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Conserved domains on  [gi|307717574|gb|ADN88840|]
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recombination factor protein, partial [Listeria ivanovii subsp. londoniensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RarA super family cl34445
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 1-191 5.21e-89

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


The actual alignment was detected with superfamily member COG2256:

Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 267.69  E-value: 5.21e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIAGSTKYAFRTLNAVTNNKKDMEVVAAEAKM----SGTVILLLDEVHRLDKVKQDFLLPLLESGAIILIG 76
Cdd:COG2256   59 GTGKTTLARLIANATDAEFVALSAVTSGVKDIREVIEEARErrayGRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIG 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  77 ATTSNPYIAINPAIRSRTQIFELKPLTVEDIMITMDRALADKDRGLGNYQVEINALAKKHFATASNGDVRSALNALELAV 156
Cdd:COG2256  139 ATTENPSFEVNSALLSRCRVFVLKPLSEEDLEQLLERALADDERGLGGYKLELDDEALEALARLADGDARRALNALELAV 218

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 307717574 157 ISSEsdEDGIVRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:COG2256  219 LSAP--PDGVIEITLELVEEALQRRALRYDKDGDE 251
 
Name Accession Description Interval E-value
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 1-191 5.21e-89

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 267.69  E-value: 5.21e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIAGSTKYAFRTLNAVTNNKKDMEVVAAEAKM----SGTVILLLDEVHRLDKVKQDFLLPLLESGAIILIG 76
Cdd:COG2256   59 GTGKTTLARLIANATDAEFVALSAVTSGVKDIREVIEEARErrayGRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIG 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  77 ATTSNPYIAINPAIRSRTQIFELKPLTVEDIMITMDRALADKDRGLGNYQVEINALAKKHFATASNGDVRSALNALELAV 156
Cdd:COG2256  139 ATTENPSFEVNSALLSRCRVFVLKPLSEEDLEQLLERALADDERGLGGYKLELDDEALEALARLADGDARRALNALELAV 218

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 307717574 157 ISSEsdEDGIVRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:COG2256  219 LSAP--PDGVIEITLELVEEALQRRALRYDKDGDE 251
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 1-191 1.27e-83

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 253.08  E-value: 1.27e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIAGSTKYAFRTLNAVTNNKKDMEVVAAEAK----MSGTVILLLDEVHRLDKVKQDFLLPLLESGAIILIG 76
Cdd:PRK13342  46 GTGKTTLARIIAGATDAPFEALSAVTSGVKDLREVIEEARqrrsAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIG 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  77 ATTSNPYIAINPAIRSRTQIFELKPLTVEDIMITMDRALADKDRGLgnyqVEINALAKKHFATASNGDVRSALNALELAV 156
Cdd:PRK13342 126 ATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGL----VELDDEALDALARLANGDARRALNLLELAA 201

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 307717574 157 ISSEsdedgivRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:PRK13342 202 LGVD-------SITLELLEEALQKRAARYDKDGDE 229
AAA_assoc_2 pfam16193
AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA ...
 123-191 3.06e-21

AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA domains in proteins ranging from archaeal to fungi, plants and mammals.


Pssm-ID: 465057  Cd Length: 81  Bit Score: 82.90  E-value: 3.06e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307717574  123 GNYQVEINALAKKHFATASNGDVRSALNALELAVISSESDeDGIVRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:pfam16193   1 GGLKIELDDEALEALAELADGDARRALNALELAVLSTPPD-DGGIHITLEILEEALQRKALRYDKDGDE 68
HLD_clamp_RarA cd18139
helical lid domain of recombination factor protein RarA; Recombination factor RarA ...
 102-179 8.27e-19

helical lid domain of recombination factor protein RarA; Recombination factor RarA (Replication associated recombination gene/protein A, also known as MgsA (Maintenance of genome stability A) or Mgs1 in yeast and WRNIP1 in mammals) is a member of the clamp-loader clade of the AAA+ superfamily. It functions as a tetramer. RarA co-localize with the replication fork throughout the cell cycle and may play a role in the rescue of stalled replication forks.


Pssm-ID: 350841 [Multi-domain]  Cd Length: 75  Bit Score: 76.52  E-value: 8.27e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 307717574 102 LTVEDIMITMDRALADKDRGlGNYQVEINALAKKHFATASNGDVRSALNALELAVISSEsdEDGIVRVTLDVAEECLQ 179
Cdd:cd18139    1 LSEEDLEKLLKRALEDKERG-GDRKVTIDDEALELLAEAADGDARSALNLLELAVLSAE--EDGGIVITLEDLEEVLQ 75
 
Name Accession Description Interval E-value
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 1-191 5.21e-89

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 267.69  E-value: 5.21e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIAGSTKYAFRTLNAVTNNKKDMEVVAAEAKM----SGTVILLLDEVHRLDKVKQDFLLPLLESGAIILIG 76
Cdd:COG2256   59 GTGKTTLARLIANATDAEFVALSAVTSGVKDIREVIEEARErrayGRRTILFVDEIHRFNKAQQDALLPHVEDGTITLIG 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  77 ATTSNPYIAINPAIRSRTQIFELKPLTVEDIMITMDRALADKDRGLGNYQVEINALAKKHFATASNGDVRSALNALELAV 156
Cdd:COG2256  139 ATTENPSFEVNSALLSRCRVFVLKPLSEEDLEQLLERALADDERGLGGYKLELDDEALEALARLADGDARRALNALELAV 218

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 307717574 157 ISSEsdEDGIVRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:COG2256  219 LSAP--PDGVIEITLELVEEALQRRALRYDKDGDE 251
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 1-191 1.27e-83

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 253.08  E-value: 1.27e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIAGSTKYAFRTLNAVTNNKKDMEVVAAEAK----MSGTVILLLDEVHRLDKVKQDFLLPLLESGAIILIG 76
Cdd:PRK13342  46 GTGKTTLARIIAGATDAPFEALSAVTSGVKDLREVIEEARqrrsAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIG 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  77 ATTSNPYIAINPAIRSRTQIFELKPLTVEDIMITMDRALADKDRGLgnyqVEINALAKKHFATASNGDVRSALNALELAV 156
Cdd:PRK13342 126 ATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGL----VELDDEALDALARLANGDARRALNLLELAA 201

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 307717574 157 ISSEsdedgivRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:PRK13342 202 LGVD-------SITLELLEEALQKRAARYDKDGDE 229
PRK13341 PRK13341
AAA family ATPase;
1-191 2.33e-63

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 207.60  E-value: 2.33e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIAGSTKYAFRTLNAVTNNKKDMEVVAAEAKMS-----GTVILLLDEVHRLDKVKQDFLLPLLESGAIILI 75
Cdd:PRK13341  62 GVGKTTLARIIANHTRAHFSSLNAVLAGVKDLRAEVDRAKERlerhgKRTILFIDEVHRFNKAQQDALLPWVENGTITLI 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  76 GATTSNPYIAINPAIRSRTQIFELKPLTVEDIMITMDRALADKDRGLGNYQVEINALAKKHFATASNGDVRSALNALELA 155
Cdd:PRK13341 142 GATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALELA 221

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 307717574 156 VISSESDEDGIVRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:PRK13341 222 VESTPPDEDGLIDITLAIAEESIQQRAVLYDKEGDA 257
AAA_assoc_2 pfam16193
AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA ...
 123-191 3.06e-21

AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA domains in proteins ranging from archaeal to fungi, plants and mammals.


Pssm-ID: 465057  Cd Length: 81  Bit Score: 82.90  E-value: 3.06e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307717574  123 GNYQVEINALAKKHFATASNGDVRSALNALELAVISSESDeDGIVRVTLDVAEECLQKKSLAHDKDGDA 191
Cdd:pfam16193   1 GGLKIELDDEALEALAELADGDARRALNALELAVLSTPPD-DGGIHITLEILEEALQRKALRYDKDGDE 68
HLD_clamp_RarA cd18139
helical lid domain of recombination factor protein RarA; Recombination factor RarA ...
 102-179 8.27e-19

helical lid domain of recombination factor protein RarA; Recombination factor RarA (Replication associated recombination gene/protein A, also known as MgsA (Maintenance of genome stability A) or Mgs1 in yeast and WRNIP1 in mammals) is a member of the clamp-loader clade of the AAA+ superfamily. It functions as a tetramer. RarA co-localize with the replication fork throughout the cell cycle and may play a role in the rescue of stalled replication forks.


Pssm-ID: 350841 [Multi-domain]  Cd Length: 75  Bit Score: 76.52  E-value: 8.27e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 307717574 102 LTVEDIMITMDRALADKDRGlGNYQVEINALAKKHFATASNGDVRSALNALELAVISSEsdEDGIVRVTLDVAEECLQ 179
Cdd:cd18139    1 LSEEDLEKLLKRALEDKERG-GDRKVTIDDEALELLAEAADGDARSALNLLELAVLSAE--EDGGIVITLEDLEEVLQ 75
PRK14700 PRK14700
recombination factor protein RarA; Provisional
 64-163 5.33e-12

recombination factor protein RarA; Provisional


Pssm-ID: 173163 [Multi-domain]  Cd Length: 300  Bit Score: 63.11  E-value: 5.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  64 LPLLESGAIILIGATTSNPYIAINPAIRSRTQIFELKPLTVEDIMITMDRALAdKDRGLGNYQVEINALAKKHFATASNG 143
Cdd:PRK14700   1 MPYVESGKIILIGATTENPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALS-QDEVLAKHKFKIDDGLYNAMHNYNEG 79

                         90       100
                 ....*....|....*....|.
gi 307717574 144 DVRSALNALE-LAVISSESDE 163
Cdd:PRK14700  80 DCRKILNLLErMFLISTRGDE 100
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 1-102 8.87e-10

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


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 54.14  E-value: 8.87e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574    1 GIGKTSIASAIAGSTKYAFRTLNA-------VTNNKKDMEVVAAEAKMSGTVILLLDEVHRL-----------DKVKQDF 62
Cdd:pfam00004   8 GTGKTTLAKAVAKELGAPFIEISGselvskyVGESEKRLRELFEAAKKLAPCVIFIDEIDALagsrgsggdseSRRVVNQ 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 307717574   63 LLPLLE-----SGAIILIGATTsNPYIaINPAIRSRTQIFELKPL 102
Cdd:pfam00004  88 LLTELDgftssNSKVIVIAATN-RPDK-LDPALLGRFDRIIEFPL 130
PRK04195 PRK04195
replication factor C large subunit; Provisional
 1-180 5.93e-09

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 54.54  E-value: 5.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIAGSTKYAFRTLNAV-TNNKKDMEVVAAEAKMSGTV------ILLLDEVHRLDkVKQDfllpllESG--A 71
Cdd:PRK04195  49 GVGKTSLAHALANDYGWEVIELNASdQRTADVIERVAGEAATSGSLfgarrkLILLDEVDGIH-GNED------RGGarA 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  72 IILIGATTSNPYIAI-----NPA---IRSRTQIFELKPLTVEDIMITMDRALADKDrglgnYQVEINALakKHFATASNG 143
Cdd:PRK04195 122 ILELIKKAKQPIILTandpyDPSlreLRNACLMIEFKRLSTRSIVPVLKRICRKEG-----IECDDEAL--KEIAERSGG 194

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 307717574 144 DVRSALNALELAVISSEsdedgivRVTLDVAEECLQK 180
Cdd:PRK04195 195 DLRSAINDLQAIAEGYG-------KLTLEDVKTLGRR 224
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
46-184 3.43e-08

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 52.12  E-value: 3.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  46 ILLLDEVHRLDKVKQDFLLPLLE--SGAIILIGATTsNPYiAINPAIRSRTQIFELKPLTVEDIMitmdRALAdkdRGLG 123
Cdd:COG2812  117 VYIIDEAHMLTTEAFNALLKTLEepPPHVVFILATT-EPQ-KLLPTILSRCQRFDFRRLPPEEIA----EHLA---KIAE 187

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 307717574 124 NYQVEINALAKKHFATASNGDVRSALNALELAVISSESDEDGIVrvtLDVAEECLQKKSLA 184
Cdd:COG2812  188 REGIEIEPEALALIARAADGSMRDALSLLDQAIAFGLLDRRELL---LDLLEALLAGDVAA 245
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 1-93 4.22e-08

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: 50.22  E-value: 4.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIA---GSTKYAFRTLNAVTNNKKDME----------VVAAEAKMSGTVILLLDEVHRLDKVKQDFLLPLL 67
Cdd:cd00009   29 GTGKTTLARAIAnelFRPGAPFLYLNASDLLEGLVVaelfghflvrLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVL 108

                         90       100       110
                 ....*....|....*....|....*....|....
gi 307717574  68 E--------SGAIILIGATTSNPYIAINPAIRSR 93
Cdd:cd00009  109 EtlndlridRENVRVIGATNRPLLGDLDRALYDR 142
PRK14961 PRK14961
DNA polymerase III subunits gamma and tau; Provisional
 46-156 1.37e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184925 [Multi-domain]  Cd Length: 363  Bit Score: 47.50  E-value: 1.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  46 ILLLDEVHRLDKVKQDFLLPLLESGA--IILIGATTSNPYIAINpaIRSRTQIFELKPLTVEDIMITMDRALADkdrglG 123
Cdd:PRK14961 122 VYLIDEVHMLSRHSFNALLKTLEEPPqhIKFILATTDVEKIPKT--ILSRCLQFKLKIISEEKIFNFLKYILIK-----E 194

                         90       100       110
                 ....*....|....*....|....*....|...
gi 307717574 124 NYQVEINALAKkhFATASNGDVRSALNALELAV 156
Cdd:PRK14961 195 SIDTDEYALKL--IAYHAHGSMRDALNLLEHAI 225
clpC CHL00095
Clp protease ATP binding subunit
 1-142 2.02e-06

Clp protease ATP binding subunit


Pssm-ID: 214361 [Multi-domain]  Cd Length: 821  Bit Score: 47.36  E-value: 2.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIA----------GSTKYAFRTLN-----AVTNNKKDMEV----VAAEAKMSGTVILLLDEVHRL------ 55
Cdd:CHL00095 210 GVGKTAIAEGLAqrivnrdvpdILEDKLVITLDiglllAGTKYRGEFEErlkrIFDEIQENNNIILVIDEVHTLigagaa 289

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  56 -DKVKQDFLL-PLLESGAIILIGATTSNPY---IAINPAIRSRTQIFELKPLTVEDImITMDRALadKDRGLGNYQVEIN 130
Cdd:CHL00095 290 eGAIDAANILkPALARGELQCIGATTLDEYrkhIEKDPALERRFQPVYVGEPSVEET-IEILFGL--RSRYEKHHNLSIS 366

                        170
                 ....*....|..
gi 307717574 131 ALAKKHFATASN 142
Cdd:CHL00095 367 DKALEAAAKLSD 378
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
46-160 7.50e-05

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 42.27  E-value: 7.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  46 ILLLDEVHRLDKVKQDFLLPLLE---SGAIILIgaTTSNPYiAINPAIRSRTQIFELKPLTVEDIMitmdRALadKDRGL 122
Cdd:COG0470  104 VVIIDEADAMNEAAANALLKTLEeppKNTPFIL--IANDPS-RLLPTIRSRCQVIRFRPPSEEEAL----AWL--REEGV 174

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 307717574 123 GnyQVEINALAKkhfatASNGDVRSALNALELAVISSE 160
Cdd:COG0470  175 D--EDALEAILR-----LAGGDPRAAINLLQALAGRKE 205
rfc PRK00440
replication factor C small subunit; Reviewed
 1-170 7.96e-05

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 42.17  E-value: 7.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIA----GST-KYAFRTLNA--------VTNNKKDMevvaAEAKMSGTV---ILLLDEVHRLDKVKQDFLL 64
Cdd:PRK00440  48 GTGKTTAALALArelyGEDwRENFLELNAsdergidvIRNKIKEF----ARTAPVGGApfkIIFLDEADNLTSDAQQALR 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  65 PLLESGA----IILIGATTSNpyiaINPAIRSRTQIFELKPLTVEDImITMDRALAdKDRGLGNYQVEINALAKkhfatA 140
Cdd:PRK00440 124 RTMEMYSqntrFILSCNYSSK----IIDPIQSRCAVFRFSPLKKEAV-AERLRYIA-ENEGIEITDDALEAIYY-----V 192

                        170       180       190
                 ....*....|....*....|....*....|.
gi 307717574 141 SNGDVRSALNALELAVISSES-DEDGIVRVT 170
Cdd:PRK00440 193 SEGDMRKAINALQAAAATGKEvTEEAVYKIT 223
PRK14963 PRK14963
DNA polymerase III subunits gamma and tau; Provisional
 22-153 8.93e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184927 [Multi-domain]  Cd Length: 504  Bit Score: 42.13  E-value: 8.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  22 LNAVTNNKKD-----MEVVAAEAKMSGTVILLLDEVHRLDKVKQDFLLPLLES--GAIILIGATTSNPYIAinPAIRSRT 94
Cdd:PRK14963  90 IDAASNNSVEdvrdlREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEppEHVIFILATTEPEKMP--PTILSRT 167

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 307717574  95 QIFELKPLTVEDIMITMDRALADKDRglgnyQVEINALAKkhFATASNGDVRSALNALE 153
Cdd:PRK14963 168 QHFRFRRLTEEEIAGKLRRLLEAEGR-----EAEPEALQL--VARLADGAMRDAESLLE 219
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 1-156 1.19e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 41.78  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574   1 GIGKTSIASAIA----------GSTKYAFRT--LNAVTNNKKD-----MEVVAAEAKMSGTVILLLDEVHRLDKVKQDFL 63
Cdd:PRK14970  49 GVGKTTCARILArkinqpgyddPNEDFSFNIfeLDAASNNSVDdirnlIDQVRIPPQTGKYKIYIIDEVHMLSSAAFNAF 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  64 LPLLES--GAIILIGATTSNPYIAinPAIRSRTQIFELKPLTVEDIMITMdRALADKDrglgNYQVEINALakKHFATAS 141
Cdd:PRK14970 129 LKTLEEppAHAIFILATTEKHKII--PTILSRCQIFDFKRITIKDIKEHL-AGIAVKE----GIKFEDDAL--HIIAQKA 199

                        170
                 ....*....|....*
gi 307717574 142 NGDVRSALNALELAV 156
Cdd:PRK14970 200 DGALRDALSIFDRVV 214
PRK06645 PRK06645
DNA polymerase III subunits gamma and tau; Validated
 46-172 2.45e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180643 [Multi-domain]  Cd Length: 507  Bit Score: 41.00  E-value: 2.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  46 ILLLDEVHRLDKVKQDFLLPLLESGA--IILIGATTSNPYIainPA-IRSRTQIFELKPLTVEDIMITMDRALADKdrgl 122
Cdd:PRK06645 131 IFIIDEVHMLSKGAFNALLKTLEEPPphIIFIFATTEVQKI---PAtIISRCQRYDLRRLSFEEIFKLLEYITKQE---- 203

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 307717574 123 gNYQVEINALakKHFATASNGDVRSALNALELAVISSESDEDGIVRVTLD 172
Cdd:PRK06645 204 -NLKTDIEAL--RIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVIN 250
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
17-156 4.23e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 40.14  E-value: 4.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  17 YAFRTLNAVTNNKKD-----MEVVAAEAKMSGTVILLLDEVHRLDKVKQDFLLPLLE---SGAIiLIGATTSNPYIAinP 88
Cdd:PRK14971  90 YNIHELDAASNNSVDdirnlIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEeppSYAI-FILATTEKHKIL--P 166

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 307717574  89 AIRSRTQIFELKPLTVEDIMITMdRALADKDrglgNYQVEINALAKkhFATASNGDVRSALNALELAV 156
Cdd:PRK14971 167 TILSRCQIFDFNRIQVADIVNHL-QYVASKE----GITAEPEALNV--IAQKADGGMRDALSIFDQVV 227
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 48-159 8.30e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 39.38  E-value: 8.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  48 LLDEVHRLDKVKQDFLLPLLESGA--IILIGATTSNPYIAInpAIRSRTQIFELKPLTVEDIMITMdRALADKDrglgNY 125
Cdd:PRK14964 121 IIDEVHMLSNSAFNALLKTLEEPAphVKFILATTEVKKIPV--TIISRCQRFDLQKIPTDKLVEHL-VDIAKKE----NI 193

                         90       100       110
                 ....*....|....*....|....*....|....
gi 307717574 126 QVEINALakKHFATASNGDVRSALNALELAVISS 159
Cdd:PRK14964 194 EHDEESL--KLIAENSSGSMRNALFLLEQAAIYS 225
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 1-103 4.34e-03

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


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 36.32  E-value: 4.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574    1 GIGKTSIASAIAGSTKYAFRT-----------LNAVTNNKKDMEVvaaeakmsgtviLLLDEVHRLDKVKQDFLLPLLES 69
Cdd:pfam05496  43 GLGKTTLANIIANEMGVNIRItsgpaierpgdLAAILTNLEPGDV------------LFIDEIHRLNRAVEEILYPAMED 110

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 307717574   70 GAI-ILIGAttsnpyiaiNPAIRSRTqiFELKPLT 103
Cdd:pfam05496 111 FRLdIVIGK---------GPSARSIR--LDLPPFT 134
DNA_pol3_delta2 pfam13177
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 46-103 4.82e-03

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: 36.03  E-value: 4.82e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 307717574   46 ILLLDEVHRLDKVKQDFLLPLLE---SGAIILIgaTTSNPYiAINPAIRSRTQIFELKPLT 103
Cdd:pfam13177 104 VYIIEDAEKMTASAANSLLKFLEeppGNTVIIL--LTENPS-RLLPTIRSRCQIIRFKPLS 161
PRK05563 PRK05563
DNA polymerase III subunits gamma and tau; Validated
 50-176 6.37e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235505 [Multi-domain]  Cd Length: 559  Bit Score: 36.77  E-value: 6.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307717574  50 DEVHrldkvkqdfllpLLESGA--------------IILIGATTSNPYIainPA-IRSRTQIFELKPLTVEDIMITMDRA 114
Cdd:PRK05563 126 DEVH------------MLSTGAfnallktleeppahVIFILATTEPHKI---PAtILSRCQRFDFKRISVEDIVERLKYI 190

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 307717574 115 LADKdrglgNYQVEINALakKHFATASNGDVRSALNALELAVisSESDEdgivRVTLDVAEE 176
Cdd:PRK05563 191 LDKE-----GIEYEDEAL--RLIARAAEGGMRDALSILDQAI--SFGDG----KVTYEDALE 239
 
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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