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Conserved domains on  [gi|564357797|ref|XP_006240831|]
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SOSS complex subunit B1 isoform X1 [Rattus norvegicus]

Protein Classification

SOSS complex subunit B family protein( domain architecture ID 10139587)

SOSS complex subunit B family protein that contains an OB-fold nucleic acid binding domain; such as human SOSS complex subunit B2 (SSB2/NABP1), a component of the SOSS multiprotein complex that functions downstream of the MRN complex to promote DNA repair and G2/M checkpoint

Gene Ontology:  GO:0006281|GO:0005634|GO:0070876|GO:0003697
PubMed:  19683501|19683490

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 18-95 5.29e-21

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


:

Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 83.06  E-value: 5.29e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797  18 NLIFIVLETGRV-TKTKDGHE--VRTCKVADKTGSINISVWDD-VGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQ 93
Cdd:cd04491    1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                 ..
gi 564357797  94 KI 95
Cdd:cd04491   81 KL 82
PRK12323 super family cl46901
DNA polymerase III subunit gamma/tau;
106-187 3.84e-07

DNA polymerase III subunit gamma/tau;


The actual alignment was detected with superfamily member PRK14971:

Pssm-ID: 481241 [Multi-domain]  Cd Length: 614  Bit Score: 49.77  E-value: 3.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797 106 PNFSEPNPEYNTQQASNKSVQNDSSPTAPQATTGPPAASPASESQNGNGLSTQPGPVggPHPSHAPSHPPSTRITRSQPN 185
Cdd:PRK14971 381 PVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPV--NPPSTAPQAVRPAQFKEEKKI 458


                 ..
gi 564357797 186 HT 187
Cdd:PRK14971 459 PV 460
 
Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 18-95 5.29e-21

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 83.06  E-value: 5.29e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797  18 NLIFIVLETGRV-TKTKDGHE--VRTCKVADKTGSINISVWDD-VGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQ 93
Cdd:cd04491    1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                 ..
gi 564357797  94 KI 95
Cdd:cd04491   81 KL 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 1-114 4.60e-18

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 76.61  E-value: 4.60e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   1 MTTETFVKDIKPGLKNLNLIFIVLETG--RVTKTKDG-HEVRTCKVADKTGSINISVWDDVGNLIQPGDIIRLTKGYASV 77
Cdd:PRK06461   1 MEMITKIKDLKPGMERVNVTVRVLEVGepKVIQTKGGpRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 564357797  78 FKGCLTLYTGRGGDLQKIGEfcmvySEVP---NFSEPNPE 114
Cdd:PRK06461  81 YRGKVQLNVGKYGSISESDD-----EEVPeaeEIPEETPE 115
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
7-97 1.53e-12

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 64.70  E-value: 1.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLTKGYASVFKGC 81
Cdd:COG1599   24 ISDLSPGDRDVNVEGRVLEIGeeRTFDRKDGSEgrVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGG 103

                         90
                 ....*....|....*.
gi 564357797  82 LTLYTGRGGDLQKIGE 97
Cdd:COG1599  104 PELNLGERTTIEKLDE 119
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
106-187 3.84e-07

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 49.77  E-value: 3.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797 106 PNFSEPNPEYNTQQASNKSVQNDSSPTAPQATTGPPAASPASESQNGNGLSTQPGPVggPHPSHAPSHPPSTRITRSQPN 185
Cdd:PRK14971 381 PVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPV--NPPSTAPQAVRPAQFKEEKKI 458


                 ..
gi 564357797 186 HT 187
Cdd:PRK14971 459 PV 460
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 129-187 4.45e-03

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. 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: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 37.18  E-value: 4.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797  129 SSPTAPQATTGPPAASPASesqngnglSTQPGPVGGPHPSHAPSH-PPSTRITRSQPNHT 187
Cdd:TIGR00601  75 SKPKTGTGKVAPPAATPTS--------APTPTPSPPASPASGMSAaPASAVEEKSPSEES 126
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 27-80 7.47e-03

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 34.13  E-value: 7.47e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 564357797   27 GRVT-KTKDGHEVRTCKVADKTGSINISVWDD----VGNLIQPGDIIRLTkGYASVFKG 80
Cdd:pfam01336   5 GRVTsIRRSGGKLLFLTLRDGTGSIQVVVFKEeaekLAKKLKEGDVVRVT-GKVKKRKG 62
 
Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 18-95 5.29e-21

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 83.06  E-value: 5.29e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797  18 NLIFIVLETGRV-TKTKDGHE--VRTCKVADKTGSINISVWDD-VGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQ 93
Cdd:cd04491    1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                 ..
gi 564357797  94 KI 95
Cdd:cd04491   81 KL 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 1-114 4.60e-18

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 76.61  E-value: 4.60e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   1 MTTETFVKDIKPGLKNLNLIFIVLETG--RVTKTKDG-HEVRTCKVADKTGSINISVWDDVGNLIQPGDIIRLTKGYASV 77
Cdd:PRK06461   1 MEMITKIKDLKPGMERVNVTVRVLEVGepKVIQTKGGpRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 564357797  78 FKGCLTLYTGRGGDLQKIGEfcmvySEVP---NFSEPNPE 114
Cdd:PRK06461  81 YRGKVQLNVGKYGSISESDD-----EEVPeaeEIPEETPE 115
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
7-97 1.53e-12

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 64.70  E-value: 1.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLTKGYASVFKGC 81
Cdd:COG1599   24 ISDLSPGDRDVNVEGRVLEIGeeRTFDRKDGSEgrVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGG 103

                         90
                 ....*....|....*.
gi 564357797  82 LTLYTGRGGDLQKIGE 97
Cdd:COG1599  104 PELNLGERTTIEKLDE 119
YhaM COG3481
3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily ...
 1-84 7.03e-08

3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily [Translation, ribosomal structure and biogenesis]; 3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 442704 [Multi-domain]  Cd Length: 316  Bit Score: 51.35  E-value: 7.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   1 MTTETFVKDIKPGlKNLNLIFIVLETgRVTKTKDGHEVRTCKVADKTGSINISVWDD---VGNLIQPGDIIRLtKGYASV 77
Cdd:COG3481    1 MMKRKFIKDLKPG-EEVDGFFLIKSK-ELRTTKNGKPYLSLTLQDKTGTIEAKIWDAseeDIEEFQPGDVVKV-RGKVQE 77


                 ....*..
gi 564357797  78 FKGCLTL 84
Cdd:COG3481   78 YQGRLQL 84
PRK07211 PRK07211
single-stranded DNA binding protein;
7-97 3.10e-07

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 49.76  E-value: 3.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL---IQPGDIIRLTKGYASVFK 79
Cdd:PRK07211 164 VEDLSLGLSDVTLVGVVLDTDsvRTFDRDDGSEgrVSNLTVGDETGRVRVTLWDDRADLaeeLDAGESVEIVDGYVRERD 243

                         90
                 ....*....|....*...
gi 564357797  80 GCLTLYTGRGGDLQKIGE 97
Cdd:PRK07211 244 GSLELHVGDRGAVEEVDE 261
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
106-187 3.84e-07

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 49.77  E-value: 3.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797 106 PNFSEPNPEYNTQQASNKSVQNDSSPTAPQATTGPPAASPASESQNGNGLSTQPGPVggPHPSHAPSHPPSTRITRSQPN 185
Cdd:PRK14971 381 PVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPV--NPPSTAPQAVRPAQFKEEKKI 458


                 ..
gi 564357797 186 HT 187
Cdd:PRK14971 459 PV 460
PRK14699 PRK14699
replication factor A; Provisional
 7-75 5.51e-07

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 49.23  E-value: 5.51e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564357797   7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGH--EVRTCKVADKTGSINISVWDDVG---NLIQPGDIIRLTKGYA 75
Cdd:PRK14699 169 IKDIKDGMGDLNLTGKVLEISeiRTFQRKDGTsgKVGNLLLGDETGTLRVTLWDDKTdflNQIEYGDTVELINAYA 244
PRK12366 PRK12366
replication factor A; Reviewed
 38-90 8.04e-07

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 48.89  E-value: 8.04e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 564357797  38 VRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLTKGYASVFKGCLTLYTGRGG 90
Cdd:PRK12366 436 VRNIELADGTGSIRLTLWDDDAEIeIKEGDAIKILHPYVKENGDYLDLSIGRYG 489
PRK15491 PRK15491
replication factor A; Provisional
 7-97 1.34e-06

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 47.95  E-value: 1.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   7 VKDIKPGLKNLNLI---FIVLETGRVTKTkDGHE--VRTCKVADKTGSINISVWDDVGNLIQPGDI-----IRLTkGYAS 76
Cdd:PRK15491  60 IADINESSSNVNFTakvVSIFEPKEFNRN-DGTTgrVGNIIVADETGSIRLTLWDDLADLIKTGDIevgksLNIS-GYAK 137

                         90       100
                 ....*....|....*....|.
gi 564357797  77 VFKGCLTLYTGRGGDLQKIGE 97
Cdd:PRK15491 138 EGYSGIEVNIGRYGGISESDE 158
PRK12366 PRK12366
replication factor A; Reviewed
 7-72 3.89e-06

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 46.58  E-value: 3.89e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564357797   7 VKDIKPGLKNLNLifivleTGRVT--------KTKDGHE--VRTCKVADKTGSINISVWDDVGNLIQP---GDIIRLTK 72
Cdd:PRK12366  66 ISDIEEGQINVEI------TGRIIeisniktfTRKDGSTgkLANITIADNTGTIRLTLWNDNAKLLKGlkeGDVIKIEN 138
PRK07218 PRK07218
Single-stranded DNA binding protein;
7-74 1.03e-05

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 45.39  E-value: 1.03e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   7 VKDIKPGLKNLNLIFIVLETGRVTKTKDG--HEVRTCKVADKTGSINISVWDDVGnlIQPGDIIRLTKGY 74
Cdd:PRK07218  61 IKELSTDDKNVTVTGRVLTIGERSIRYQGddHVIYEGILADETGTISYTAWKDFG--LSPGDTVTIGNAG 128
PRK15491 PRK15491
replication factor A; Provisional
 7-75 1.38e-04

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 41.79  E-value: 1.38e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564357797   7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL---IQPGDIIRLTKGYA 75
Cdd:PRK15491 169 ISDIKDGDSDINIVGKVLDISdvRTFQKKDGSQgrVRNITIGDETGKIRVTLWDGKTDLadkLENGDSVEIINGYA 244
PRK07211 PRK07211
single-stranded DNA binding protein;
7-77 3.95e-04

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 40.51  E-value: 3.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   7 VKDIKPGLKNLNLIFIVLETGRV-TKTKDGHE----VRTCKVADKTGSINISVWDD-----VGNLiQPGDIIRL----TK 72
Cdd:PRK07211  56 IADIEPGMDEVKFLAKVLSIGDLrTFERDGEDedgrVINVEVADETGSVRVAFWDEqavaaEEEL-EVGQVLRIkgrpKD 134


                 ....*
gi 564357797  73 GYASV 77
Cdd:PRK07211 135 GYNGL 139
PRK14699 PRK14699
replication factor A; Provisional
 4-94 7.82e-04

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 39.60  E-value: 7.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797   4 ETF--VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHEVRTCKV--ADKTGSINISVWDDVGNLIQPGDI---IRLTKGY 74
Cdd:PRK14699 274 EEFtpIEDIKADMNNINISGRVLDISevRTFEKKDGSPGRVGNLllGDSTGKIRLTLWDEKTNFLDEIDFdetVEVLNAY 353

                         90       100
                 ....*....|....*....|..
gi 564357797  75 A--SVFKGCLTLYTGRGGDLQK 94
Cdd:PRK14699 354 SreNTFSQQVELNLGARGIIQK 375
PRK12366 PRK12366
replication factor A; Reviewed
 19-76 1.97e-03

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 38.49  E-value: 1.97e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564357797  19 LIFIVLETGRVTKtKDGHE--VRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLtKGYAS 76
Cdd:PRK12366 192 EVTKAYPIKEFTR-KDGSEgkLKSFILKDDTGSIRVTLWNDLTDIeVNKGDIVRV-KGYVK 250
YhaM_OBF_like cd04492
YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and ...
 31-80 2.71e-03

YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.


Pssm-ID: 239938 [Multi-domain]  Cd Length: 83  Bit Score: 35.64  E-value: 2.71e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 564357797  31 KTKDGHEVRTCKVADKTGSINISVWDDVGNL---IQPGDIIRLtKGYASVFKG 80
Cdd:cd04492   13 TAKNGKPYLALTLQDKTGEIEAKLWDASEEDeekFKPGDIVHV-KGRVEEYRG 64
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 129-187 4.45e-03

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. 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: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 37.18  E-value: 4.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564357797  129 SSPTAPQATTGPPAASPASesqngnglSTQPGPVGGPHPSHAPSH-PPSTRITRSQPNHT 187
Cdd:TIGR00601  75 SKPKTGTGKVAPPAATPTS--------APTPTPSPPASPASGMSAaPASAVEEKSPSEES 126
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 106-182 5.47e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 37.27  E-value: 5.47e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564357797 106 PNFSEPNPEYNTQQASNKSVQNDSSPTAPQATTGPPAASPASESQNGNGLSTQPGPVGGPhPSHAPSHPPSTRITRS 182
Cdd:PRK07764 590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAA-PEHHPKHVAVPDASDG 665
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 27-80 7.47e-03

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 34.13  E-value: 7.47e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 564357797   27 GRVT-KTKDGHEVRTCKVADKTGSINISVWDD----VGNLIQPGDIIRLTkGYASVFKG 80
Cdd:pfam01336   5 GRVTsIRRSGGKLLFLTLRDGTGSIQVVVFKEeaekLAKKLKEGDVVRVT-GKVKKRKG 62
 
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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