTMEKYMS 157
Cdd:PRK14964  74 HNCISIKNSNHPDVIEIDAASNTSVddikVILE------NSCYLPISSK--FKVYIIDEVHMLSNSAFNALLKTLEEPAP 145

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4506489   158 TCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCE 231
Cdd:PRK14964 146 HVKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLE 219
PRK05564 PRK05564
DNA polymerase III subunit delta'; Validated
 128-192 2.44e-05

DNA polymerase III subunit delta'; Validated


Pssm-ID: 180132 [Multi-domain]  Cd Length: 313  Bit Score: 45.41  E-value: 2.44e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4506489   128 DFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDI 192
Cdd:PRK05564  93 DKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEI 157
PRK05707 PRK05707
DNA polymerase III subunit delta'; Validated
 22-191 2.86e-05

DNA polymerase III subunit delta'; Validated


Pssm-ID: 180215 [Multi-domain]  Cd Length: 328  Bit Score: 45.46  E-value: 2.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    22 QAAQLRNLVQCGDFPH-LLVYGPSGAGKK---TRIMCIL-----RELYGVGveklriehqtittpSKKKIEISTIAS--- 89
Cdd:PRK05707   8 QQSLWQQLAGRGRHPHaYLLHGPAGIGKRalaERLAAALlceapQGGGACG--------------SCKGCQLLRAGShpd 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    90 NYHLEvnPSDAGNSDRV-VIQEMLKTVAQSQQletnsQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNST 168
Cdd:PRK05707  74 NFVLE--PEEADKTIKVdQVRELVSFVVQTAQ-----LGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQP 146

                        170       180
                 ....*....|....*....|...
gi 4506489   169 SKVIPPIRSRCLAVRVPAPSIED 191
Cdd:PRK05707 147 SRLLPTIKSRCQQQACPLPSNEE 169
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
 7-319 6.44e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 44.70  E-value: 6.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKTrimcILRELygvgVEKLRIEHQTITTPSKKKIEIS 85
Cdd:PRK08691   9 KWRPKTFADLVGQEHVVKALQNALDEGRLHHaYLLTGTRGVGKTT----IARIL----AKSLNCENAQHGEPCGVCQSCT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    86 TIASNYHLEVNPSDAGNSDRVviqEMLKTVAQSQQLETNSQRdFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCC 165
Cdd:PRK08691  81 QIDAGRYVDLLEIDAASNTGI---DNIREVLENAQYAPTAGK-YKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILAT 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   166 NSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQQYPFTADQE 245
Cdd:PRK08691 157 TDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALGSGKVAEND 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   246 IPETDWEV---YLRETANAIVSQQTPQRLLEVR-------------GRLYELLTH-----CIPPEIIMKGLLSELLHNCD 304
Cdd:PRK08691 237 VRQMIGAVdkqYLYELLTGIINQDGAALLAKAQemaacavgfdnalGELAILLQQlaliqAVPSALAHDDPDSDILHRLA 316

                        330
                 ....*....|....*
gi 4506489   305 GQLKGEVAQMaaYYE 319
Cdd:PRK08691 317 QTISGEQIQL--YYQ 329
PRK06305 PRK06305
DNA polymerase III subunits gamma and tau; Validated
 87-226 1.42e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180523 [Multi-domain]  Cd Length: 451  Bit Score: 43.61  E-value: 1.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    87 IASNYHLEVNPSDaGNSDRVV--IQEMLKTVaqsqqLETNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILC 164
Cdd:PRK06305  84 ISSGTSLDVLEID-GASHRGIedIRQINETV-----LFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLA 157

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4506489   165 CNSTSKVIPPIRSRC---LAVRVPAPSIEDichVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKA 226
Cdd:PRK06305 158 TTEIHKIPGTILSRCqkmHLKRIPEETIID---KLALIAKQEGIETSREALLPIARAAQGSLRDA 219
PRK04132 PRK04132
replication factor C small subunit; Provisional
 4-48 1.82e-04

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 43.29  E-value: 1.82e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 4506489     4 WVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPHLLVYGPSGAGK 48
Cdd:PRK04132   9 WVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGK 53
PRK06645 PRK06645
DNA polymerase III subunits gamma and tau; Validated
 39-234 1.89e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180643 [Multi-domain]  Cd Length: 507  Bit Score: 43.31  E-value: 1.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    39 LVYGPSGAGKKTRIMCILRelyGVGVEKLRIEHQTITTPSKKKIEIStIASNYHLEVNPSDAGNSDRVviqEMLKTVAQS 118
Cdd:PRK06645  47 LLTGIRGVGKTTSARIIAK---AVNCSALITENTTIKTCEQCTNCIS-FNNHNHPDIIEIDAASKTSV---DDIRRIIES 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   119 QQLETnSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLST 198
Cdd:PRK06645 120 AEYKP-LQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEY 198

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 4506489   199 VCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACR 234
Cdd:PRK06645 199 ITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAA 234
PRK14963 PRK14963
DNA polymerase III subunits gamma and tau; Provisional
 130-222 1.92e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184927 [Multi-domain]  Cd Length: 504  Bit Score: 43.29  E-value: 1.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   130 KVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPS 209
Cdd:PRK14963 118 KVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEP 197

                         90
                 ....*....|....*.
gi 4506489   210 ---QLAHRLAEKSCRN 222
Cdd:PRK14963 198 ealQLVARLADGAMRD 213
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 187-252 2.23e-04

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: 39.05  E-value: 2.23e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4506489  187 PSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKALLMCEACRVQqypftaDQEIPETDWE 252
Cdd:cd18140   1 LSKEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAG------GGVITEEDVY 60
PRK07132 PRK07132
DNA polymerase III subunit delta'; Validated
 121-192 3.14e-04

DNA polymerase III subunit delta'; Validated


Pssm-ID: 180855 [Multi-domain]  Cd Length: 299  Bit Score: 42.02  E-value: 3.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4506489   121 LETNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDI 192
Cdd:PRK07132  83 FSSFVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKI 154
PRK14969 PRK14969
DNA polymerase III subunits gamma and tau; Provisional
 129-227 4.17e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237873 [Multi-domain]  Cd Length: 527  Bit Score: 42.04  E-value: 4.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   129 FKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAV---RVPAPSI-EDICHVLStvckKEG 204
Cdd:PRK14969 120 FKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFnlkQMPPPLIvSHLQHILE----QEN 195

                         90       100
                 ....*....|....*....|...
gi 4506489   205 LNLPSQLAHRLAEKSCRNLRKAL 227
Cdd:PRK14969 196 IPFDATALQLLARAAAGSMRDAL 218
PRK09112 PRK09112
DNA polymerase III subunit delta'; Validated
 123-229 8.63e-04

DNA polymerase III subunit delta'; Validated


Pssm-ID: 169667 [Multi-domain]  Cd Length: 351  Bit Score: 40.79  E-value: 8.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489   123 TNSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVckk 202
Cdd:PRK09112 136 TSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHL--- 212

                         90       100
                 ....*....|....*....|....*....
gi 4506489   203 eGLNLPSQLAHR--LAEKSCRNLRKALLM 229
Cdd:PRK09112 213 -GSSQGSDGEITeaLLQRSKGSVRKALLL 240
Rad17 pfam03215
Rad17 P-loop domain;
3-169 8.97e-04

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 39.94  E-value: 8.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489      3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPH-----LLVYGPSGAGKKTRIMCILRELygvgVEKLR--IEHQTIT 75
Cdd:pfam03215   8 QWYEKYKPNCLEQLAVHKRKIKDVQEWLDAMFLENakhriLLISGPSGCGKSTVIKELSKEL----GPKYRewSNPTSFR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     76 TPSKKKieistiaSNYHLEVNPSDAGNSDRVVIQEMLKTVAQS---QQLETNSQRDFKVVLLTEVDKLTKDAQHALRRTM 152
Cdd:pfam03215  84 SPPNQV-------TDFRGDCIVNSRFLSQMESFSEFELKGARYlvmQKRGKNAQGNKKLILIEDLPNVFHIDTRRFQQVI 156

                         170       180
                  ....*....|....*....|...
gi 4506489    153 EKYMSTCR---LILC---CNSTS 169
Cdd:pfam03215 157 RQWLYSSEplpLIICiteCEILE 179
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 3-164 1.06e-03

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: 41.10  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489      3 LWVDKYRPCSLGRLDYHKEQAAQLRNLVQCGDFPH-----LLVYGPSGAGKKTRIMCILRELygvgVEKLR--IEHQTIT 75
Cdd:TIGR00602  73 PWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENapkriLLITGPSGCGKSTTIKILSKEL----GIQVQewSNPTLPD 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     76 TPSKKKIEISTIASNYHLEVnpsdagnSDRVVIQEMLKTVAQS-QQLETNSQRDFKVVLLTEVDK---LTKDAQHALRRT 151
Cdd:TIGR00602 149 FQKNDHKVTLSLESCFSNFQ-------SQIEVFSEFLLRATNKlQMLGDDLMTDKKIILVEDLPNqfyRDTRALHEILRW 221

                         170
                  ....*....|...
gi 4506489    152 MEKYMSTCRLILC 164
Cdd:TIGR00602 222 KYVSIGRCPLVFI 234
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 7-227 2.37e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 39.79  E-value: 2.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489     7 KYRPCSLGRLDYHKEQAAQLRNLVQCGDFPH-LLVYGPSGAGKKTrimcilrelygvgVEKLRIEHQTITTPSKKKIEIS 85
Cdd:PRK14950   9 KWRSQTFAELVGQEHVVQTLRNAIAEGRVAHaYLFTGPRGVGKTS-------------TARILAKAVNCTTNDPKGRPCG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4506489    86 T------IASNYHLEVNPSDAGNSDRVV-IQEMLKTVAQSQqletnSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMST 158
Cdd:PRK14950  76 TcemcraIAEGSAVDVIEMDAASHTSVDdAREIIERVQFRP-----ALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPH 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4506489   159 CRLILCCNSTSKVIPPIRSRCLAVRVPAPSIEDICHVLSTVCKKEGLNLPSQLAHRLAEKSCRNLRKAL 227
Cdd:PRK14950 151 AIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAE 219
 
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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