Citrus Sinensis ID: 021274

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-------280-------290-------300-------310-----
MMYSLRRVMAQIGRSQTTVKRIILYSPAHFTRPFSSRAHQFTKATTKTTTSKDVVWPKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLNLIEPTSQKRMFFVSKKQEAATVDHSVKISSSKKDGDSALSSWRDLLDNPEQWRDYRSDKLKGLVKPRYPDFKRKDGTLPLWLNSAPDWVLSELEGVVFDKSKPVLDDQTRKSNYVKKSKGVVFDKSKPVLDDQTQKSNYVKKSKGMKLLLFCSNLMQ
ccHHHHHHHHHHcccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccccEEEEcccccEEEEEEEEEcccccccEEEEEEEcHHHHHHHHHcccccEEEEEEEEEEccccccccEEEEEEEcEEcccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccEEcccccHHHHHHHcccccccccccccccccccccHHccccccccccccccccccccccccccccccEEEEEEccccc
ccHHHHHHHHHHHccccccccEEEEcccccccccccccccccccccEEcccccccccccccccccHHHHcEEEEEEEccccEEEEEcccccEEEEEEEEEEccccccEEEEEEcHHHHHHHHHHHccccEEEEEEEEEEcccccccccEEEEEEEEEEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHccHHHHHccccccccccccccccccccccccEEEEccccHHHHHHHHccccccccccccccccccccHHHHHHHHccccccccccccccccccEcccHHHHHHHHHHHcc
MMYSLRRVMAQIGRSQTTVKRIIlyspahftrpfssrahqftkattktttskdvvwpkpseipfqvkVANSVnlighvdapvqfqtssdgkhwAGTVIVQHAashslwipilfegdLAHIAsshlkkddhvhiagqltadppaiegqaNVQVMVHSLnlieptsqkRMFFVSKkqeaatvdhsvkissskkdgdsaLSSWRDlldnpeqwrDYRSDKlkglvkprypdfkrkdgtlplwlnsapdwvlselegvvfdkskpvlddqtrksnyvkkskgvvfdkskpvlddqtqksnyvkkskgMKLLLFCSNLMQ
MMYSLRrvmaqigrsqttvKRIILYSPAhftrpfssrahqftkattktttskdvvwpkpsEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLNLIEPTSQKRMFFVSKKqeaatvdhsvkissskkdgdsalsswrdlldnpeqwrdyrsdklkglvkprypdfkrkdgtlpLWLNSAPDWVLSELEgvvfdkskpvlddqtrksnyvkkskgvvfdkskpvlddqtqksnyvkkskgmkLLLFCSNLMQ
MMYSLRRVMAQIGRSQTTVKRIILYSPAHFTRPFSSRAHQFtkattktttskDVVWPKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLNLIEPTSQKRMFFVSKKQEAATVDHSVKISSSKKDGDSALSSWRDLLDNPEQWRDYRSDKLKGLVKPRYPDFKRKDGTLPLWLNSAPDWVLSELEGVVFDKSKPVLDDQTRKSNYVKKSKGVVFDKSKPVLDDQTQKSNYVKKSKGMKLLLFCSNLMQ
********MAQIGRSQTTVKRIILYSPAHFTRPFSS*AHQFT*******TSKDVVWPKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLNLIEP*****MFF***************************************WRDYR*DKLKGLVKPRYPDFKRKDGTLPLWLNSAPDWVLSELEGVVFDK*********************************************MKLLLFC*****
********************************************************PKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLN*******************************************DLLDNPEQWRDYRS************DFKRKDGTLPLWLNSAPDWVLSELEG*********************KSKGVVFDKSKPVLDDQTQKSNYVKKSKGMKLLLFCSNLM*
MMYSLRRVMAQIGRSQTTVKRIILYSPAHFTRPFSSRAHQFTKATTKTTTSKDVVWPKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLNLIEPTSQKRMFFVSK************************SSWRDLLDNPEQWRDYRSDKLKGLVKPRYPDFKRKDGTLPLWLNSAPDWVLSELEGVVFDKSKPVLDDQTRKSNYVKKSKGVVFDKSKPVLDDQTQKSNYVKKSKGMKLLLFCSNLMQ
**YSLRRVMAQIGRSQTTVKRIILYSPAHFT**************TK*****DVVWPKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLNLIEPT******************************DSALSSWRDLLDNPEQWRDYRSDKLKGLVKPRYPDFKRKDGTLPLWLNSAPDWVLSELEGVVFDK************NYVKKSKGVVFDKSKPVLDDQTQKSNYVKKSKGMKLLLFCSNLM*
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MMYSLRRVMAQIGRSQTTVKRIILYSPAHFTRPFSSRAHQFTKATTKTTTSKDVVWPKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPPAIEGQANVQVMVHSLNLIEPTSQKRMFFVSKKQEAATVDHSVKISSSKKDGDSALSSWRDLLDNPEQWRDYRSDKLKGLVKPRYPDFKRKDGTLPLWLNSAPDWVLSELEGVVFDKSKPVLDDQTRKSNYVKKSKGVVFDKSKPVLDDQTQKSNYVKKSKGMKLLLFCSNLMQ
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 ?
Query315 2.2.26 [Sep-21-2011]
Q8GXH3371 Protein OSB2, chloroplast yes no 0.707 0.601 0.475 3e-53
Q8GWJ4 440 Protein OSB3, chloroplast no no 0.631 0.452 0.458 4e-45
Q9FYJ2360 Protein OSB4, chloroplast no no 0.631 0.552 0.438 2e-44
Q9SX99261 Protein OSB1, mitochondri no no 0.657 0.793 0.278 2e-11
>sp|Q8GXH3|OSB2_ARATH Protein OSB2, chloroplastic OS=Arabidopsis thaliana GN=OSB2 PE=1 SV=2 Back     alignment and function desciption
 Score =  209 bits (531), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 117/246 (47%), Positives = 160/246 (65%), Gaps = 23/246 (9%)

Query: 44  ATTKTTTSKDVVWPKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAA 103
           A+   TT  ++  P+P+EI ++ +VAN VNLIG VD PVQF+ SSDGK WAGTVI Q +A
Sbjct: 75  ASVTATTENEL--PRPNEIAYESEVANWVNLIGFVDQPVQFEASSDGKFWAGTVISQRSA 132

Query: 104 SHS--LWIPILFEGDLAHIASSHLKKDDHVHIAGQLTAD--PPAIE-GQANVQVMVHSLN 158
           S S   WIPI+FEGDLA  A+ ++ KDD +H++G+L  D  PP +   QANVQV+V +LN
Sbjct: 133 SDSSGFWIPIIFEGDLAKTAARYVSKDDQIHVSGKLFIDSPPPNMTYAQANVQVLVQNLN 192

Query: 159 LIEPTSQKRMFFV----SKKQEAATVDHSVKISSSKKDG--DSALSSWRDLLDNPEQWRD 212
            I+P S     F+    S+K+E+       +   +K+D   D A  SW  L++NP++W D
Sbjct: 193 FIQPMSPSPSPFMVMSSSEKEESGIKKQPAR---AKQDIVIDEASDSWNHLIENPKEWWD 249

Query: 213 YRSDKLKGLVKPRYPDFKRKDGTLPLWLNSAPDWVLSELEGVVFDKSKPVLDDQTRKSNY 272
           +R +K+ GLVKPR+PDFK KD +  LWLN AP+WVL +LEG+ FD   P       K+  
Sbjct: 250 HRENKVNGLVKPRHPDFKSKDSSFSLWLNKAPNWVLPKLEGLEFDVLVP-------KARV 302

Query: 273 VKKSKG 278
           VK+ KG
Sbjct: 303 VKQLKG 308
Binds preferentially single-stranded DNA. Does not bind to RNA.
Arabidopsis thaliana (taxid: 3702)
>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
>sp|Q9SX99|OSB1_ARATH Protein OSB1, mitochondrial OS=Arabidopsis thaliana GN=OSB1 PE=1 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 ?
Query315
224121612354 predicted protein [Populus trichocarpa] 0.8 0.711 0.455 4e-52
79325179371 protein OSB2 [Arabidopsis thaliana] gi|3 0.717 0.609 0.473 6e-52
18415421371 protein OSB2 [Arabidopsis thaliana] gi|2 0.707 0.601 0.475 2e-51
297804136365 hypothetical protein ARALYDRAFT_492872 [ 0.634 0.547 0.509 3e-51
26451527371 unknown protein [Arabidopsis thaliana] 0.707 0.601 0.471 5e-51
359806154309 uncharacterized protein LOC100788700 [Gl 0.625 0.637 0.524 1e-46
297851580357 single-stranded DNA binding protein [Ara 0.695 0.613 0.408 3e-44
2660671395 hypothetical protein [Arabidopsis thalia 0.631 0.503 0.458 1e-43
297791323 441 hypothetical protein ARALYDRAFT_494502 [ 0.631 0.451 0.458 2e-43
18422482 440 protein OSB3 [Arabidopsis thaliana] gi|7 0.631 0.452 0.458 2e-43
>gi|224121612|ref|XP_002330744.1| predicted protein [Populus trichocarpa] gi|222872520|gb|EEF09651.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  211 bits (537), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 127/279 (45%), Positives = 164/279 (58%), Gaps = 27/279 (9%)

Query: 7   RVMAQIGRSQTTVKRI----ILYSPAHFTRPFSSRAHQFTKATTKTT------TSKDVVW 56
           RV+A+I  SQ T +RI    IL          + + H     T K T      +     +
Sbjct: 9   RVLAKIATSQPTTRRISPPLILLLQQSSCYSTNEKEHNPPTTTLKKTPPLYKKSPSSTDF 68

Query: 57  PKPSEIPFQVKVANSVNLIGHVDAPVQFQTSS-DGKHWAGTVIVQHAASHS--LWIPILF 113
           P+P EIPFQ KVANS+NLIG++D P+Q Q SS D K  A TVI Q  + HS  L IPI+F
Sbjct: 69  PRPKEIPFQAKVANSINLIGYIDMPIQTQVSSPDEKFRAATVITQEPSYHSPALRIPIIF 128

Query: 114 EGDLAHIASSHLKKDDHVHIAGQLTADPPA---IEGQANVQVMVHSLNLIEPTSQKRMFF 170
           EGDLAHIA+SHLKK D V+I GQL+ DPP    ++ Q  VQV+V+S+N IE + Q +   
Sbjct: 129 EGDLAHIAASHLKKGDFVYIDGQLSTDPPPFPEMQDQTQVQVLVNSINFIEGSFQVKKSI 188

Query: 171 VSKKQEAATVDHSVKISSSKKDGDSALSSWRDLLDNPEQWRDYRSDKLKGLVKPRYPDFK 230
           + ++ E    D          DG+S  +SW DLL+NP QW DYRS K  GLVKP++PDFK
Sbjct: 189 LEQQLEVPLDD----------DGESGSNSWTDLLENPNQWWDYRSSKRSGLVKPKHPDFK 238

Query: 231 RKDGTLPLWLNSAPDWVLSELEGVVFDKSKPVLDDQTRK 269
            K+    +WL  AP W+ S LE V FD  K  L  QT++
Sbjct: 239 HKNNNQSVWLTGAPSWIFSGLEKVKFD-VKTALPTQTKQ 276

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|79325179|ref|NP_001031674.1| protein OSB2 [Arabidopsis thaliana] gi|332658861|gb|AEE84261.1| protein OSB2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|18415421|ref|NP_567593.1| protein OSB2 [Arabidopsis thaliana] gi|259517764|sp|Q8GXH3.2|OSB2_ARATH RecName: Full=Protein OSB2, chloroplastic; AltName: Full=Organellar single-stranded DNA-binding protein 2; AltName: Full=Protein FLORAL ABSCISSION ASSOCIATED; AltName: Full=Protein PLASTID TRANSCRIPTIONALLY ACTIVE 9; Flags: Precursor gi|2827655|emb|CAA16609.1| hypothetical protein [Arabidopsis thaliana] gi|7268796|emb|CAB79001.1| hypothetical protein [Arabidopsis thaliana] gi|111074390|gb|ABH04568.1| At4g20010 [Arabidopsis thaliana] gi|332658860|gb|AEE84260.1| protein OSB2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297804136|ref|XP_002869952.1| hypothetical protein ARALYDRAFT_492872 [Arabidopsis lyrata subsp. lyrata] gi|297315788|gb|EFH46211.1| hypothetical protein ARALYDRAFT_492872 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|26451527|dbj|BAC42861.1| unknown protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|359806154|ref|NP_001241452.1| uncharacterized protein LOC100788700 [Glycine max] gi|255635066|gb|ACU17891.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|297851580|ref|XP_002893671.1| single-stranded DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi|297339513|gb|EFH69930.1| single-stranded DNA binding protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|2660671|gb|AAC79142.1| hypothetical protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297791323|ref|XP_002863546.1| hypothetical protein ARALYDRAFT_494502 [Arabidopsis lyrata subsp. lyrata] gi|297309381|gb|EFH39805.1| hypothetical protein ARALYDRAFT_494502 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|18422482|ref|NP_568639.1| protein OSB3 [Arabidopsis thaliana] gi|75328911|sp|Q8GWJ4.1|OSB3_ARATH RecName: Full=Protein OSB3, chloroplastic/mitochondrial; AltName: Full=Organellar single-stranded DNA-binding protein 3; Flags: Precursor gi|26452626|dbj|BAC43396.1| unknown protein [Arabidopsis thaliana] gi|28973013|gb|AAO63831.1| unknown protein [Arabidopsis thaliana] gi|30102734|gb|AAP21285.1| At5g44785 [Arabidopsis thaliana] gi|110743279|dbj|BAE99530.1| hypothetical protein [Arabidopsis thaliana] gi|332007779|gb|AED95162.1| protein OSB3 [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 ?
Query315
TAIR|locus:2119767371 PTAC9 "plastid transcriptional 0.682 0.579 0.491 1.9e-51
TAIR|locus:505006672 442 OSB3 "organellar single-strand 0.752 0.536 0.414 2.7e-45
TAIR|locus:2015721360 OSB4 "organellar single-strand 0.631 0.552 0.373 2.1e-29
TAIR|locus:2015353261 OSB1 "Organellar Single-strand 0.657 0.793 0.291 2.9e-16
TAIR|locus:2119767 PTAC9 "plastid transcriptionally active 9" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 534 (193.0 bits), Expect = 1.9e-51, P = 1.9e-51
 Identities = 113/230 (49%), Positives = 150/230 (65%)

Query:    57 PKPSEIPFQVKVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAASHS--LWIPILFE 114
             P+P+EI ++ +VAN VNLIG VD PVQF+ SSDGK WAGTVI Q +AS S   WIPI+FE
Sbjct:    86 PRPNEIAYESEVANWVNLIGFVDQPVQFEASSDGKFWAGTVISQRSASDSSGFWIPIIFE 145

Query:   115 GDLAHIASSHLKKDDHVHIAGQLTAD--PPAIE-GQANVQVMVHSLNLIEPTSQKRM-FF 170
             GDLA  A+ ++ KDD +H++G+L  D  PP +   QANVQV+V +LN I+P S     F 
Sbjct:   146 GDLAKTAARYVSKDDQIHVSGKLFIDSPPPNMTYAQANVQVLVQNLNFIQPMSPSPSPFM 205

Query:   171 VSKKQEAATVDHSVKISSSKKDG--DSALSSWRDLLDNPEQWRDYRSDKLKGLVKPRYPD 228
             V    E        + + +K+D   D A  SW  L++NP++W D+R +K+ GLVKPR+PD
Sbjct:   206 VMSSSEKEESGIKKQPARAKQDIVIDEASDSWNHLIENPKEWWDHRENKVNGLVKPRHPD 265

Query:   229 FKRKDGTLPLWLNSAPDWVLSELEGVVFDKSKPVLDDQTRKSNYVKKSKG 278
             FK KD +  LWLN AP+WVL +LEG+ FD   P       K+  VK+ KG
Sbjct:   266 FKSKDSSFSLWLNKAPNWVLPKLEGLEFDVLVP-------KARVVKQLKG 308
GO:0003697 "single-stranded DNA binding" evidence=IEA
GO:0008150 "biological_process" evidence=ND
GO:0009507 "chloroplast" evidence=ISM
GO:0009295 "nucleoid" evidence=IDA
GO:0009508 "plastid chromosome" evidence=IDA
TAIR|locus:505006672 OSB3 "organellar single-stranded DNA binding protein 3" [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:2015353 OSB1 "Organellar Single-stranded" [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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 315
PRK06752112 single-stranded DNA-binding protein; Validated 99.94
PRK07275162 single-stranded DNA-binding protein; Provisional 99.94
PRK07459121 single-stranded DNA-binding protein; Provisional 99.94
PRK08486182 single-stranded DNA-binding protein; Provisional 99.93
PRK06751173 single-stranded DNA-binding protein; Provisional 99.92
PRK08182148 single-stranded DNA-binding protein; Provisional 99.92
PRK07274131 single-stranded DNA-binding protein; Provisional 99.92
PRK08763164 single-stranded DNA-binding protein; Provisional 99.91
PRK13732175 single-stranded DNA-binding protein; Provisional 99.91
PRK06293161 single-stranded DNA-binding protein; Provisional 99.91
PRK06642152 single-stranded DNA-binding protein; Provisional 99.91
PRK09010177 single-stranded DNA-binding protein; Provisional 99.9
PRK06863168 single-stranded DNA-binding protein; Provisional 99.9
PRK06958182 single-stranded DNA-binding protein; Provisional 99.9
PRK05733172 single-stranded DNA-binding protein; Provisional 99.89
TIGR00621164 ssb single stranded DNA-binding protein (ssb). Thi 99.89
PF00436104 SSB: Single-strand binding protein family; InterPr 99.88
PRK06341166 single-stranded DNA-binding protein; Provisional 99.88
PRK05813219 single-stranded DNA-binding protein; Provisional 99.87
PRK02801101 primosomal replication protein N; Provisional 99.87
COG0629167 Ssb Single-stranded DNA-binding protein [DNA repli 99.86
PRK07772186 single-stranded DNA-binding protein; Provisional 99.85
PRK05853161 hypothetical protein; Validated 99.79
cd04496100 SSB_OBF SSB_OBF: A subfamily of OB folds similar t 99.79
PRK05813219 single-stranded DNA-binding protein; Provisional 99.74
KOG1653175 consensus Single-stranded DNA-binding protein [Rep 99.55
PRK00036107 primosomal replication protein N; Reviewed 98.49
COG2965103 PriB Primosomal replication protein N [DNA replica 98.23
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 97.32
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 97.06
cd0448482 polC_OBF polC_OBF: A subfamily of OB folds corresp 96.46
cd0448773 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f 96.09
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 95.97
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 95.92
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 95.55
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 94.65
PF1374299 tRNA_anti_2: OB-fold nucleic acid binding domain 94.35
PRK07211 485 replication factor A; Reviewed 93.47
cd0448291 RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara 93.13
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 92.81
TIGR00237 432 xseA exodeoxyribonuclease VII, large subunit. This 92.65
PRK00286 438 xseA exodeoxyribonuclease VII large subunit; Revie 92.52
cd0410085 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant 91.9
cd04320102 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r 90.24
PF11506104 DUF3217: Protein of unknown function (DUF3217); In 89.95
PRK15491374 replication factor A; Provisional 89.86
cd0449182 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil 89.22
PRK07373449 DNA polymerase III subunit alpha; Reviewed 89.19
PRK06461129 single-stranded DNA-binding protein; Reviewed 89.18
cd04317135 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod 88.75
cd0448875 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f 88.52
PRK15491374 replication factor A; Provisional 88.22
COG3390196 Uncharacterized protein conserved in archaea [Func 87.7
PRK056731135 dnaE DNA polymerase III subunit alpha; Validated 87.61
cd0432384 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a 87.45
PRK07211485 replication factor A; Reviewed 86.61
PRK12366 637 replication factor A; Reviewed 86.43
PF1132584 DUF3127: Domain of unknown function (DUF3127); Int 85.85
cd04316108 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a 85.57
cd04475101 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor 84.79
PRK14699 484 replication factor A; Provisional 84.65
COG1570 440 XseA Exonuclease VII, large subunit [DNA replicati 84.44
cd0432186 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, a 84.42
PRK13480314 3'-5' exoribonuclease YhaM; Provisional 83.8
PRK08402355 replication factor A; Reviewed 83.54
cd04322108 LysRS_N LysRS_N: N-terminal, anticodon recognition 83.13
PRK00448 1437 polC DNA polymerase III PolC; Validated 83.04
PRK068261151 dnaE DNA polymerase III DnaE; Reviewed 82.21
PRK069201107 dnaE DNA polymerase III DnaE; Reviewed 81.7
>PRK06752 single-stranded DNA-binding protein; Validated Back     alignment and domain information 
Probab=99.94  E-value=2.8e-26  Score=189.30  Aligned_cols=98  Identities=16%  Similarity=0.210  Sum_probs=90.8

Q ss_pred             CccEEEEEEEeCCCceEEEcCCCcEEEEEEEEEcCC-------CCCeEEEEEEecchHHHHHhhcCCCCeEEEEEEeEec
Q 021274           68 VANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAA-------SHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTAD  140 (315)
Q Consensus        68 l~NsV~LIGrLg~DPElr~T~~Gk~VA~ftLAV~r~-------~~T~wI~Vv~wGkLAE~aakhLKKGD~V~VeGRL~sr  140 (315)
                      |+|+|+|||||++|||++++++|..++.|+||+++.       .+++||+|++||++|+.+++||+|||+|+|+|+|+++
T Consensus         1 MmN~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~~   80 (112)
T PRK06752          1 MMNRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITGRIHTR   80 (112)
T ss_pred             CceEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEEEEEeC
Confidence            789999999999999999999999999999999972       2589999999999999999999999999999999999


Q ss_pred             CCCcC---CeEEEEEEEeEEeeecCCcc
Q 021274          141 PPAIE---GQANVQVMVHSLNLIEPTSQ  165 (315)
Q Consensus       141 s~edk---~rs~~eVvVe~I~FV~~k~q  165 (315)
                      +|+++   .++.++|+|++|.|++++.+
T Consensus        81 ~~~~~~G~~~~~~ei~a~~i~~l~~~~~  108 (112)
T PRK06752         81 NYEDDQGKRIYITEVVIESITFLERRRE  108 (112)
T ss_pred             ccCCCCCcEEEEEEEEEEEEEECCCCCc
Confidence            99876   46789999999999987653

>PRK07275 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07459 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
>PRK08182 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07274 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08763 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK13732 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06293 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06642 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK09010 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06863 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06958 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK05733 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>TIGR00621 ssb single stranded DNA-binding protein (ssb) 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
>PRK05813 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK02801 primosomal replication protein N; Provisional Back     alignment and domain information
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07772 single-stranded DNA-binding protein; 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
>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
>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
>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
>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
>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
>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
>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
>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
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit Back     alignment and domain information
>PRK00286 xseA exodeoxyribonuclease VII large subunit; 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
>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
>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
>PRK15491 replication factor A; Provisional 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
>PRK07373 DNA polymerase III subunit alpha; Reviewed Back     alignment and domain information
>PRK06461 single-stranded DNA-binding protein; Reviewed 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
>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
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>COG3390 Uncharacterized protein conserved in archaea [Function unknown] Back     alignment and domain information
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated Back     alignment and domain information
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs Back     alignment and domain information
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>PRK12366 replication factor A; Reviewed Back     alignment and domain information
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function 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
>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
>PRK14699 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
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS) Back     alignment and domain information
>PRK13480 3'-5' exoribonuclease YhaM; Provisional Back     alignment and domain information
>PRK08402 replication factor A; 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
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed Back     alignment and domain information
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed 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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query315
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-04
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
 Score = 42.1 bits (98), Expect = 2e-04
 Identities = 18/141 (12%), Positives = 36/141 (25%), Gaps = 50/141 (35%)

Query: 201 RDLLDNPEQWRDYRSDKLKGLV------------KPRYPDFK--RKDGTLP------LWL 240
           RD L   + W+    DKL  ++            +  +           +P      +W 
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397

Query: 241 NSA---PDWVLSELE-----------------GVVFDKSKPVLDDQT--RK--SNYVKKS 276
           +        V+++L                   +  +    + ++    R    +Y    
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK 457

Query: 277 KGVVFDKSKPVLDDQTQKSNY 297
                D   P LD       Y
Sbjct: 458 TFDSDDLIPPYLD------QY 472

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query315
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 99.94
3vdy_A116 SSB, single-stranded DNA-binding protein SSBB; OB 99.93
3ull_A132 DNA binding protein; DNA replication, mitochondrio 99.92
3ulp_A124 Single-strand binding protein; OB-fold, DNA bindin 99.92
2vw9_A134 Single-stranded DNA binding protein; DNA replicati 99.92
1z9f_A153 Single-strand binding protein; TM0604, single stra 99.91
1qvc_A145 Single stranded DNA binding protein monomer; beta- 99.91
1txy_A104 Primosomal replication protein N; OB fold, dimer, 99.91
3tqy_A158 Single-stranded DNA-binding protein; DNA replicati 99.91
3lgj_A169 Single-stranded DNA-binding protein; niaid, CAT sc 99.9
1v1q_A134 Primosomal replication protein N; primosome, DNA r 99.9
4gs3_A107 Single-stranded DNA-binding protein; primosome, ol 99.9
4dam_A128 Single-stranded DNA-binding protein 1; OB-fold; 1. 99.89
3afp_A168 Single-stranded DNA-binding protein; OB-fold, quat 99.89
3pgz_A193 Single-stranded DNA-binding protein; ssgcid, singl 99.89
1eqq_A178 Single stranded DNA binding protein; beta barrel, 99.88
3fhw_A115 Primosomal replication protein N; PRIB BPR162 X-RA 99.88
3k7u_C148 MP18 RNA editing complex protein; OB-fold, RNA-edi 99.88
3k8a_A103 Putative primosomal replication protein; beta-barr 99.87
3k81_C164 MP18 RNA editing complex protein; krepa6, single d 99.87
3eiv_A199 Single-stranded DNA-binding protein 2; DNA damage, 99.87
2fxq_A264 Single-strand binding protein; strand beta-sheet e 99.87
1se8_A301 Single-strand binding protein; DNA binding protein 99.86
2fxq_A264 Single-strand binding protein; strand beta-sheet e 99.86
1se8_A301 Single-strand binding protein; DNA binding protein 99.84
3en2_A101 Probable primosomal replication protein N; PRIB RS 99.8
4dni_A257 Fusion protein of RNA-editing complex proteins MP 99.79
4dni_A257 Fusion protein of RNA-editing complex proteins MP 99.72
3stb_C148 RNA-editing complex protein MP42; editosome, nanob 99.67
4dka_C105 RNA-editing complex protein MP81; krepa1, VHH, sin 97.38
2k50_A115 Replication factor A related protein; uncharacteri 96.06
3dm3_A105 Replication factor A; probably plays AN essential 95.81
3e0e_A97 Replication protein A; structural genomics, PSI-2, 95.69
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 94.05
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 92.07
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 91.78
2hql_A110 Hypothetical protein Mg376 homolog; structural gen 90.24
3f2b_A 1041 DNA-directed DNA polymerase III alpha chain; DNA p 88.52
4gop_B136 Putative uncharacterized protein; OB fold, ssDNA b 84.79
1eov_A 487 ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy 82.99
3kdf_D132 Replication protein A 32 kDa subunit; wheat GERM c 81.86
>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
Probab=99.94  E-value=2.1e-26  Score=189.62  Aligned_cols=92  Identities=16%  Similarity=0.159  Sum_probs=81.0

Q ss_pred             CCccEEEEEEEeCCCceEEEcCCC-cEEEEEEEEEcC---CCCCeEEEEEEecchHHHHHhhcCCCCeEEEEEEeEecCC
Q 021274           67 KVANSVNLIGHVDAPVQFQTSSDG-KHWAGTVIVQHA---ASHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQLTADPP  142 (315)
Q Consensus        67 ~l~NsV~LIGrLg~DPElr~T~~G-k~VA~ftLAV~r---~~~T~wI~Vv~wGkLAE~aakhLKKGD~V~VeGRL~srs~  142 (315)
                      ..+|+|+|||||++|||+|+|++| .++|+|+||+++   .++++||+|++||++||.|++||+|||+|+|+|+|++++|
T Consensus         9 ~~~~~v~LiGrL~~DPelR~t~~g~~~va~f~lAv~~~~~~~~t~fi~vv~wgk~AE~~~~yl~KG~~V~VeGrL~~r~y   88 (108)
T 3koj_A            9 SHMNSCILQATVVEAPQLRYAQDNQTPVAEMVVQFPGLSSKDAPARLKVVGWGAVAQELQDRCRLNDEVVLEGRLRINSL   88 (108)
T ss_dssp             SSCEEEEEEEEEEEEEEEEECTTSSSEEEEEEEEECC-----CCEEEEEEEETHHHHHHHHHCCTTCEEEEEEEEEEEC-
T ss_pred             cccceEEEEEEECCCCEEEEeCCCCEEEEEEEEEECCcccCCCcEEEEEEEEhHHHHHHHHhCCCCCEEEEEEEEEeeeE
Confidence            358999999999999999999998 999999999995   3479999999999999999999999999999999999999


Q ss_pred             CcC---CeEEEEEEEeEEe
Q 021274          143 AIE---GQANVQVMVHSLN  158 (315)
Q Consensus       143 edk---~rs~~eVvVe~I~  158 (315)
                      +++   .++.+||+|++|.
T Consensus        89 ~~kdG~kr~~tEVva~~i~  107 (108)
T 3koj_A           89 LKPDGNREKQTELTVTRVH  107 (108)
T ss_dssp             -------CCEEEEEEEEEE
T ss_pred             ECCCCCEEEEEEEEEEEEE
Confidence            985   5788999999874
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis} 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
>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
>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
>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
>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
>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
>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
>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
>4gs3_A Single-stranded DNA-binding protein; primosome, oligonucleotide/oligosaccharide binding domain, D binding protein; 1.09A {Thermoanaerobacter tengcongensis} Back     alignment and structure
>4dam_A Single-stranded DNA-binding protein 1; OB-fold; 1.70A {Streptomyces coelicolor} 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
>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
>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
>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
>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090} 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
>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor} 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
>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
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 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
>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
>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
>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
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} 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
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Back     alignment and structure
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} 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
>2hql_A Hypothetical protein Mg376 homolog; structural genomics, conserved hypothetical protein, GI:1673959, MPN554, OB fold; 2.00A {Mycoplasma pneumoniae} Back     alignment and structure
>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA polymerase III; HET: DGT; 2.39A {Geobacillus kaustophilus} PDB: 3f2c_A* 3f2d_A* 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
>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

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 315
d1v1qa_111 b.40.4.3 (A:) Primosomal replication protein N, Pr 0.001
d1ue1a_118 b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium 0.004
>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 = 0.001
 Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 70  NSVNLIGHV-DAPVQFQTSSDGKHWAGTVIVQHAASHS-------LWIPILFEGDLAHIA 121
           N + L G V  AP++  + S   H    +  +     +         +P++  G      
Sbjct: 7   NRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAI 66

Query: 122 SSHLKKDDHVHIAGQLT 138
           +  +     + + G ++
Sbjct: 67  THSITVGSRITVQGFIS 83
>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 ?
Query315
d1qvca_145 ssDNA-binding protein {Escherichia coli [TaxId: 56 99.91
d3ulla_115 ssDNA-binding protein {Human (Homo sapiens), mitoc 99.91
d1ue1a_118 ssDNA-binding protein {Mycobacterium tuberculosis 99.9
d1v1qa_111 Primosomal replication protein N, PriB {Escherichi 99.88
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.86
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.86
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 93.47
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 93.33
d1b8aa1103 Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ 91.02
d1eova1134 Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S 89.02
d1c0aa1106 Aspartyl-tRNA synthetase (AspRS) {Escherichia coli 83.13
d1wjja_145 Hypothetical protein At4g28440 (F20O9.120) {Thale 81.55
d1l0wa1104 Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph 80.25
>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=99.91  E-value=3.9e-24  Score=179.88  Aligned_cols=98  Identities=21%  Similarity=0.359  Sum_probs=87.2

Q ss_pred             CCccEEEEEEEeCCCceEEEcCCCcEEEEEEEEEcCC----------CCCeEEEEEEecchHHHHHhhcCCCCeEEEEEE
Q 021274           67 KVANSVNLIGHVDAPVQFQTSSDGKHWAGTVIVQHAA----------SHSLWIPILFEGDLAHIASSHLKKDDHVHIAGQ  136 (315)
Q Consensus        67 ~l~NsV~LIGrLg~DPElr~T~~Gk~VA~ftLAV~r~----------~~T~wI~Vv~wGkLAE~aakhLKKGD~V~VeGR  136 (315)
                      +-||+|+|||||++|||++++++|..++.|+||+++.          +.++||+|++||++|+.+++||+|||+|+|+|+
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            5689999999999999999999999999999999861          368999999999999999999999999999999


Q ss_pred             eEecCCCcC---CeEEEEEEEe---EEeeecCCc
Q 021274          137 LTADPPAIE---GQANVQVMVH---SLNLIEPTS  164 (315)
Q Consensus       137 L~srs~edk---~rs~~eVvVe---~I~FV~~k~  164 (315)
                      |+++.|+++   .++.++|+|+   .|.|+.++.
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            999999976   4678899997   566665443
>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
>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]} 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
>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
>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1c0aa1 b.40.4.1 (A:1-106) Aspartyl-tRNA synthetase (AspRS) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]} Back     information, alignment and structure