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Conserved domains on  [gi|449033057|gb|AGE68484|]
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hypothetical protein K60_025740 [Mycobacterium tuberculosis variant bovis BCG str. Korea 1168P]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10792691)

single-stranded DNA (ssDNA)-binding protein plays a key role in DNA replication, recombination, and repair

CATH:  2.40.50.140
Gene Ontology:  GO:0003697|GO:0006260
PubMed:  27838363
SCOP:  4000346

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PRK05853 PRK05853
hypothetical protein; Validated
 8-168 4.61e-88

hypothetical protein; Validated


:

Pssm-ID: 235626  Cd Length: 161  Bit Score: 254.38  E-value: 4.61e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   8 VVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYED 87
Cdd:PRK05853   1 VVGHIVNDPQRRKVGDQEVIKFRVASNSRRRTADGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYED 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057  88 RDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDLPAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPIS 167
Cdd:PRK05853  81 RDGNRRSSLEMRATSVGPDLSRCIVRIEKPRYTGPSAGEAPAATGTGAADAADAPASAADSVSDVVDDDAATGHNPLPLS 160


                 .
gi 449033057 168 A 168
Cdd:PRK05853 161 A 161
 
Name Accession Description Interval E-value
PRK05853 PRK05853
hypothetical protein; Validated
 8-168 4.61e-88

hypothetical protein; Validated


Pssm-ID: 235626  Cd Length: 161  Bit Score: 254.38  E-value: 4.61e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   8 VVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYED 87
Cdd:PRK05853   1 VVGHIVNDPQRRKVGDQEVIKFRVASNSRRRTADGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYED 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057  88 RDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDLPAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPIS 167
Cdd:PRK05853  81 RDGNRRSSLEMRATSVGPDLSRCIVRIEKPRYTGPSAGEAPAATGTGAADAADAPASAADSVSDVVDDDAATGHNPLPLS 160


                 .
gi 449033057 168 A 168
Cdd:PRK05853 161 A 161
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
7-109 2.86e-25

Single-stranded DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 440394  Cd Length: 116  Bit Score: 93.75  E-value: 2.86e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   7 TVVGHIVNDLQRRKVGD-QEVVKFRVASNSRRRTSDGGWEPGnSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEY 85
Cdd:COG0629    5 TLVGRLGKDPELRYTPSgTAVANFRLAVNRRYKDQDGEWKDE-TDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSW 83

                         90       100
                 ....*....|....*....|....
gi 449033057  86 EDRDGIRRSSLEMRATSVGPDLSR 109
Cdd:COG0629   84 EDKDGQKRYTTEVVADEIQFLGSR 107
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 7-106 4.09e-21

SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart at forks that have stalled at sites of DNA damage. It also plays a role in the assembly of primosome during replication initiation at the bacteriophage phiX174 origin. PriB physically interacts with SSB and binds ssDNA with high affinity.


Pssm-ID: 239942  Cd Length: 100  Bit Score: 82.27  E-value: 4.09e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   7 TVVGHIVNDLQRRKV-GDQEVVKFRVASNSRRRtsDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEY 85
Cdd:cd04496    2 ILIGRLGKDPELRYTpSGTPVARFSLAVNRRRK--DRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSW 79

                         90       100
                 ....*....|....*....|.
gi 449033057  86 EDRDGIRRSSLEMRATSVGPD 106
Cdd:cd04496   80 EDKDGQKRYGTEVVADRIEFL 100
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-103 1.70e-13

Single-strand binding protein family; This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.


Pssm-ID: 425680  Cd Length: 103  Bit Score: 63.02  E-value: 1.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057    6 LTVVGHIVNDLQRRKVGDQ-EVVKFRVASNSRRRtsDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSE 84
Cdd:pfam00436   4 VILVGRLTRDPELRYTPNGnAVANFTLATNRRFK--DRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRK 81

                          90
                  ....*....|....*....
gi 449033057   85 YEDRDGIRRSSLEMRATSV 103
Cdd:pfam00436  82 YEDQEGQKRYVTEIVADEV 100
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 7-104 5.21e-12

single stranded DNA-binding protein (ssb); All proteins in this family for which functions are known are single-stranded DNA binding proteins that function in many processes including transcription, repair, replication and recombination. Members encoded between genes for ribosomal proteins S6 and S18 should be annotated as primosomal protein N (PriB). Forms in gamma-protoeobacteria are much shorter and poorly recognized by this model. Additional members of this family include phage proteins. Eukaryotic members are organellar proteins. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273179 [Multi-domain]  Cd Length: 164  Bit Score: 60.51  E-value: 5.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057    7 TVVGHIVNDLQRRKV-GDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNcWGRLVTGVGAALGKGAPVIVVGHVYTSEY 85
Cdd:TIGR00621   8 ILVGRLTRDPELRYTpSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVI-FGRLAEVAAQYLKKGSLVYVEGRLRTRKW 86

                          90
                  ....*....|....*....
gi 449033057   86 EDRDGIRRSSLEMRATSVG 104
Cdd:TIGR00621  87 EDQNGQKRSKTEIIADNVQ 105
 
Name Accession Description Interval E-value
PRK05853 PRK05853
hypothetical protein; Validated
 8-168 4.61e-88

hypothetical protein; Validated


Pssm-ID: 235626  Cd Length: 161  Bit Score: 254.38  E-value: 4.61e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   8 VVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYED 87
Cdd:PRK05853   1 VVGHIVNDPQRRKVGDQEVIKFRVASNSRRRTADGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYED 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057  88 RDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDLPAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPIS 167
Cdd:PRK05853  81 RDGNRRSSLEMRATSVGPDLSRCIVRIEKPRYTGPSAGEAPAATGTGAADAADAPASAADSVSDVVDDDAATGHNPLPLS 160


                 .
gi 449033057 168 A 168
Cdd:PRK05853 161 A 161
Ssb COG0629
Single-stranded DNA-binding protein [Replication, recombination and repair];
7-109 2.86e-25

Single-stranded DNA-binding protein [Replication, recombination and repair];


Pssm-ID: 440394  Cd Length: 116  Bit Score: 93.75  E-value: 2.86e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   7 TVVGHIVNDLQRRKVGD-QEVVKFRVASNSRRRTSDGGWEPGnSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEY 85
Cdd:COG0629    5 TLVGRLGKDPELRYTPSgTAVANFRLAVNRRYKDQDGEWKDE-TDWHRVVAWGKLAENAAEYLKKGDKVYVEGRLRTRSW 83

                         90       100
                 ....*....|....*....|....
gi 449033057  86 EDRDGIRRSSLEMRATSVGPDLSR 109
Cdd:COG0629   84 EDKDGQKRYTTEVVADEIQFLGSR 107
PRK07772 PRK07772
single-stranded DNA-binding protein; Provisional
 1-125 1.51e-23

single-stranded DNA-binding protein; Provisional


Pssm-ID: 236092 [Multi-domain]  Cd Length: 186  Bit Score: 91.25  E-value: 1.51e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   1 MFETPLTVVGHIVNDLQRRKVGD-QEVVKFRVASNSRR--RTSdGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVV 77
Cdd:PRK07772   2 AGDTTITVVGNLTADPELRFTPSgAAVANFTVASTPRTfdRQT-NEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVT 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 449033057  78 GHVYTSEYEDRDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAG 125
Cdd:PRK07772  81 GRLKQRSYETREGEKRTVVELEVDEIGPSLRYATAKVTRASRGGGGGG 128
SSB_OBF cd04496
SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs ...
 7-106 4.09e-21

SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart at forks that have stalled at sites of DNA damage. It also plays a role in the assembly of primosome during replication initiation at the bacteriophage phiX174 origin. PriB physically interacts with SSB and binds ssDNA with high affinity.


Pssm-ID: 239942  Cd Length: 100  Bit Score: 82.27  E-value: 4.09e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   7 TVVGHIVNDLQRRKV-GDQEVVKFRVASNSRRRtsDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEY 85
Cdd:cd04496    2 ILIGRLGKDPELRYTpSGTPVARFSLAVNRRRK--DRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGRLRTRSW 79

                         90       100
                 ....*....|....*....|.
gi 449033057  86 EDRDGIRRSSLEMRATSVGPD 106
Cdd:cd04496   80 EDKDGQKRYGTEVVADRIEFL 100
SSB pfam00436
Single-strand binding protein family; This family includes single stranded binding proteins ...
 6-103 1.70e-13

Single-strand binding protein family; This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.


Pssm-ID: 425680  Cd Length: 103  Bit Score: 63.02  E-value: 1.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057    6 LTVVGHIVNDLQRRKVGDQ-EVVKFRVASNSRRRtsDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSE 84
Cdd:pfam00436   4 VILVGRLTRDPELRYTPNGnAVANFTLATNRRFK--DRGEGDEETDFHRVVVFGKLAEVAAQYLKKGSLVYVEGRLQTRK 81

                          90
                  ....*....|....*....
gi 449033057   85 YEDRDGIRRSSLEMRATSV 103
Cdd:pfam00436  82 YEDQEGQKRYVTEIVADEV 100
ssb TIGR00621
single stranded DNA-binding protein (ssb); All proteins in this family for which functions are ...
 7-104 5.21e-12

single stranded DNA-binding protein (ssb); All proteins in this family for which functions are known are single-stranded DNA binding proteins that function in many processes including transcription, repair, replication and recombination. Members encoded between genes for ribosomal proteins S6 and S18 should be annotated as primosomal protein N (PriB). Forms in gamma-protoeobacteria are much shorter and poorly recognized by this model. Additional members of this family include phage proteins. Eukaryotic members are organellar proteins. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273179 [Multi-domain]  Cd Length: 164  Bit Score: 60.51  E-value: 5.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057    7 TVVGHIVNDLQRRKV-GDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNcWGRLVTGVGAALGKGAPVIVVGHVYTSEY 85
Cdd:TIGR00621   8 ILVGRLTRDPELRYTpSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVI-FGRLAEVAAQYLKKGSLVYVEGRLRTRKW 86

                          90
                  ....*....|....*....
gi 449033057   86 EDRDGIRRSSLEMRATSVG 104
Cdd:TIGR00621  87 EDQNGQKRSKTEIIADNVQ 105
PRK06293 PRK06293
single-stranded DNA-binding protein; Provisional
 10-103 2.06e-08

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180517 [Multi-domain]  Cd Length: 161  Bit Score: 50.67  E-value: 2.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057  10 GHIVNDL-----QRRKVGDQEVVKFRVASNSRRRTSDggwepgNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSE 84
Cdd:PRK06293   4 GYIVGRLgadpeERMTSKGKRVVVLRLGVKSRVGSKD------ETVWCRCNIWGNRYDKMLPYLKKGSGVIVAGEMSPES 77

                         90
                 ....*....|....*....
gi 449033057  85 YEDRDGIRRSSLEMRATSV 103
Cdd:PRK06293  78 YVDKDGSPQSSLVVSVDTI 96
PRK08182 PRK08182
single-stranded DNA-binding protein; Provisional
 22-124 3.48e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 169261  Cd Length: 148  Bit Score: 38.89  E-value: 3.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057  22 GDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYEDRDGIRRSSLEMRAT 101
Cdd:PRK08182  26 EPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEGRMERDEWTDNEDNERVTFKVEAR 105

                         90       100
                 ....*....|....*....|....*
gi 449033057 102 SVGPDLSRV--IVRIEKPAYTGPSA 124
Cdd:PRK08182 106 RVGILPYRIesVTLSPKPAATEPEA 130
PRK07274 PRK07274
single-stranded DNA-binding protein; Provisional
 8-116 5.27e-04

single-stranded DNA-binding protein; Provisional


Pssm-ID: 180914  Cd Length: 131  Bit Score: 38.20  E-value: 5.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 449033057   8 VVGHIVNDLQRRKV-GDQEVVKFRVASNSRRRTSDGGWEPGnslFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYe 86
Cdd:PRK07274   7 LIGRLTATPELVKTaNDKSVARVTLAVNRRFKNQNGEREAD---FINVVLWGKLAETLASYASKGSLISIDGELRTRKY- 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 449033057  87 DRDGIR----------------RSSLEMRATSVGPDLSRVIVRIEK 116
Cdd:PRK07274  83 EKDGQThyvtevlcqsfqllesRAQRAMRENNVGNDLADLVLEEEE 128
 
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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