Citrus Sinensis ID: 024247

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270
MIARRIGQSLRTVCRFSLRRVAPFCSSSSDHPRFSSVYSDAKRGGSAVYRHALKFQRPTTIKWQPQLENSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYVRECGQGLAFKKSVESKSRGGEAGMEKYENRFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMMEERGSRDLGSLSRVSTWVYDE
ccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccEEEEEEEcccccEEcccccEEEEEEEEcccccccccEEEEEEcHHHHHHHHHcccccEEEEEEEEEEEccccccccEEEEEEEEEEEEcHHHHccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccEEEccccccHHHHHHHHHHcHHHHHcccccccccccccccEEcc
ccHHHHHHHHHcccHHHHHHHccHcccccccccccccccccccccccHHHHHcccccccccccccHHHcEEEEEEEccccEEEcccEEEEEEEEEEcccccccEEEEEEEcHHHHHHHHHHHccccEEEEEEEEEEccccccccccEEEEEEEEEEEEEEEcccccccccccccccccccccHHHcccHHHHHHHHHHHccHHHHHccccccccccccccccccccEEEEcccccHHHHHHHHHHHHHHcccccccccccccccEEEEcc
MIARRIGQSLRTVCRFSlrrvapfcssssdhprfssvysdakrggsavYRHAlkfqrpttikwqpqlensvnfigtvvrplersnvFGVYTLLHVknshsdrgFDILLAVGGDMAQLCqkhlkpndfiyvtgqlhsyskvdkngklcLCYKVVVEDFNYVRECGQGLAFKKSvesksrggeagmEKYENRFYLWHVYFanpyewwdnrknklypgapdfkhkstgealwldpkdppwvkKQLQRIDSMMEergsrdlgslsrvstwvyde
miarrigqslrtVCRFSLRRVapfcssssdhprfssVYSDAKRGGSAVYRHALKFQrpttikwqpqlenSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYVRECgqglafkksvesksrggEAGMEKYENRFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTgealwldpkdppWVKKQLQRIDSMmeergsrdlgslsrvstwvyde
MIARRIGQSLRTVCRFSLRRVAPFCSSSSDHPRFSSVYSDAKRGGSAVYRHALKFQRPTTIKWQPQLENSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYVRECGQGLAFKKSVESKSRGGEAGMEKYENRFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMMEERGSRDLGSLSRVSTWVYDE
********SLRTVCRFSLRRVAPFC*******************GSAVYRHALKFQRPTTIKWQPQLENSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYVRECGQGLAFK***************KYENRFYLWHVYFANPYEWWDNRKNKLYPGAPDFKH***GEALWLD***************************************
****R***SLRTV*****************************************FQRPTTIKWQPQLENSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDF**************************************VYFANPYEWWD***********DF*HKSTGEALWLDPKDPPWVKKQLQ***************************
MIARRIGQSLRTVCRFSLRRVAPF******************RGGSAVYRHALKFQRPTTIKWQPQLENSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYVRECGQGLAFKK**********AGMEKYENRFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMMEERGSRDLGSLSRVSTWVYDE
*I*RRIGQSLRTVCRFSLRRVAPFCS******************GSAVYRHALKFQRPTTIKWQPQLENSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYVREC**********************KYENRFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMME********************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MIARRIGQSLRTVCRFSLRRVAPFCSSSSDHPRFSSVYSDAKRGGSAVYRHALKFQRPTTIKWQPQLENSVNFIGTVVRPLERSNVFGVYTLLHVKNSHSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYVRECGQGLAFKKSVESKSRGGEAGMEKYENRFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMMEERGSRDLGSLSRVSTWVYDE
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query270 2.2.26 [Sep-21-2011]
Q9SX99261 Protein OSB1, mitochondri yes no 0.862 0.892 0.414 7e-39
Q8GXH3371 Protein OSB2, chloroplast no no 0.707 0.514 0.274 9e-15
Q8GWJ4 440 Protein OSB3, chloroplast no no 0.770 0.472 0.271 4e-12
Q9FYJ2360 Protein OSB4, chloroplast no no 0.633 0.475 0.251 3e-09
>sp|Q9SX99|OSB1_ARATH Protein OSB1, mitochondrial OS=Arabidopsis thaliana GN=OSB1 PE=1 SV=1 Back     alignment and function desciption
 Score =  160 bits (406), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 104/251 (41%), Positives = 141/251 (56%), Gaps = 18/251 (7%)

Query: 18  LRRVAPFCSSSSDHPRFSSVYSDAKRGGSAVYRHALKFQRPTTIKWQPQLENSVNFIGTV 77
           ++R A   SSS    RF   +SD   G SAVY HA  F++P + K +  L NSV+ +G V
Sbjct: 11  IQRTASQISSSFPKSRF---FSD---GESAVYHHARLFKKPLSTKLKFNLVNSVSLMGFV 64

Query: 78  VRPLERSNV----FGVYTLLHVKNS-HSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTG 132
            R ++  N     FGV+T+L VK+  + +R F I L +   MA+ C  HLK ND I V+G
Sbjct: 65  DRSIQVMNTGPDRFGVFTILRVKDPLNPNRSFRISLRMWDAMARTCIAHLKLNDHILVSG 124

Query: 133 QLHSYSKV--DKNGKLCLCYKVVVEDFNYVREC-GQGLAFKKSVESKSRGGEAGMEKYEN 189
           +L SYSK   D    L L Y+V V + NYV       L  + S   K++  +   E  ++
Sbjct: 125 RLESYSKSSSDVYSGLNLDYQVKVAEVNYVAAPPSHVLDSQISKNPKTKTEDDIEESKKD 184

Query: 190 RFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMM 249
             YLW V+F+NPY+WWDNR+NK  P  PDFKHK TGEALWL    P W+ ++L+  D   
Sbjct: 185 EIYLWQVFFSNPYDWWDNRRNKKNPKQPDFKHKDTGEALWLCSDLPDWITRRLELFDQKN 244

Query: 250 ----EERGSRD 256
               EE+  RD
Sbjct: 245 RFYDEEKTRRD 255
Regulates mitochondrial DNA recombination. Represses homologous recombination, preventing mitochondrial genome instability and unbalanced transmission of alternative mtDNA configurations. Binds preferentially single-stranded DNA. Does not bind to RNA.
Arabidopsis thaliana (taxid: 3702)
>sp|Q8GXH3|OSB2_ARATH Protein OSB2, chloroplastic OS=Arabidopsis thaliana GN=OSB2 PE=1 SV=2 Back     alignment and function description
>sp|Q8GWJ4|OSB3_ARATH Protein OSB3, chloroplastic/mitochondrial OS=Arabidopsis thaliana GN=OSB3 PE=2 SV=1 Back     alignment and function description
>sp|Q9FYJ2|OSB4_ARATH Protein OSB4, chloroplastic OS=Arabidopsis thaliana GN=OSB4 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query270
356553917270 PREDICTED: protein OSB1, mitochondrial-l 0.855 0.855 0.5 6e-56
356553921271 PREDICTED: protein OSB1, mitochondrial-l 0.859 0.856 0.5 4e-55
357437947268 Protein OSB1 [Medicago truncatula] gi|35 0.870 0.876 0.478 9e-54
302142377273 unnamed protein product [Vitis vinifera] 0.918 0.908 0.490 2e-53
255538426 378 conserved hypothetical protein [Ricinus 0.937 0.669 0.433 2e-53
147795684273 hypothetical protein VITISV_012535 [Viti 0.918 0.908 0.486 4e-52
224137350 371 predicted protein [Populus trichocarpa] 0.896 0.652 0.422 6e-51
449470037263 PREDICTED: protein OSB1, mitochondrial-l 0.940 0.965 0.417 3e-41
297852370261 organellar single-stranded [Arabidopsis 0.885 0.915 0.412 5e-41
30694139261 protein OSB1 [Arabidopsis thaliana] gi|7 0.862 0.892 0.414 4e-37
>gi|356553917|ref|XP_003545297.1| PREDICTED: protein OSB1, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
 Score =  223 bits (568), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 125/250 (50%), Positives = 156/250 (62%), Gaps = 19/250 (7%)

Query: 29  SDHPRFSSVYSDAKRGGSAVYRHALKFQRPTTIKWQPQLENSVNFIGTVVRPLERSNV-- 86
           S H R S  + +A  G SAVY+H LKFQRP TI+W P LEN+ +FIGTV R   R N   
Sbjct: 32  STHNRHS--FDEAVPGCSAVYQHVLKFQRPPTIRWSPHLENTASFIGTVAREPTRVNSTT 89

Query: 87  --FGVYTLLHVKNSHSDRG--FDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVDK 142
             FGVYT+L V  S+      F +LL +  ++A+L  +HLK ND I+V G L S++K D 
Sbjct: 90  GKFGVYTVLKVPKSNQSNSSFFRLLLMMRNNVAKLASEHLKSNDLIHVLGSLGSFTKPDA 149

Query: 143 NGKLCLCYKVVVEDFNYVRECGQGLAFKK--SVESKSRGGEAGMEKYENRFYLWHVYFAN 200
           NG L L YK+ V++F +V +    L  KK  SVE      +AGM K +NR +LW V+F+N
Sbjct: 150 NGILRLNYKLEVKEFEFVAQSSGYLGDKKLESVE------DAGMHKNQNRLHLWQVFFSN 203

Query: 201 PYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMMEERGSRDLGSL 260
           P EWWD RK+K  P  PDFKHK TGEALWL   DPPWVK+QLQ  DS +        G  
Sbjct: 204 PNEWWDQRKSKRNPKQPDFKHKDTGEALWLSEYDPPWVKRQLQLFDSKI---AGGSAGRR 260

Query: 261 SRVSTWVYDE 270
           SRV+ WVYDE
Sbjct: 261 SRVTNWVYDE 270

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356553921|ref|XP_003545299.1| PREDICTED: protein OSB1, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
>gi|357437947|ref|XP_003589249.1| Protein OSB1 [Medicago truncatula] gi|355478297|gb|AES59500.1| Protein OSB1 [Medicago truncatula] Back     alignment and taxonomy information
>gi|302142377|emb|CBI19580.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255538426|ref|XP_002510278.1| conserved hypothetical protein [Ricinus communis] gi|223550979|gb|EEF52465.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|147795684|emb|CAN72175.1| hypothetical protein VITISV_012535 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224137350|ref|XP_002327104.1| predicted protein [Populus trichocarpa] gi|222835419|gb|EEE73854.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449470037|ref|XP_004152725.1| PREDICTED: protein OSB1, mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297852370|ref|XP_002894066.1| organellar single-stranded [Arabidopsis lyrata subsp. lyrata] gi|297339908|gb|EFH70325.1| organellar single-stranded [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|30694139|ref|NP_175203.2| protein OSB1 [Arabidopsis thaliana] gi|75337810|sp|Q9SX99.1|OSB1_ARATH RecName: Full=Protein OSB1, mitochondrial; AltName: Full=Organellar single-stranded DNA-binding protein 1; Flags: Precursor gi|5668791|gb|AAD46017.1|AC007519_2 F16N3.2 [Arabidopsis thaliana] gi|26453224|dbj|BAC43686.1| unknown protein [Arabidopsis thaliana] gi|28950819|gb|AAO63333.1| At1g47720 [Arabidopsis thaliana] gi|332194083|gb|AEE32204.1| protein OSB1 [Arabidopsis thaliana] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query270
TAIR|locus:2015353261 OSB1 "Organellar Single-strand 0.862 0.892 0.414 2.1e-38
TAIR|locus:2119767371 PTAC9 "plastid transcriptional 0.770 0.560 0.276 1.4e-15
TAIR|locus:2015721360 OSB4 "organellar single-strand 0.177 0.133 0.489 9.2e-15
TAIR|locus:505006672 442 OSB3 "organellar single-strand 0.770 0.470 0.268 7.4e-13
TAIR|locus:2015353 OSB1 "Organellar Single-stranded" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 104/251 (41%), Positives = 141/251 (56%)

Query:    18 LRRVAPFCSSSSDHPRFSSVYSDAKRGGSAVYRHALKFQRPTTIKWQPQLENSVNFIGTV 77
             ++R A   SSS    RF   +SD   G SAVY HA  F++P + K +  L NSV+ +G V
Sbjct:    11 IQRTASQISSSFPKSRF---FSD---GESAVYHHARLFKKPLSTKLKFNLVNSVSLMGFV 64

Query:    78 VRPLERSNV----FGVYTLLHVKNS-HSDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTG 132
              R ++  N     FGV+T+L VK+  + +R F I L +   MA+ C  HLK ND I V+G
Sbjct:    65 DRSIQVMNTGPDRFGVFTILRVKDPLNPNRSFRISLRMWDAMARTCIAHLKLNDHILVSG 124

Query:   133 QLHSYSKV--DKNGKLCLCYKVVVEDFNYVREC-GQGLAFKKSVESKSRGGEAGMEKYEN 189
             +L SYSK   D    L L Y+V V + NYV       L  + S   K++  +   E  ++
Sbjct:   125 RLESYSKSSSDVYSGLNLDYQVKVAEVNYVAAPPSHVLDSQISKNPKTKTEDDIEESKKD 184

Query:   190 RFYLWHVYFANPYEWWDNRKNKLYPGAPDFKHKSTGEALWLDPKDPPWVKKQLQRIDSMM 249
               YLW V+F+NPY+WWDNR+NK  P  PDFKHK TGEALWL    P W+ ++L+  D   
Sbjct:   185 EIYLWQVFFSNPYDWWDNRRNKKNPKQPDFKHKDTGEALWLCSDLPDWITRRLELFDQKN 244

Query:   250 ----EERGSRD 256
                 EE+  RD
Sbjct:   245 RFYDEEKTRRD 255
GO:0003697 "single-stranded DNA binding" evidence=IEA;IDA
GO:0009507 "chloroplast" evidence=ISM
GO:0000002 "mitochondrial genome maintenance" evidence=IMP
GO:0005739 "mitochondrion" evidence=IDA
GO:0045910 "negative regulation of DNA recombination" evidence=IMP
GO:0048046 "apoplast" evidence=IDA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA
GO:0043687 "post-translational protein modification" evidence=RCA
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA
TAIR|locus:2119767 PTAC9 "plastid transcriptionally active 9" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2015721 OSB4 "organellar single-stranded DNA binding protein 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:505006672 OSB3 "organellar single-stranded DNA binding protein 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q9SX99OSB1_ARATHNo assigned EC number0.41430.86290.8927yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00014749001
SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (273 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query270
cd04496100 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds 0.002
>gnl|CDD|239942 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB) Back     alignment and domain information 
 Score = 36.1 bits (84), Expect = 0.002
 Identities = 14/34 (41%), Positives = 22/34 (64%)

Query: 112 GDMAQLCQKHLKPNDFIYVTGQLHSYSKVDKNGK 145
           G +A+   K+LK  D +YV G+L + S  DK+G+
Sbjct: 52  GKLAENAAKYLKKGDLVYVEGRLRTRSWEDKDGQ 85

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. Length = 100

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 270
PRK07459121 single-stranded DNA-binding protein; Provisional 99.96
PRK06752112 single-stranded DNA-binding protein; Validated 99.96
PRK07275162 single-stranded DNA-binding protein; Provisional 99.96
PRK08486182 single-stranded DNA-binding protein; Provisional 99.95
PRK06751173 single-stranded DNA-binding protein; Provisional 99.94
PRK07274131 single-stranded DNA-binding protein; Provisional 99.94
PRK06293161 single-stranded DNA-binding protein; Provisional 99.94
PRK08763164 single-stranded DNA-binding protein; Provisional 99.94
PRK06642152 single-stranded DNA-binding protein; Provisional 99.94
PRK08182148 single-stranded DNA-binding protein; Provisional 99.94
PRK09010177 single-stranded DNA-binding protein; Provisional 99.93
PRK06958182 single-stranded DNA-binding protein; Provisional 99.93
PRK13732175 single-stranded DNA-binding protein; Provisional 99.93
PRK06863168 single-stranded DNA-binding protein; Provisional 99.93
TIGR00621164 ssb single stranded DNA-binding protein (ssb). Thi 99.92
PRK05733172 single-stranded DNA-binding protein; Provisional 99.92
PF00436104 SSB: Single-strand binding protein family; InterPr 99.92
PRK06341166 single-stranded DNA-binding protein; Provisional 99.91
COG0629167 Ssb Single-stranded DNA-binding protein [DNA repli 99.89
PRK05813219 single-stranded DNA-binding protein; Provisional 99.89
PRK07772186 single-stranded DNA-binding protein; Provisional 99.89
PRK02801101 primosomal replication protein N; Provisional 99.89
PRK05853161 hypothetical protein; Validated 99.86
cd04496100 SSB_OBF SSB_OBF: A subfamily of OB folds similar t 99.84
PRK05813219 single-stranded DNA-binding protein; Provisional 99.79
KOG1653175 consensus Single-stranded DNA-binding protein [Rep 99.63
PRK00036107 primosomal replication protein N; Reviewed 97.96
COG2965103 PriB Primosomal replication protein N [DNA replica 97.53
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 97.41
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 96.35
cd0448773 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f 96.33
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 95.61
cd0448291 RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara 94.9
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 94.43
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 93.35
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 92.91
cd04320102 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r 92.68
cd04317135 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod 92.22
PF1374299 tRNA_anti_2: OB-fold nucleic acid binding domain 92.2
PRK07211 485 replication factor A; Reviewed 91.85
cd0410085 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant 91.6
cd04475101 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor 91.33
PF11506104 DUF3217: Protein of unknown function (DUF3217); In 91.08
COG3390196 Uncharacterized protein conserved in archaea [Func 90.99
PLN02903 652 aminoacyl-tRNA ligase 90.74
cd0448482 polC_OBF polC_OBF: A subfamily of OB folds corresp 89.85
cd04319103 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticod 89.0
PRK00286 438 xseA exodeoxyribonuclease VII large subunit; Revie 88.92
cd04322108 LysRS_N LysRS_N: N-terminal, anticodon recognition 88.56
TIGR00237 432 xseA exodeoxyribonuclease VII, large subunit. This 88.05
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 87.75
PRK07373449 DNA polymerase III subunit alpha; Reviewed 86.74
cd04316108 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a 86.02
PRK15491374 replication factor A; Provisional 85.36
COG1570 440 XseA Exonuclease VII, large subunit [DNA replicati 85.33
PRK07211 485 replication factor A; Reviewed 85.28
cd0448875 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f 84.82
cd0449182 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil 82.1
PRK15491 374 replication factor A; Provisional 81.75
PRK056731135 dnaE DNA polymerase III subunit alpha; Validated 81.33
TIGR00458 428 aspS_arch aspartyl-tRNA synthetase, archaeal type. 81.27
>PRK07459 single-stranded DNA-binding protein; Provisional Back     alignment and domain information 
Probab=99.96  E-value=1.1e-28  Score=203.05  Aligned_cols=100  Identities=23%  Similarity=0.184  Sum_probs=93.7

Q ss_pred             CcceEEEEEEcCCCCc----cCCeeEEEEEEEEcCCC-CCCCeeEEEEEechhHHHHHhhcCCCCeEEEEEEeeecceec
Q 024247           67 LENSVNFIGTVVRPLE----RSNVFGVYTLLHVKNSH-SDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHSYSKVD  141 (270)
Q Consensus        67 l~NsV~LIGrLg~DPE----~~G~~va~fsLAV~~~~-~~~t~wI~Vv~wGkLAE~~~~yLkKGd~V~VsGrL~t~sy~d  141 (270)
                      ++|+|+||||||+|||    ++|+.++.|+||+++.+ .++++||+|++||++||.+++||+||++|+|+|+|++++|+|
T Consensus         2 ~~N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~~~~d   81 (121)
T PRK07459          2 SLNSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITGSLKFDRWTD   81 (121)
T ss_pred             CccEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEEEEEecceEc
Confidence            4899999999999999    79999999999999766 467999999999999999999999999999999999999999


Q ss_pred             CC-CcEEEEEEEEEEEEEeeecCCCC
Q 024247          142 KN-GKLCLCYKVVVEDFNYVRECGQG  166 (270)
Q Consensus       142 kd-G~kr~~~eVvV~~v~Fl~~~~q~  166 (270)
                      +| |++++.++|+|++|.||+.+.+.
T Consensus        82 ~d~G~~r~~~ei~a~~i~~L~~k~~~  107 (121)
T PRK07459         82 RNTGEDRSKPVIRVDRLELLGSKRDS  107 (121)
T ss_pred             CCCCeEEEEEEEEEeEEEECcCCCcc
Confidence            87 99999999999999999877644

>PRK06752 single-stranded DNA-binding protein; Validated Back     alignment and domain information
>PRK07275 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08486 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06751 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07274 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06293 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08763 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06642 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08182 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK09010 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06958 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK13732 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06863 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>TIGR00621 ssb single stranded DNA-binding protein (ssb) Back     alignment and domain information
>PRK05733 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids Back     alignment and domain information
>PRK06341 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK05813 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07772 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK02801 primosomal replication protein N; Provisional Back     alignment and domain information
>PRK05853 hypothetical protein; Validated Back     alignment and domain information
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB) Back     alignment and domain information
>PRK05813 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>KOG1653 consensus Single-stranded DNA-binding protein [Replication, recombination and repair] Back     alignment and domain information
>PRK00036 primosomal replication protein N; Reviewed Back     alignment and domain information
>COG2965 PriB Primosomal replication protein N [DNA replication, recombination, and repair] Back     alignment and domain information
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands Back     alignment and domain information
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit Back     alignment and domain information
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ Back     alignment and domain information
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32) Back     alignment and domain information
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32) Back     alignment and domain information
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70) Back     alignment and domain information
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1) Back     alignment and domain information
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE) Back     alignment and domain information
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS) Back     alignment and domain information
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS Back     alignment and domain information
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain Back     alignment and domain information
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs) Back     alignment and domain information
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70) Back     alignment and domain information
>PF11506 DUF3217: Protein of unknown function (DUF3217); InterPro: IPR024506 This family of proteins with unknown function appears to be restricted to Mycoplasma Back     alignment and domain information
>COG3390 Uncharacterized protein conserved in archaea [Function unknown] Back     alignment and domain information
>PLN02903 aminoacyl-tRNA ligase Back     alignment and domain information
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC) Back     alignment and domain information
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS) Back     alignment and domain information
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed Back     alignment and domain information
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS) Back     alignment and domain information
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit Back     alignment and domain information
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit Back     alignment and domain information
>PRK07373 DNA polymerase III subunit alpha; Reviewed Back     alignment and domain information
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS) Back     alignment and domain information
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG Back     alignment and domain information
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB) Back     alignment and domain information
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated Back     alignment and domain information
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query270
3vdy_A116 SSB, single-stranded DNA-binding protein SSBB; OB 99.96
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 99.95
3ull_A132 DNA binding protein; DNA replication, mitochondrio 99.95
2vw9_A134 Single-stranded DNA binding protein; DNA replicati 99.94
3ulp_A124 Single-strand binding protein; OB-fold, DNA bindin 99.94
1qvc_A145 Single stranded DNA binding protein monomer; beta- 99.94
1z9f_A153 Single-strand binding protein; TM0604, single stra 99.94
3tqy_A158 Single-stranded DNA-binding protein; DNA replicati 99.94
3lgj_A169 Single-stranded DNA-binding protein; niaid, CAT sc 99.93
4dam_A128 Single-stranded DNA-binding protein 1; OB-fold; 1. 99.92
3pgz_A193 Single-stranded DNA-binding protein; ssgcid, singl 99.92
1eqq_A178 Single stranded DNA binding protein; beta barrel, 99.92
3afp_A168 Single-stranded DNA-binding protein; OB-fold, quat 99.92
1txy_A104 Primosomal replication protein N; OB fold, dimer, 99.92
4gs3_A107 Single-stranded DNA-binding protein; primosome, ol 99.92
3k7u_C148 MP18 RNA editing complex protein; OB-fold, RNA-edi 99.92
2fxq_A264 Single-strand binding protein; strand beta-sheet e 99.91
1v1q_A134 Primosomal replication protein N; primosome, DNA r 99.91
3eiv_A199 Single-stranded DNA-binding protein 2; DNA damage, 99.9
3k81_C164 MP18 RNA editing complex protein; krepa6, single d 99.9
1se8_A301 Single-strand binding protein; DNA binding protein 99.89
2fxq_A264 Single-strand binding protein; strand beta-sheet e 99.89
3fhw_A115 Primosomal replication protein N; PRIB BPR162 X-RA 99.88
1se8_A301 Single-strand binding protein; DNA binding protein 99.88
3k8a_A103 Putative primosomal replication protein; beta-barr 99.85
4dni_A257 Fusion protein of RNA-editing complex proteins MP 99.84
3stb_C148 RNA-editing complex protein MP42; editosome, nanob 99.78
4dni_A257 Fusion protein of RNA-editing complex proteins MP 99.78
3en2_A101 Probable primosomal replication protein N; PRIB RS 99.77
4dka_C105 RNA-editing complex protein MP81; krepa1, VHH, sin 97.39
3dm3_A105 Replication factor A; probably plays AN essential 95.07
3e0e_A97 Replication protein A; structural genomics, PSI-2, 94.88
2k50_A115 Replication factor A related protein; uncharacteri 93.09
2hql_A110 Hypothetical protein Mg376 homolog; structural gen 91.26
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 90.16
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 88.87
1eov_A 487 ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy 87.19
3kdf_D132 Replication protein A 32 kDa subunit; wheat GERM c 86.98
4gop_B136 Putative uncharacterized protein; OB fold, ssDNA b 84.43
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 83.46
3au7_A402 TIAS, putative uncharacterized protein; ATP hydrol 82.69
3bju_A 521 Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, 82.01
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis} Back     alignment and structure
Probab=99.96  E-value=2.1e-28  Score=197.12  Aligned_cols=100  Identities=12%  Similarity=0.130  Sum_probs=87.4

Q ss_pred             CCcceEEEEEEcCCCCc----cCCeeEEEEEEEEcCCC-----CCCCeeEEEEEechhHHHHHhhcCCCCeEEEEEEeee
Q 024247           66 QLENSVNFIGTVVRPLE----RSNVFGVYTLLHVKNSH-----SDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQLHS  136 (270)
Q Consensus        66 ~l~NsV~LIGrLg~DPE----~~G~~va~fsLAV~~~~-----~~~t~wI~Vv~wGkLAE~~~~yLkKGd~V~VsGrL~t  136 (270)
                      .|||+|+|+|||++|||    ++|..++.|+||+++.+     +.+++||+|++||++||.+++||+||++|+|+|+|++
T Consensus         3 ~mmN~v~l~G~l~~dpe~r~t~~G~~v~~f~la~~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~   82 (116)
T 3vdy_A            3 HMFNQVMLVGRLTKDPDLRYTSAGAAVAHVTLAVNRSFKNASGEIEADYVNCTLWRKTAENTALYCQKGSLVGVSGRIQT   82 (116)
T ss_dssp             CCCCCEEEEEEESSCCEEEECTTSCEEEEEEEEEECSSCCSSSCCCEEEEEEEEEHHHHHHHHHHCCTTCEEEEEEEEEE
T ss_pred             ceEeEEEEEEEEccCcEEEECCCCCEEEEEEEEEeccccCCCCccccEEEEEEEECHHHHHHHHhCCCCCEEEEEEEEEe
Confidence            59999999999999999    78999999999998754     2478999999999999999999999999999999999


Q ss_pred             cceecCCCcEEEEEEEEEEEEEeeecCCC
Q 024247          137 YSKVDKNGKLCLCYKVVVEDFNYVRECGQ  165 (270)
Q Consensus       137 ~sy~dkdG~kr~~~eVvV~~v~Fl~~~~q  165 (270)
                      ++|+|+||++++.++|+|++|+||+++++
T Consensus        83 ~~~~d~dG~~~~~~ev~a~~i~~l~~~~~  111 (116)
T 3vdy_A           83 RSYENEEGVNVYVTEVLADTVRFMDPKPR  111 (116)
T ss_dssp             EEEC----CCEEEEEEEEEEEEECC----
T ss_pred             eEEECCCCCEEEEEEEEEEEEEEccCCCc
Confidence            99999999999999999999999988754
>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301} Back     alignment and structure
>3ull_A DNA binding protein; DNA replication, mitochondrion, transit peptide; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 PDB: 1s3o_A* 2dud_A Back     alignment and structure
>2vw9_A Single-stranded DNA binding protein; DNA replication, single-stranded DNA, single-stranded DNA binding protein, oligonucleotide/oligosaccharide binding fold, OB-fold; 2.30A {Helicobacter pylori} Back     alignment and structure
>3ulp_A Single-strand binding protein; OB-fold, DNA binding, single-stranded DNA, apicoplast, DNA B protein-DNA complex; HET: DNA; 2.10A {Plasmodium falciparum} Back     alignment and structure
>1qvc_A Single stranded DNA binding protein monomer; beta-barrel; 2.20A {Escherichia coli} SCOP: b.40.4.3 PDB: 1kaw_A 1eyg_A 1sru_A Back     alignment and structure
>1z9f_A Single-strand binding protein; TM0604, single stranded DNA-binding protein, structural GENO joint center for structural genomics, JCSG; 2.30A {Thermotoga maritima} Back     alignment and structure
>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii} Back     alignment and structure
>3lgj_A Single-stranded DNA-binding protein; niaid, CAT scratch fever, rochalimaea, LYME disease, ALS collaborative crystallography, DNA replication; 2.50A {Bartonella henselae} Back     alignment and structure
>4dam_A Single-stranded DNA-binding protein 1; OB-fold; 1.70A {Streptomyces coelicolor} Back     alignment and structure
>3pgz_A Single-stranded DNA-binding protein; ssgcid, single-strand binding protein, structural genomics center for infectious disease; 2.10A {Bartonella henselae} Back     alignment and structure
>1eqq_A Single stranded DNA binding protein; beta barrel, protein-DNA complex, replication/RNA complex; HET: 5MU; 3.20A {Escherichia coli} SCOP: b.40.4.3 Back     alignment and structure
>3afp_A Single-stranded DNA-binding protein; OB-fold, quaternary structure and stability, changes on oligomerisation, water-bridges, DNA damage; 2.05A {Mycobacterium leprae} PDB: 3afq_A 1ue1_A 1ue5_A 1ue6_A 1ue7_A 1x3e_A 1x3f_A 1x3g_A 3a5u_A* Back     alignment and structure
>1txy_A Primosomal replication protein N; OB fold, dimer, DNA binding protein; 2.00A {Escherichia coli} SCOP: b.40.4.3 PDB: 1woc_A 2pnh_A 4apv_A Back     alignment and structure
>4gs3_A Single-stranded DNA-binding protein; primosome, oligonucleotide/oligosaccharide binding domain, D binding protein; 1.09A {Thermoanaerobacter tengcongensis} Back     alignment and structure
>3k7u_C MP18 RNA editing complex protein; OB-fold, RNA-editing proteins, kinetoplastids, system, RNA binding protein; 2.10A {Trypanosoma brucei} PDB: 3k80_D 3stb_D Back     alignment and structure
>2fxq_A Single-strand binding protein; strand beta-sheet extended loops, DNA binding protein; 1.85A {Thermus aquaticus} PDB: 2ihe_A 2cwa_A 2ihf_A Back     alignment and structure
>1v1q_A Primosomal replication protein N; primosome, DNA replication, DNA binding; 2.1A {Escherichia coli} SCOP: b.40.4.3 PDB: 2ccz_A Back     alignment and structure
>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor} Back     alignment and structure
>3k81_C MP18 RNA editing complex protein; krepa6, single domain antibody, immune system, RNA BIND protein; 3.40A {Trypanosoma brucei} Back     alignment and structure
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 Back     alignment and structure
>2fxq_A Single-strand binding protein; strand beta-sheet extended loops, DNA binding protein; 1.85A {Thermus aquaticus} PDB: 2ihe_A 2cwa_A 2ihf_A Back     alignment and structure
>3fhw_A Primosomal replication protein N; PRIB BPR162 X-RAY NESG, structural genomics, PSI-2, protein initiative; 1.90A {Bordetella parapertussis} PDB: 3dm4_A 3klw_A Back     alignment and structure
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 Back     alignment and structure
>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090} Back     alignment and structure
>4dni_A Fusion protein of RNA-editing complex proteins MP MP18; krepa3, krepa6, editosome, protein/RNA binding, protein BIND binding protein; 2.55A {Trypanosoma brucei} Back     alignment and structure
>3stb_C RNA-editing complex protein MP42; editosome, nanobody, single domain antibody, VH krepa3, krepa6, RNA binding protein-immune system complex; 2.50A {Trypanosoma brucei} Back     alignment and structure
>4dni_A Fusion protein of RNA-editing complex proteins MP MP18; krepa3, krepa6, editosome, protein/RNA binding, protein BIND binding protein; 2.55A {Trypanosoma brucei} Back     alignment and structure
>3en2_A Probable primosomal replication protein N; PRIB RSR213C NESG X-RAY Q8XZT7 Q8XZT7_ralso, structural genomics, PSI-2; 2.30A {Ralstonia solanacearum} Back     alignment and structure
>4dka_C RNA-editing complex protein MP81; krepa1, VHH, single domain antibody, protein binding, RNA BI protein-immune system complex; 1.97A {Trypanosoma brucei} PDB: 4dk3_C 4dk6_C Back     alignment and structure
>3dm3_A Replication factor A; probably plays AN essential for replication of the chromosome, DNA recombination and repair; 2.40A {Methanocaldococcus jannaschii} Back     alignment and structure
>3e0e_A Replication protein A; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.60A {Methanococcus maripaludis} PDB: 2k5v_A Back     alignment and structure
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Back     alignment and structure
>2hql_A Hypothetical protein Mg376 homolog; structural genomics, conserved hypothetical protein, GI:1673959, MPN554, OB fold; 2.00A {Mycoplasma pneumoniae} Back     alignment and structure
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Back     alignment and structure
>1eov_A ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA synthetase, tRNA ligase, APO-enzyme, OB-fold,; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.1 d.104.1.1 PDB: 1asy_A* 1asz_A* Back     alignment and structure
>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_A 1quq_A 1l1o_B Back     alignment and structure
>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} Back     alignment and structure
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum} Back     alignment and structure
>3au7_A TIAS, putative uncharacterized protein; ATP hydrolysis, RNA binding protein; 2.60A {Archaeoglobus fulgidus} PDB: 3amt_A* 3amu_A* Back     alignment and structure
>3bju_A Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP- binding, cytoplasm, ligase, nucleotide-binding, phosphoprotein, polymorphism; HET: LYS ATP; 2.31A {Homo sapiens} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 270
d1v1qa_111 b.40.4.3 (A:) Primosomal replication protein N, Pr 7e-04
d1se8a_231 b.40.4.3 (A:) ssDNA-binding protein {Deinococcus r 0.003
d1ue1a_118 b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium 0.003
>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]} Length = 111 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: Primosomal replication protein N, PriB
species: Escherichia coli [TaxId: 562]

 Score = 36.0 bits (83), Expect = 7e-04
 Identities = 18/102 (17%), Positives = 32/102 (31%), Gaps = 14/102 (13%)

Query: 69  NSVNFIGTVVR-PLERSNVFGV----YTLLHVKNSHSDRG-----FDILLAVGGDMAQLC 118
           N +   GTV R PL + +  G+    + L H                + + V G   Q  
Sbjct: 7   NRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAI 66

Query: 119 QKHLKPNDFIYVTGQLHSYSKVDKNGKLCLCYKVVVEDFNYV 160
              +     I V G +  +   +   K+     +  E    +
Sbjct: 67  THSITVGSRITVQGFISCHKAKNGLSKM----VLHAEQIELI 104
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Length = 231 Back     information, alignment and structure
>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]} Length = 118 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query270
d1qvca_145 ssDNA-binding protein {Escherichia coli [TaxId: 56 99.94
d3ulla_115 ssDNA-binding protein {Human (Homo sapiens), mitoc 99.94
d1ue1a_118 ssDNA-binding protein {Mycobacterium tuberculosis 99.93
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.9
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.9
d1v1qa_111 Primosomal replication protein N, PriB {Escherichi 99.86
d1eova1134 Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S 94.04
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 91.66
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 90.64
d1b8aa1103 Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ 83.24
>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Single strand DNA-binding domain, SSB
domain: ssDNA-binding protein
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=1.3e-26  Score=191.45  Aligned_cols=99  Identities=18%  Similarity=0.192  Sum_probs=90.1

Q ss_pred             CCcceEEEEEEcCCCCc----cCCeeEEEEEEEEcCCC--------CCCCeeEEEEEechhHHHHHhhcCCCCeEEEEEE
Q 024247           66 QLENSVNFIGTVVRPLE----RSNVFGVYTLLHVKNSH--------SDRGFDILLAVGGDMAQLCQKHLKPNDFIYVTGQ  133 (270)
Q Consensus        66 ~l~NsV~LIGrLg~DPE----~~G~~va~fsLAV~~~~--------~~~t~wI~Vv~wGkLAE~~~~yLkKGd~V~VsGr  133 (270)
                      +-||+|+||||||+|||    ++|..++.|+||+++..        .+.|+||+|++||++||.+++||+|||+|+|+|+
T Consensus         3 ~~mN~v~LiG~l~~dpe~r~~~~G~~v~~f~va~~~~~~~~~~~~~~~~t~w~~v~~~g~~Ae~~~~~l~KG~~V~V~G~   82 (145)
T d1qvca_           3 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQ   82 (145)
T ss_dssp             CCEEEEEEEEEESSCCEEECCSSSCCEEEEEEEECCCCSCCSSSSCCCCCEEEEEEEETHHHHHHHHHCCTTCEEEEEEE
T ss_pred             CcceEEEEEEECCCCCEEEECCCCCEEEEEEEEecccccccccccccccceEEeeEEecchhhhHhhhcccCCEEEEEEE
Confidence            57999999999999999    78999999999998643        3578999999999999999999999999999999


Q ss_pred             eeecceecCCCcEEEEEEEEEE---EEEeeecCC
Q 024247          134 LHSYSKVDKNGKLCLCYKVVVE---DFNYVRECG  164 (270)
Q Consensus       134 L~t~sy~dkdG~kr~~~eVvV~---~v~Fl~~~~  164 (270)
                      |+++.|+|+||++++.++|+|+   .|.|+..+.
T Consensus        83 l~~~~~~~kdG~~r~~~ei~~~~~~~l~~l~~r~  116 (145)
T d1qvca_          83 LRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQ  116 (145)
T ss_dssp             EEEEEECSSSSCEEEEEEEECTTCEEEECCCCSC
T ss_pred             EEEeeeECCCCCEEEEEEEEEecCCcEEECcCcc
Confidence            9999999999999999999997   566665554
>d3ulla_ b.40.4.3 (A:) ssDNA-binding protein {Human (Homo sapiens), mitochondria [TaxId: 9606]} Back     information, alignment and structure
>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1jmca1 b.40.4.3 (A:183-298) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1b8aa1 b.40.4.1 (A:1-103) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]} Back     information, alignment and structure