NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|28076937|ref|NP_081533|]
View 

SOSS complex subunit B1 isoform 1 [Mus musculus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 5.42e-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: 5.42e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937  18 NLIFIVLETGRV-TKTKDGHE--VRTCKVADKTGSINISVWDD-VGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQ 93
Cdd:cd04491   1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                ..
gi 28076937  94 KI 95
Cdd:cd04491  81 KL 82
PRK12323 super family cl46901
DNA polymerase III subunit gamma/tau;
106-179 5.78e-05

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: 43.23  E-value: 5.78e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28076937  106 PNFSEPNPEYNTQQAPNKSVQNNDNSpTAPQATTGPPAASPASENQNGN---GLSTQLGPVGGPHPSHTPSHPPSTR 179
Cdd:PRK14971 381 PVFTQPAAAPQPSAAAAASPSPSQSS-AAAQPSAPQSATQPAGTPPTVSvdpPAAVPVNPPSTAPQAVRPAQFKEEK 456
 
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 5.42e-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: 5.42e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937  18 NLIFIVLETGRV-TKTKDGHE--VRTCKVADKTGSINISVWDD-VGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQ 93
Cdd:cd04491   1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                ..
gi 28076937  94 KI 95
Cdd:cd04491  81 KL 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 1-114 5.75e-18

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 76.61  E-value: 5.75e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    1 MTTETFVKDIKPGLKNLNLIFIVLETG--RVTKTKDG-HEVRTCKVADKTGSINISVWDDVGNLIQPGDIIRLTKGYASV 77
Cdd:PRK06461   1 MEMITKIKDLKPGMERVNVTVRVLEVGepKVIQTKGGpRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 28076937   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 1.56e-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: 1.56e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937   7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLTKGYASVFKGC 81
Cdd:COG1599  24 ISDLSPGDRDVNVEGRVLEIGeeRTFDRKDGSEgrVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGG 103

                        90
                ....*....|....*.
gi 28076937  82 LTLYTGRGGDLQKIGE 97
Cdd:COG1599 104 PELNLGERTTIEKLDE 119
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
106-179 5.78e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 43.23  E-value: 5.78e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28076937  106 PNFSEPNPEYNTQQAPNKSVQNNDNSpTAPQATTGPPAASPASENQNGN---GLSTQLGPVGGPHPSHTPSHPPSTR 179
Cdd:PRK14971 381 PVFTQPAAAPQPSAAAAASPSPSQSS-AAAQPSAPQSATQPAGTPPTVSvdpPAAVPVNPPSTAPQAVRPAQFKEEK 456
Metaviral_G pfam09595
Metaviral_G glycoprotein; This is a viral attachment glycoprotein from region G of metaviruses. ...
 103-210 5.26e-03

Metaviral_G glycoprotein; This is a viral attachment glycoprotein from region G of metaviruses. It is high in serine and threonine suggesting it is highly glycosylated.


Pssm-ID: 462833 [Multi-domain]  Cd Length: 183  Bit Score: 36.47  E-value: 5.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937   103 SEVPNFSEPNPEYNTQQApNKSVQNNDNSPTAPQATTGPPAASPASENQNGNGLSTQLGPVGGPHPSHTPSHPPstriTR 182
Cdd:pfam09595  75 KEAPSESEDAPDIDPNNQ-HPSQDRSEAPPLEPAAKTKPSEHEPANPPDASNRLSPPDASTAAIREARTFRKPS----TG 149

                          90       100
                  ....*....|....*....|....*...
gi 28076937   183 SQPNhtPSGPPGPSSNPVSNGKETRRSS 210
Cdd:pfam09595 150 KRNN--PSSAQSDQSPPRANHEAIGRAN 175
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 27-80 7.52e-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: 7.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 28076937    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 5.42e-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: 5.42e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937  18 NLIFIVLETGRV-TKTKDGHE--VRTCKVADKTGSINISVWDD-VGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQ 93
Cdd:cd04491   1 SVEGKVLSISEPrEFTRDGSEgkVQSGLVGDETGTIRFTLWDEkAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80


                ..
gi 28076937  94 KI 95
Cdd:cd04491  81 KL 82
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 1-114 5.75e-18

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 76.61  E-value: 5.75e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    1 MTTETFVKDIKPGLKNLNLIFIVLETG--RVTKTKDG-HEVRTCKVADKTGSINISVWDDVGNLIQPGDIIRLTKGYASV 77
Cdd:PRK06461   1 MEMITKIKDLKPGMERVNVTVRVLEVGepKVIQTKGGpRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 28076937   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 1.56e-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: 1.56e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937   7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLTKGYASVFKGC 81
Cdd:COG1599  24 ISDLSPGDRDVNVEGRVLEIGeeRTFDRKDGSEgrVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYVREFNGG 103

                        90
                ....*....|....*.
gi 28076937  82 LTLYTGRGGDLQKIGE 97
Cdd:COG1599 104 PELNLGERTTIEKLDE 119
YhaM COG3481
3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily ...
 1-84 7.14e-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: 7.14e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937   1 MTTETFVKDIKPGlKNLNLIFIVLETgRVTKTKDGHEVRTCKVADKTGSINISVWDD---VGNLIQPGDIIRLtKGYASV 77
Cdd:COG3481   1 MMKRKFIKDLKPG-EEVDGFFLIKSK-ELRTTKNGKPYLSLTLQDKTGTIEAKIWDAseeDIEEFQPGDVVKV-RGKVQE 77


                ....*..
gi 28076937  78 FKGCLTL 84
Cdd:COG3481  78 YQGRLQL 84
PRK07211 PRK07211
single-stranded DNA binding protein;
7-97 3.15e-07

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 49.76  E-value: 3.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL---IQPGDIIRLTKGYASVFK 79
Cdd:PRK07211 164 VEDLSLGLSDVTLVGVVLDTDsvRTFDRDDGSEgrVSNLTVGDETGRVRVTLWDDRADLaeeLDAGESVEIVDGYVRERD 243

                         90
                 ....*....|....*...
gi 28076937   80 GCLTLYTGRGGDLQKIGE 97
Cdd:PRK07211 244 GSLELHVGDRGAVEEVDE 261
PRK14699 PRK14699
replication factor A; Provisional
 7-131 4.52e-07

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 49.61  E-value: 4.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGH--EVRTCKVADKTGSINISVWDDVG---NLIQPGDIIRLTKGYA--SV 77
Cdd:PRK14699 169 IKDIKDGMGDLNLTGKVLEISeiRTFQRKDGTsgKVGNLLLGDETGTLRVTLWDDKTdflNQIEYGDTVELINAYAreNA 248

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 28076937   78 FKGCLTLYTGRGGDLQKigefcmvysevpnfSEPNPEYNTQQAPNKSVQNNDNS 131
Cdd:PRK14699 249 FTQKVELQVGNRSIIRK--------------SEKKVEYEEEFTPIEDIKADMNN 288
PRK12366 PRK12366
replication factor A; Reviewed
 38-90 8.17e-07

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 48.89  E-value: 8.17e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 28076937   38 VRTCKVADKTGSINISVWDDVGNL-IQPGDIIRLTKGYASVFKGCLTLYTGRGG 90
Cdd:PRK12366 436 VRNIELADGTGSIRLTLWDDDAEIeIKEGDAIKILHPYVKENGDYLDLSIGRYG 489
PRK15491 PRK15491
replication factor A; Provisional
 7-97 8.47e-07

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 48.34  E-value: 8.47e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    7 VKDIKPGLKNLNLI---FIVLETGRVTKTkDGHE--VRTCKVADKTGSINISVWDDVGNLIQPGDI-----IRLTkGYAS 76
Cdd:PRK15491  60 IADINESSSNVNFTakvVSIFEPKEFNRN-DGTTgrVGNIIVADETGSIRLTLWDDLADLIKTGDIevgksLNIS-GYAK 137

                         90       100
                 ....*....|....*....|.
gi 28076937   77 VFKGCLTLYTGRGGDLQKIGE 97
Cdd:PRK15491 138 EGYSGIEVNIGRYGGISESDE 158
PRK12366 PRK12366
replication factor A; Reviewed
 7-72 3.95e-06

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 46.58  E-value: 3.95e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28076937    7 VKDIKPGLKNLNLifivleTGRVT--------KTKDGHE--VRTCKVADKTGSINISVWDDVGNLIQP---GDIIRLTK 72
Cdd:PRK12366  66 ISDIEEGQINVEI------TGRIIeisniktfTRKDGSTgkLANITIADNTGTIRLTLWNDNAKLLKGlkeGDVIKIEN 138
PRK07218 PRK07218
Single-stranded DNA binding protein;
7-74 1.05e-05

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 45.39  E-value: 1.05e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    7 VKDIKPGLKNLNLIFIVLETGRVTKTKDG--HEVRTCKVADKTGSINISVWDDVGnlIQPGDIIRLTKGY 74
Cdd:PRK07218  61 IKELSTDDKNVTVTGRVLTIGERSIRYQGddHVIYEGILADETGTISYTAWKDFG--LSPGDTVTIGNAG 128
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
106-179 5.78e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 43.23  E-value: 5.78e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28076937  106 PNFSEPNPEYNTQQAPNKSVQNNDNSpTAPQATTGPPAASPASENQNGN---GLSTQLGPVGGPHPSHTPSHPPSTR 179
Cdd:PRK14971 381 PVFTQPAAAPQPSAAAAASPSPSQSS-AAAQPSAPQSATQPAGTPPTVSvdpPAAVPVNPPSTAPQAVRPAQFKEEK 456
PRK15491 PRK15491
replication factor A; Provisional
 7-75 9.93e-05

replication factor A; Provisional


Pssm-ID: 185388 [Multi-domain]  Cd Length: 374  Bit Score: 42.18  E-value: 9.93e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28076937    7 VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHE--VRTCKVADKTGSINISVWDDVGNL---IQPGDIIRLTKGYA 75
Cdd:PRK15491 169 ISDIKDGDSDINIVGKVLDISdvRTFQKKDGSQgrVRNITIGDETGKIRVTLWDGKTDLadkLENGDSVEIINGYA 244
PRK07211 PRK07211
single-stranded DNA binding protein;
7-77 4.00e-04

single-stranded DNA binding protein;


Pssm-ID: 180887 [Multi-domain]  Cd Length: 485  Bit Score: 40.51  E-value: 4.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    7 VKDIKPGLKNLNLIFIVLETGRV-TKTKDGHE----VRTCKVADKTGSINISVWDD-----VGNLiQPGDIIRL----TK 72
Cdd:PRK07211  56 IADIEPGMDEVKFLAKVLSIGDLrTFERDGEDedgrVINVEVADETGSVRVAFWDEqavaaEEEL-EVGQVLRIkgrpKD 134


                 ....*
gi 28076937   73 GYASV 77
Cdd:PRK07211 135 GYNGL 139
PRK14699 PRK14699
replication factor A; Provisional
 4-94 7.92e-04

replication factor A; Provisional


Pssm-ID: 173162 [Multi-domain]  Cd Length: 484  Bit Score: 39.60  E-value: 7.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937    4 ETF--VKDIKPGLKNLNLIFIVLETG--RVTKTKDGHEVRTCKV--ADKTGSINISVWDDVGNLIQPGDI---IRLTKGY 74
Cdd:PRK14699 274 EEFtpIEDIKADMNNINISGRVLDISevRTFEKKDGSPGRVGNLllGDSTGKIRLTLWDEKTNFLDEIDFdetVEVLNAY 353

                         90       100
                 ....*....|....*....|..
gi 28076937   75 A--SVFKGCLTLYTGRGGDLQK 94
Cdd:PRK14699 354 SreNTFSQQVELNLGARGIIQK 375
PRK10856 PRK10856
cytoskeleton protein RodZ;
118-203 1.16e-03

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 38.85  E-value: 1.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937  118 QQAPNK--SVQNNDNSpTAPQATTGPPAASPASENQNGNGLSTQLGPVGGPHPSHTPSHPPstritrSQPNHTPSGPPGP 195
Cdd:PRK10856 153 ELSQNSgqSVPLDTST-TTDPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVAP------SQANVDTAATPAP 225


                 ....*...
gi 28076937  196 SSNPVSNG 203
Cdd:PRK10856 226 AAPATPDG 233
PRK12366 PRK12366
replication factor A; Reviewed
 19-76 1.99e-03

replication factor A; Reviewed


Pssm-ID: 237078 [Multi-domain]  Cd Length: 637  Bit Score: 38.49  E-value: 1.99e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28076937   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 2.73e-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: 2.73e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 28076937  31 KTKDGHEVRTCKVADKTGSINISVWDDVGNL---IQPGDIIRLtKGYASVFKG 80
Cdd:cd04492  13 TAKNGKPYLALTLQDKTGEIEAKLWDASEEDeekFKPGDIVHV-KGRVEEYRG 64
PHA03247 PHA03247
large tegument protein UL36; Provisional
 109-199 3.70e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 38.00  E-value: 3.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937   109 SEPNPEYNTQQAPNKSVQnndnSPTAPQATTGPPAASPASENQNGNGLSTQLGPVGGPHPSH-------TPSHPPSTRIT 181
Cdd:PHA03247 2812 LAPAAALPPAASPAGPLP----PPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRspaakpaAPARPPVRRLA 2887

                          90
                  ....*....|....*...
gi 28076937   182 RSQPNHTPSGPPGPSSNP 199
Cdd:PHA03247 2888 RPAVSRSTESFALPPDQP 2905
PHA03247 PHA03247
large tegument protein UL36; Provisional
 132-203 4.31e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 37.61  E-value: 4.31e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28076937   132 PTAPQATTGPPAASPASENQNGNGLSTQLGPVGGPHPSHTPSHPPSTRITRSQPNHT------PSGPPGPSSNPVSNG 203
Cdd:PHA03247 2776 AAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTsaqptaPPPPPGPPPPSLPLG 2853
Metaviral_G pfam09595
Metaviral_G glycoprotein; This is a viral attachment glycoprotein from region G of metaviruses. ...
 103-210 5.26e-03

Metaviral_G glycoprotein; This is a viral attachment glycoprotein from region G of metaviruses. It is high in serine and threonine suggesting it is highly glycosylated.


Pssm-ID: 462833 [Multi-domain]  Cd Length: 183  Bit Score: 36.47  E-value: 5.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28076937   103 SEVPNFSEPNPEYNTQQApNKSVQNNDNSPTAPQATTGPPAASPASENQNGNGLSTQLGPVGGPHPSHTPSHPPstriTR 182
Cdd:pfam09595  75 KEAPSESEDAPDIDPNNQ-HPSQDRSEAPPLEPAAKTKPSEHEPANPPDASNRLSPPDASTAAIREARTFRKPS----TG 149

                          90       100
                  ....*....|....*....|....*...
gi 28076937   183 SQPNhtPSGPPGPSSNPVSNGKETRRSS 210
Cdd:pfam09595 150 KRNN--PSSAQSDQSPPRANHEAIGRAN 175
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 27-80 7.52e-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: 7.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 28076937    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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH