Citrus Sinensis ID: 029088

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-------20
MAALTRRFYRSLLLNPKFSQSPKPFFTSNIFSSSSRVDSDLDESAIHSDADPLPDSSPTQNSGQQRESFDRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIFF
ccHHHHHHHHHHccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccEEEcccccEEEEEEcccccccccccccccccccccccccccccEEEEEEcccHHHHHHHHcccccEEEEEcEEccEEEccccccEEEEEEEEEEEccccEEEcc
cccHcHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccEEEEEEcccccccEEEcccccEEEEEEEEEccccccccccccccccHHHccccccEEEEEEEcHHHHHHHHHHHccccEEEEEEEEEEEEEEccccccEEEEEEEEEEcccEEEEEc
MAALTRRFYRSLllnpkfsqspkpfftsnifssssrvdsdldesaihsdadplpdssptqnsgqqresfdrplengldpgiFKAILVGqvgqspvqkklksgrtvtlfslgtggirnnrrplenenpteyanrcavqwhrvsvyperlggvvmkhlvpgstiyvegnleqkvfndpiTGLVRRIREIAIRRngtyliff
MAALTRRFYRSLllnpkfsqspkpfFTSNIFSSSSRVDSDLDESAIhsdadplpdssptqnsgQQRESFDRPLENGLDPGIFKAILVGQVGQspvqkklksgrtvtlfslgtggirnnrrplenenpteYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIyvegnleqkvfndpitglvRRIREiairrngtyliff
MAALTRRFYRSLLLNPKFSQSPKPFFTSNIFSSSSRVDSDLDESAIHSDADPLPDSSPTQNSGQQRESFDRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIrnnrrplenenpTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIFF
*******FYRSLLL***************************************************************DPGIFKAILVGQVGQS*V***LKSGRTVTLFSLGTGGI*************EYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIF*
****************************************************************************LDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNN***********YANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIFF
MAALTRRFYRSLLLNPKFSQSPKPFFTSNIFSSSSRVDSDLDESAIHSDA*******************DRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIFF
*********************************************************************DRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNN******ENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIFF
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MAALTRRFYRSLLLNPKFSQSPKPFFTSNIFSSSSRVDSDLDESAIHSDADPLPDSSPTQNSGQQRESFDRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIFF
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 ?
Query199 2.2.26 [Sep-21-2011]
Q84J78201 Single-stranded DNA-bindi no no 0.567 0.562 0.412 2e-22
Q89A53166 Single-stranded DNA-bindi yes no 0.527 0.632 0.321 6e-09
Q8D254163 Single-stranded DNA-bindi yes no 0.527 0.644 0.339 1e-08
Q1RK72150 Single-stranded DNA-bindi yes no 0.542 0.72 0.299 1e-08
Q92G30152 Single-stranded DNA-bindi yes no 0.542 0.710 0.299 1e-08
Q4UJW3152 Single-stranded DNA-bindi yes no 0.542 0.710 0.299 2e-08
Q68Y11152 Single-stranded DNA-bindi yes no 0.542 0.710 0.290 5e-08
Q9ZCC2152 Single-stranded DNA-bindi yes no 0.542 0.710 0.290 5e-08
P57610171 Single-stranded DNA-bindi yes no 0.547 0.637 0.294 6e-08
Q8P778172 Single-stranded DNA-bindi yes no 0.396 0.459 0.382 7e-08
>sp|Q84J78|SSBP_ARATH Single-stranded DNA-binding protein, mitochondrial OS=Arabidopsis thaliana GN=At4g11060 PE=2 SV=1 Back     alignment and function desciption
 Score =  105 bits (262), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/126 (41%), Positives = 82/126 (65%), Gaps = 13/126 (10%)

Query: 75  NGLDP-------GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENP 127
           +G+DP       G+ +AI+ G+VGQ+P+QK L++GRTVT+F++GTGG+ + R       P
Sbjct: 58  HGVDPRKGWGFRGVHRAIICGKVGQAPLQKILRNGRTVTIFTVGTGGMFDQRLVGATNQP 117

Query: 128 TEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREI 187
                    QWHR++V+ E LG   ++ L   S++YVEG++E +V+ND I+  V+ I EI
Sbjct: 118 K------PAQWHRIAVHNEVLGSYAVQKLAKNSSVYVEGDIETRVYNDSISSEVKSIPEI 171

Query: 188 AIRRNG 193
            +RR+G
Sbjct: 172 CVRRDG 177
Binds to ss-DNA.
Arabidopsis thaliana (taxid: 3702)
>sp|Q89A53|SSB_BUCBP Single-stranded DNA-binding protein OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q8D254|SSB_WIGBR Single-stranded DNA-binding protein OS=Wigglesworthia glossinidia brevipalpis GN=ssb PE=3 SV=2 Back     alignment and function description
>sp|Q1RK72|SSB_RICBR Single-stranded DNA-binding protein OS=Rickettsia bellii (strain RML369-C) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q92G30|SSB_RICCN Single-stranded DNA-binding protein OS=Rickettsia conorii (strain ATCC VR-613 / Malish 7) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q4UJW3|SSB_RICFE Single-stranded DNA-binding protein OS=Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q68Y11|SSB_RICTY Single-stranded DNA-binding protein OS=Rickettsia typhi (strain ATCC VR-144 / Wilmington) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q9ZCC2|SSB_RICPR Single-stranded DNA-binding protein OS=Rickettsia prowazekii (strain Madrid E) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|P57610|SSB_BUCAI Single-stranded DNA-binding protein OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q8P778|SSB_XANCP Single-stranded DNA-binding protein OS=Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568) GN=ssb PE=3 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 ?
Query199
297834764223 single-strand-binding family protein [Ar 0.954 0.852 0.664 1e-66
15229675217 single-strand DNA-binding protein [Arabi 0.944 0.866 0.663 3e-65
449439377234 PREDICTED: single-stranded DNA-binding p 0.979 0.833 0.598 8e-62
255541852223 Single-stranded DNA-binding protein, mit 0.959 0.856 0.645 2e-61
224118858220 predicted protein [Populus trichocarpa] 0.979 0.886 0.625 2e-60
225427470221 PREDICTED: single-stranded DNA-binding p 0.743 0.669 0.706 5e-57
356511595207 PREDICTED: single-stranded DNA-binding p 0.879 0.845 0.584 7e-55
357135683214 PREDICTED: single-stranded DNA-binding p 0.904 0.841 0.562 9e-53
115438823224 Os01g0642900 [Oryza sativa Japonica Grou 0.688 0.611 0.686 2e-51
125527031224 hypothetical protein OsI_03039 [Oryza sa 0.688 0.611 0.678 4e-51
>gi|297834764|ref|XP_002885264.1| single-strand-binding family protein [Arabidopsis lyrata subsp. lyrata] gi|297331104|gb|EFH61523.1| single-strand-binding family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 131/197 (66%), Positives = 156/197 (79%), Gaps = 7/197 (3%)

Query: 1   MAALTRRFYRSLLLNPKFSQSPKPFFTSNIFSSSSRVDSDLDESAIHSDAD----PLPDS 56
           +A L+RR YRSLL NP+ SQS   F T+NI   SSR DSD DE + +SD +    P    
Sbjct: 5   VATLSRRLYRSLLSNPRISQSSMSFCTNNI---SSREDSDFDELSANSDTESPIEPKASD 61

Query: 57  SPTQNSGQQRESFDRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIR 116
             ++ SG++R   +RPLENGLD GIFKAILVGQVGQ P+QKKLKSGRTVTLFS+GTGGIR
Sbjct: 62  PVSRFSGEERVMEERPLENGLDSGIFKAILVGQVGQLPLQKKLKSGRTVTLFSVGTGGIR 121

Query: 117 NNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDP 176
           NNRRPL NE+P EYA+R AVQWHRVSVYPERL  +V+K++ PG+ IY+EGNLE K+F DP
Sbjct: 122 NNRRPLINEDPREYASRSAVQWHRVSVYPERLAELVLKNVEPGTVIYLEGNLETKIFTDP 181

Query: 177 ITGLVRRIREIAIRRNG 193
           +TGLVRRIRE+AIRRNG
Sbjct: 182 VTGLVRRIREVAIRRNG 198

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|15229675|ref|NP_188488.1| single-strand DNA-binding protein [Arabidopsis thaliana] gi|9294319|dbj|BAB02216.1| unnamed protein product [Arabidopsis thaliana] gi|332642598|gb|AEE76119.1| single-strand DNA-binding protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|449439377|ref|XP_004137462.1| PREDICTED: single-stranded DNA-binding protein, mitochondrial-like [Cucumis sativus] gi|449486863|ref|XP_004157425.1| PREDICTED: single-stranded DNA-binding protein, mitochondrial-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255541852|ref|XP_002511990.1| Single-stranded DNA-binding protein, mitochondrial precursor, putative [Ricinus communis] gi|223549170|gb|EEF50659.1| Single-stranded DNA-binding protein, mitochondrial precursor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224118858|ref|XP_002317924.1| predicted protein [Populus trichocarpa] gi|222858597|gb|EEE96144.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225427470|ref|XP_002270678.1| PREDICTED: single-stranded DNA-binding protein, mitochondrial [Vitis vinifera] gi|296088446|emb|CBI37437.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|356511595|ref|XP_003524509.1| PREDICTED: single-stranded DNA-binding protein, mitochondrial-like [Glycine max] Back     alignment and taxonomy information
>gi|357135683|ref|XP_003569438.1| PREDICTED: single-stranded DNA-binding protein, mitochondrial-like [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|115438823|ref|NP_001043691.1| Os01g0642900 [Oryza sativa Japonica Group] gi|55297106|dbj|BAD68750.1| single-strand DNA binding protein-like [Oryza sativa Japonica Group] gi|113533222|dbj|BAF05605.1| Os01g0642900 [Oryza sativa Japonica Group] gi|125571356|gb|EAZ12871.1| hypothetical protein OsJ_02792 [Oryza sativa Japonica Group] gi|215686631|dbj|BAG88884.1| unnamed protein product [Oryza sativa Japonica Group] gi|215707058|dbj|BAG93518.1| unnamed protein product [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|125527031|gb|EAY75145.1| hypothetical protein OsI_03039 [Oryza sativa Indica Group] 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 ?
Query199
TAIR|locus:2086889217 AT3G18580 [Arabidopsis thalian 0.944 0.866 0.611 2.9e-55
TAIR|locus:2136083201 MTSSB "mitochondrially targete 0.592 0.587 0.406 2.1e-20
UNIPROTKB|P09380146 ssbp1-a "Single-stranded DNA-b 0.582 0.794 0.291 1.6e-08
UNIPROTKB|E2RST4148 SSBP1 "Single-stranded DNA-bin 0.577 0.777 0.291 4.2e-08
UNIPROTKB|E1BTE0149 SSBP1 "Single-stranded DNA-bin 0.577 0.771 0.283 5.3e-08
UNIPROTKB|F1N1S0148 SSBP1 "Single-stranded DNA-bin 0.577 0.777 0.291 5.3e-08
UNIPROTKB|F1SRQ7148 SSBP1 "Single-stranded DNA-bin 0.577 0.777 0.283 6.8e-08
UNIPROTKB|Q95KK4148 SSBP1 "Single-stranded DNA-bin 0.577 0.777 0.291 6.8e-08
UNIPROTKB|P09381148 ssbp1-b "Single-stranded DNA-b 0.628 0.844 0.285 8.7e-08
ZFIN|ZDB-GENE-050417-340146 ssbp1 "single-stranded DNA bin 0.577 0.787 0.291 8.7e-08
TAIR|locus:2086889 AT3G18580 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 570 (205.7 bits), Expect = 2.9e-55, P = 2.9e-55
 Identities = 118/193 (61%), Positives = 141/193 (73%)

Query:     1 MAALTRRFYRSLLLNPKFSQSPKPFFTSNIFSSSSRVDSDLDESAIHSDADPLPDSSPTQ 60
             MA L+RR YRSLL NP+ SQ+   F T+NI S     DSD DE  + S  +P      ++
Sbjct:     5 MATLSRRLYRSLLSNPRISQASMSFCTNNITSPE---DSDFDE--LESPIEPKASDPVSR 59

Query:    61 NSGQQRESFDRPLENGLDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXX 120
              SG++R   +RPLENGLD GIFKAILVGQVGQ P+QKKLKSGRTVTLFS+GTGGI     
Sbjct:    60 FSGEERVMEERPLENGLDSGIFKAILVGQVGQLPLQKKLKSGRTVTLFSVGTGGIRNNRR 119

Query:   121 XXXXXXXTEYANRCAVQWHRVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGL 180
                     EYA+R AVQWHRVSVYPERL  +V+K++ PG+ IY+EGNLE K+F DP+TGL
Sbjct:   120 PLINEDPREYASRSAVQWHRVSVYPERLADLVLKNVEPGTVIYLEGNLETKIFTDPVTGL 179

Query:   181 VRRIREIAIRRNG 193
             VRRIRE+AIRRNG
Sbjct:   180 VRRIREVAIRRNG 192
GO:0003697 "single-stranded DNA binding" evidence=IEA;ISS
GO:0005739 "mitochondrion" evidence=ISM
GO:0008150 "biological_process" evidence=ND
TAIR|locus:2136083 MTSSB "mitochondrially targeted single-stranded DNA binding protein" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|P09380 ssbp1-a "Single-stranded DNA-binding protein 1-A, mitochondrial" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
UNIPROTKB|E2RST4 SSBP1 "Single-stranded DNA-binding protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|E1BTE0 SSBP1 "Single-stranded DNA-binding protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1N1S0 SSBP1 "Single-stranded DNA-binding protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1SRQ7 SSBP1 "Single-stranded DNA-binding protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q95KK4 SSBP1 "Single-stranded DNA-binding protein, mitochondrial" [Oryctolagus cuniculus (taxid:9986)] Back     alignment and assigned GO terms
UNIPROTKB|P09381 ssbp1-b "Single-stranded DNA-binding protein 1-B, mitochondrial" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-050417-340 ssbp1 "single-stranded DNA binding protein 1" [Danio rerio (taxid:7955)] 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

Your Input:
fgenesh2_kg.3__2064__AT3G18580.1
annotation not avaliable (223 aa)
(Arabidopsis lyrata)
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 ?
Query199
pfam00436104 pfam00436, SSB, Single-strand binding protein fami 3e-15
cd04496100 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds 3e-14
PRK06642152 PRK06642, PRK06642, single-stranded DNA-binding pr 5e-11
PRK08763164 PRK08763, PRK08763, single-stranded DNA-binding pr 2e-09
PRK05733172 PRK05733, PRK05733, single-stranded DNA-binding pr 2e-08
PRK06341166 PRK06341, PRK06341, single-stranded DNA-binding pr 2e-08
PRK09010177 PRK09010, PRK09010, single-stranded DNA-binding pr 4e-08
PRK13732175 PRK13732, PRK13732, single-stranded DNA-binding pr 8e-08
TIGR00621164 TIGR00621, ssb, single stranded DNA-binding protei 7e-07
PRK06863168 PRK06863, PRK06863, single-stranded DNA-binding pr 4e-06
PRK06958182 PRK06958, PRK06958, single-stranded DNA-binding pr 1e-05
COG0629167 COG0629, Ssb, Single-stranded DNA-binding protein 5e-05
>gnl|CDD|215919 pfam00436, SSB, Single-strand binding protein family Back     alignment and domain information 
 Score = 68.0 bits (167), Expect = 3e-15
 Identities = 28/111 (25%), Positives = 47/111 (42%), Gaps = 11/111 (9%)

Query: 81  IFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHR 140
           + K ILVG++ + P  +   +G  V  F+L       ++    +E            + R
Sbjct: 1   MNKVILVGRLTRDPELRYTPNGNAVANFTLAVNRRFKDQNGEGDE---------ETDFIR 51

Query: 141 VSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRR 191
           V V+  +L     ++L  GS +YVEG L  + + D   G  R + EI    
Sbjct: 52  VVVWG-KLAENAAEYLKKGSLVYVEGRLRTRKYEDQ-EGQKRYVTEIVADE 100

This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA. Length = 104
>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
>gnl|CDD|135984 PRK06642, PRK06642, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|181549 PRK08763, PRK08763, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|235585 PRK05733, PRK05733, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|236362 PRK09010, PRK09010, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|184284 PRK13732, PRK13732, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|233057 TIGR00621, ssb, single stranded DNA-binding protein (ssb) Back     alignment and domain information
>gnl|CDD|136097 PRK06863, PRK06863, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|223702 COG0629, Ssb, Single-stranded DNA-binding protein [DNA replication, recombination, and repair] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 199
PRK09010177 single-stranded DNA-binding protein; Provisional 99.97
PRK06642152 single-stranded DNA-binding protein; Provisional 99.97
PRK05733172 single-stranded DNA-binding protein; Provisional 99.97
PRK06752112 single-stranded DNA-binding protein; Validated 99.96
PRK08763164 single-stranded DNA-binding protein; Provisional 99.96
PRK07275162 single-stranded DNA-binding protein; Provisional 99.96
PRK13732175 single-stranded DNA-binding protein; Provisional 99.96
PRK06863168 single-stranded DNA-binding protein; Provisional 99.96
PRK06341166 single-stranded DNA-binding protein; Provisional 99.96
PRK07459121 single-stranded DNA-binding protein; Provisional 99.96
PRK06958182 single-stranded DNA-binding protein; Provisional 99.96
PRK08486182 single-stranded DNA-binding protein; Provisional 99.96
PRK07274131 single-stranded DNA-binding protein; Provisional 99.96
PRK06751173 single-stranded DNA-binding protein; Provisional 99.95
PRK08182148 single-stranded DNA-binding protein; Provisional 99.95
TIGR00621164 ssb single stranded DNA-binding protein (ssb). Thi 99.95
PRK06293161 single-stranded DNA-binding protein; Provisional 99.95
KOG1653175 consensus Single-stranded DNA-binding protein [Rep 99.94
PF00436104 SSB: Single-strand binding protein family; InterPr 99.94
PRK07772186 single-stranded DNA-binding protein; Provisional 99.94
COG0629167 Ssb Single-stranded DNA-binding protein [DNA repli 99.93
PRK05853161 hypothetical protein; Validated 99.92
PRK05813219 single-stranded DNA-binding protein; Provisional 99.91
PRK02801101 primosomal replication protein N; Provisional 99.89
cd04496100 SSB_OBF SSB_OBF: A subfamily of OB folds similar t 99.88
PRK05813 219 single-stranded DNA-binding protein; Provisional 99.78
PRK00036107 primosomal replication protein N; Reviewed 97.91
COG2965103 PriB Primosomal replication protein N [DNA replica 97.52
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 96.44
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 95.67
cd0448482 polC_OBF polC_OBF: A subfamily of OB folds corresp 95.66
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 95.6
PF11506104 DUF3217: Protein of unknown function (DUF3217); In 94.2
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 93.9
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 93.75
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 92.84
PRK07211 485 replication factor A; Reviewed 91.7
PF1132584 DUF3127: Domain of unknown function (DUF3127); Int 90.95
cd0448773 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f 90.24
PRK15491374 replication factor A; Provisional 89.38
PRK15491 374 replication factor A; Provisional 86.76
PRK06461129 single-stranded DNA-binding protein; Reviewed 86.62
cd0448875 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f 85.87
PRK07211 485 replication factor A; Reviewed 85.73
PRK00286 438 xseA exodeoxyribonuclease VII large subunit; Revie 84.68
PF1374299 tRNA_anti_2: OB-fold nucleic acid binding domain 83.07
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 82.5
cd0448291 RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara 81.88
PRK13480 314 3'-5' exoribonuclease YhaM; Provisional 80.95
TIGR00237 432 xseA exodeoxyribonuclease VII, large subunit. This 80.01
>PRK09010 single-stranded DNA-binding protein; Provisional Back     alignment and domain information 
Probab=99.97  E-value=2.7e-30  Score=213.45  Aligned_cols=110  Identities=30%  Similarity=0.558  Sum_probs=101.8

Q ss_pred             ccCceEEEEEEeCCCCeEEEeCCCcEEEEEEEEeCCeecCCCCCCCCCCccccccCceeEEEEEEeCcchHHHHhhcCCC
Q 029088           79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP  158 (199)
Q Consensus        79 ~~~N~viLiG~Ig~dPe~k~~~~G~~v~~FsVAv~~~~~~r~~g~~ge~~e~~d~~~t~w~~V~~~g~~lAe~v~~~L~K  158 (199)
                      ++||+|+|+||||+||++|++++|..+++|+||+++.|+++..   +   +|  .+.++||+|++|+ ++|+.+.++|+|
T Consensus         4 r~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~---G---e~--~e~t~w~~V~~fg-k~Ae~~~~~L~K   74 (177)
T PRK09010          4 RGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQT---G---EM--KEQTEWHRVVLFG-KLAEVAGEYLRK   74 (177)
T ss_pred             cCceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCcc---c---cc--ccceEEEEEEEeh-hHHHHHHHhcCC
Confidence            7899999999999999999999999999999999999986532   3   33  2379999999998 899999999999


Q ss_pred             CCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEec
Q 029088          159 GSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIF  198 (199)
Q Consensus       159 G~~V~VeGrL~~~~~~d~~dG~~r~~~eI~v~~~g~l~fl  198 (199)
                      |++|+|+|+|+++.|+|+ +|++++.++|+|+.+|+|+||
T Consensus        75 Gs~V~VeGrL~~~~yedk-dG~~r~~~eVvv~~~~~~~~l  113 (177)
T PRK09010         75 GSQVYIEGQLRTRKWTDQ-SGQDRYTTEVVVNVGGTMQML  113 (177)
T ss_pred             CCEEEEEEEEEeccccCC-CCCEEEEEEEEEecCCcEEEc
Confidence            999999999999999998 999999999999999999998

>PRK06642 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK05733 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06752 single-stranded DNA-binding protein; Validated Back     alignment and domain information
>PRK08763 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07275 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
>PRK06341 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07459 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06958 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08486 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07274 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
>TIGR00621 ssb single stranded DNA-binding protein (ssb) Back     alignment and domain information
>PRK06293 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
>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
>PRK07772 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
>PRK05853 hypothetical protein; Validated 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
>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
>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
>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
>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
>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
>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
>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
>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
>PRK07211 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
>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
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>PRK06461 single-stranded DNA-binding protein; 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
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed Back     alignment and domain information
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain 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
>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
>PRK13480 3'-5' exoribonuclease YhaM; Provisional Back     alignment and domain information
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query199
3ulp_A124 Plasmodium Falciparum Ssb Complex With Ssdna Length 2e-07
3tqy_A158 Structure Of A Single-Stranded Dna-Binding Protein 8e-07
3pgz_A193 Crystal Structure Of A Single Strand Binding Protei 1e-06
1eqq_A178 Single Stranded Dna Binding Protein And Ssdna Compl 4e-06
1sru_A113 Crystal Structure Of Full Length E. Coli Ssb Protei 1e-05
3lgj_A169 Crystal Structure Of Single-Stranded Binding Protei 2e-05
1qvc_A145 Crystal Structure Analysis Of Single Stranded Dna B 2e-05
1eyg_A116 Crystal Structure Of Chymotryptic Fragment Of E. Co 2e-05
3ull_A132 Human Mitochondrial Single-Stranded Dna Binding Pro 2e-05
2dud_A133 Crystal Structure Of Human Mitochondrial Single-Str 2e-05
1kaw_A135 Structure Of Single Stranded Dna Binding Protein (S 6e-05
>pdb|3ULP|A Chain A, Plasmodium Falciparum Ssb Complex With Ssdna Length = 124 Back     alignment and structure 
Iteration: 1

 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 54/118 (45%), Gaps = 9/118 (7%)
Query: 83  KAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIXXXXXXXXXXXXTEYANRCAVQWHRVS 142
           K +L+G+VG  P  K L  G  V  FSL T               T+        WHR+ 
Sbjct: 8   KIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTD--------WHRIV 59
Query: 143 VYPERLGGVVMKHLVPGSTIYVEGNLE-QKVFNDPITGLVRRIREIAIRRNGTYLIFF 199
           VY + +  ++ K+L  G  +YV+G+L  +K   + +    ++I EI +  N   LIF 
Sbjct: 60  VYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFL 117
>pdb|3TQY|A Chain A, Structure Of A Single-Stranded Dna-Binding Protein (Ssb), From Coxiella Burnetii Length = 158 Back     alignment and structure
>pdb|3PGZ|A Chain A, Crystal Structure Of A Single Strand Binding Protein (Ssb) From Bartonella Henselae Length = 193 Back     alignment and structure
>pdb|1EQQ|A Chain A, Single Stranded Dna Binding Protein And Ssdna Complex Length = 178 Back     alignment and structure
>pdb|1SRU|A Chain A, Crystal Structure Of Full Length E. Coli Ssb Protein Length = 113 Back     alignment and structure
>pdb|3LGJ|A Chain A, Crystal Structure Of Single-Stranded Binding Protein (Ssb) From Bartonella Henselae Length = 169 Back     alignment and structure
>pdb|1QVC|A Chain A, Crystal Structure Analysis Of Single Stranded Dna Binding Protein (Ssb) From E.Coli Length = 145 Back     alignment and structure
>pdb|1EYG|A Chain A, Crystal Structure Of Chymotryptic Fragment Of E. Coli Ssb Bound To Two 35-Mer Single Strand Dnas Length = 116 Back     alignment and structure
>pdb|3ULL|A Chain A, Human Mitochondrial Single-Stranded Dna Binding Protein Length = 132 Back     alignment and structure
>pdb|2DUD|A Chain A, Crystal Structure Of Human Mitochondrial Single-Stranded Dna-Binding Protein(Hmtssb) Length = 133 Back     alignment and structure
>pdb|1KAW|A Chain A, Structure Of Single Stranded Dna Binding Protein (Ssb) Length = 135 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query199
3ulp_A124 Single-strand binding protein; OB-fold, DNA bindin 4e-14
3ull_A132 DNA binding protein; DNA replication, mitochondrio 3e-13
3lgj_A169 Single-stranded DNA-binding protein; niaid, CAT sc 5e-13
1qvc_A145 Single stranded DNA binding protein monomer; beta- 1e-12
3pgz_A193 Single-stranded DNA-binding protein; ssgcid, singl 1e-12
1eqq_A178 Single stranded DNA binding protein; beta barrel, 5e-12
3tqy_A158 Single-stranded DNA-binding protein; DNA replicati 9e-12
1z9f_A153 Single-strand binding protein; TM0604, single stra 2e-08
2fxq_A 264 Single-strand binding protein; strand beta-sheet e 2e-08
2fxq_A264 Single-strand binding protein; strand beta-sheet e 9e-06
3vdy_A116 SSB, single-stranded DNA-binding protein SSBB; OB 1e-07
2vw9_A134 Single-stranded DNA binding protein; DNA replicati 2e-07
3afp_A168 Single-stranded DNA-binding protein; OB-fold, quat 3e-07
1se8_A 301 Single-strand binding protein; DNA binding protein 3e-07
1se8_A301 Single-strand binding protein; DNA binding protein 5e-06
3eiv_A199 Single-stranded DNA-binding protein 2; DNA damage, 5e-07
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 1e-05
3k7u_C148 MP18 RNA editing complex protein; OB-fold, RNA-edi 8e-05
>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} Length = 124 Back     alignment and structure
 Score = 65.1 bits (159), Expect = 4e-14
 Identities = 37/120 (30%), Positives = 60/120 (50%), Gaps = 9/120 (7%)

Query: 80  GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWH 139
            + K +L+G+VG  P  K L  G  V  FSL T     +R   E ++ T+        WH
Sbjct: 5   SLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTD--------WH 56

Query: 140 RVSVYPERLGGVVMKHLVPGSTIYVEGNLE-QKVFNDPITGLVRRIREIAIRRNGTYLIF 198
           R+ VY + +  ++ K+L  G  +YV+G+L  +K   + +    ++I EI +  N   LIF
Sbjct: 57  RIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIF 116
>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 Length = 132 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} Length = 169 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 Length = 145 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} Length = 193 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 Length = 178 Back     alignment and structure
>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii} Length = 158 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} Length = 153 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 Length = 264 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 Length = 264 Back     alignment and structure
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis} Length = 116 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} Length = 134 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* Length = 168 Back     alignment and structure
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 Length = 301 Back     alignment and structure
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 Length = 301 Back     alignment and structure
>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor} Length = 199 Back     alignment and structure
>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301} Length = 108 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 Length = 148 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query199
3ulp_A124 Single-strand binding protein; OB-fold, DNA bindin 99.97
3ull_A132 DNA binding protein; DNA replication, mitochondrio 99.97
3pgz_A193 Single-stranded DNA-binding protein; ssgcid, singl 99.97
3tqy_A158 Single-stranded DNA-binding protein; DNA replicati 99.96
3lgj_A169 Single-stranded DNA-binding protein; niaid, CAT sc 99.96
3vdy_A116 SSB, single-stranded DNA-binding protein SSBB; OB 99.96
3k7u_C148 MP18 RNA editing complex protein; OB-fold, RNA-edi 99.96
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 99.96
1qvc_A145 Single stranded DNA binding protein monomer; beta- 99.96
2vw9_A134 Single-stranded DNA binding protein; DNA replicati 99.96
4dam_A128 Single-stranded DNA-binding protein 1; OB-fold; 1. 99.96
3afp_A168 Single-stranded DNA-binding protein; OB-fold, quat 99.96
1z9f_A153 Single-strand binding protein; TM0604, single stra 99.96
1eqq_A178 Single stranded DNA binding protein; beta barrel, 99.95
3eiv_A199 Single-stranded DNA-binding protein 2; DNA damage, 99.94
3k81_C164 MP18 RNA editing complex protein; krepa6, single d 99.94
1se8_A 301 Single-strand binding protein; DNA binding protein 99.93
4dni_A257 Fusion protein of RNA-editing complex proteins MP 99.93
2fxq_A264 Single-strand binding protein; strand beta-sheet e 99.93
2fxq_A 264 Single-strand binding protein; strand beta-sheet e 99.93
4gs3_A107 Single-stranded DNA-binding protein; primosome, ol 99.92
1v1q_A134 Primosomal replication protein N; primosome, DNA r 99.92
1se8_A301 Single-strand binding protein; DNA binding protein 99.92
1txy_A104 Primosomal replication protein N; OB fold, dimer, 99.92
3fhw_A115 Primosomal replication protein N; PRIB BPR162 X-RA 99.89
3k8a_A103 Putative primosomal replication protein; beta-barr 99.89
3en2_A101 Probable primosomal replication protein N; PRIB RS 99.84
3stb_C148 RNA-editing complex protein MP42; editosome, nanob 99.83
4dni_A 257 Fusion protein of RNA-editing complex proteins MP 99.81
4dka_C105 RNA-editing complex protein MP81; krepa1, VHH, sin 97.14
3e0e_A97 Replication protein A; structural genomics, PSI-2, 95.22
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 94.21
3dm3_A105 Replication factor A; probably plays AN essential 94.05
2k50_A115 Replication factor A related protein; uncharacteri 93.92
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 93.89
2hql_A110 Hypothetical protein Mg376 homolog; structural gen 93.88
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 93.74
3f2b_A 1041 DNA-directed DNA polymerase III alpha chain; DNA p 84.81
1jmc_A 246 Protein (replication protein A (RPA)); human ssDNA 84.74
4gop_C 444 Putative uncharacterized protein; OB fold, ssDNA b 80.44
>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
Probab=99.97  E-value=2.3e-30  Score=200.64  Aligned_cols=112  Identities=29%  Similarity=0.531  Sum_probs=99.3

Q ss_pred             ccCceEEEEEEeCCCCeEEEeCCCcEEEEEEEEeCCeecCCCCCCCCCCccccccCceeEEEEEEeCcchHHHHhhcCCC
Q 029088           79 PGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHLVP  158 (199)
Q Consensus        79 ~~~N~viLiG~Ig~dPe~k~~~~G~~v~~FsVAv~~~~~~r~~g~~ge~~e~~d~~~t~w~~V~~~g~~lAe~v~~~L~K  158 (199)
                      ++||+|+|+|+||+||+++++++|.++++|+||+++.|+++.+   |   +|.  ..++||+|++||+++|+.+.++|+|
T Consensus         4 ~~~N~v~l~Grl~~dpelr~t~~G~~v~~f~lA~~~~~~~~~~---G---~~~--~~t~~~~v~~wg~~~Ae~~~~~l~K   75 (124)
T 3ulp_A            4 KSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNT---N---ELK--SKTDWHRIVVYDQNIVDLIDKYLRK   75 (124)
T ss_dssp             CCEEEEEEEEEECSCCEEEECTTSCEEEEEEEEEEEEEECTTT---C---CEE--EEEEEEEEEECCHHHHHHHHHHCCT
T ss_pred             ccceEEEEEEEECCCcEEEECCCCCEEEEEEEEEccceecccC---C---cEe--cccEEEEEEEEEchHHHHHHhhcCC
Confidence            6899999999999999999999999999999999999987632   3   342  3799999999974699999999999


Q ss_pred             CCEEEEEEEeEeeeeeCCC-CCeEEEEEEEEEEe-CCcEEec
Q 029088          159 GSTIYVEGNLEQKVFNDPI-TGLVRRIREIAIRR-NGTYLIF  198 (199)
Q Consensus       159 G~~V~VeGrL~~~~~~d~~-dG~~r~~~eI~v~~-~g~l~fl  198 (199)
                      |++|+|+|+|+++.|+++. ||++++.++|+|+. +++|+||
T Consensus        76 G~~V~V~G~L~~~~~~d~~~dG~~~~~~ev~a~~~g~~i~~l  117 (124)
T 3ulp_A           76 GRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFL  117 (124)
T ss_dssp             TCEEEEEEEEEEEEECC----CCCEEEEEEEECTTTCEEEEC
T ss_pred             CCEEEEEEEEEeEEEeCCCCCCCEEEEEEEEEEcCCCcEEEe
Confidence            9999999999999999864 79999999999996 6799998
>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
>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
>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
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>4gs3_A Single-stranded DNA-binding protein; primosome, oligonucleotide/oligosaccharide binding domain, D binding protein; 1.09A {Thermoanaerobacter tengcongensis} 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
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 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
>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
>3k8a_A Putative primosomal replication protein; beta-barrel, OB-fold, DNA binding protein; 2.70A {Neisseria gonorrhoeae fa 1090} 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
>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
>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
>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
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum} 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
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Back     alignment and structure
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} 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
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 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
>1jmc_A Protein (replication protein A (RPA)); human ssDNA binding replication protein A(RPA), single stranded DNA-binding protein, protein-ssDNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 1fgu_A Back     alignment and structure
>4gop_C Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} 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 199
d1se8a_ 231 b.40.4.3 (A:) ssDNA-binding protein {Deinococcus r 7e-11
d1se8a_231 b.40.4.3 (A:) ssDNA-binding protein {Deinococcus r 4e-07
d3ulla_115 b.40.4.3 (A:) ssDNA-binding protein {Human (Homo s 4e-09
d1ue1a_118 b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium 7e-09
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Length = 231 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: Deinococcus radiodurans [TaxId: 1299]

 Score = 57.3 bits (138), Expect = 7e-11
 Identities = 23/112 (20%), Positives = 40/112 (35%), Gaps = 10/112 (8%)

Query: 80  GIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWH 139
           G+    L+G + + P  +   +G  V   ++            E   P          +H
Sbjct: 2   GMNHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLP---------WYH 52

Query: 140 RVSVYPERLGGVVMKHLVPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRR 191
           RVS+  +       ++L  G  + VEG LE + +  P  G  R    +   R
Sbjct: 53  RVSILGKPAEWQAERNLKGGDAVVVEGTLEYRQWEAP-EGGKRSAVNVKALR 103
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Length = 231 Back     information, alignment and structure
>d3ulla_ b.40.4.3 (A:) ssDNA-binding protein {Human (Homo sapiens), mitochondria [TaxId: 9606]} Length = 115 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 ?
Query199
d3ulla_115 ssDNA-binding protein {Human (Homo sapiens), mitoc 99.97
d1qvca_145 ssDNA-binding protein {Escherichia coli [TaxId: 56 99.97
d1ue1a_118 ssDNA-binding protein {Mycobacterium tuberculosis 99.96
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.94
d1se8a_ 231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.93
d1v1qa_111 Primosomal replication protein N, PriB {Escherichi 99.89
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 95.49
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 94.61
d1wjja_145 Hypothetical protein At4g28440 (F20O9.120) {Thale 90.39
>d3ulla_ b.40.4.3 (A:) ssDNA-binding protein {Human (Homo sapiens), mitochondria [TaxId: 9606]} 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: Human (Homo sapiens), mitochondria [TaxId: 9606]

Probab=99.97  E-value=4.9e-32  Score=205.07  Aligned_cols=115  Identities=26%  Similarity=0.469  Sum_probs=98.9

Q ss_pred             cCccCceEEEEEEeCCCCeEEEeCCCcEEEEEEEEeCCeecCCCCCCCCCCccccccCceeEEEEEEeCcchHHHHhhcC
Q 029088           77 LDPGIFKAILVGQVGQSPVQKKLKSGRTVTLFSLGTGGIRNNRRPLENENPTEYANRCAVQWHRVSVYPERLGGVVMKHL  156 (199)
Q Consensus        77 ~~~~~N~viLiG~Ig~dPe~k~~~~G~~v~~FsVAv~~~~~~r~~g~~ge~~e~~d~~~t~w~~V~~~g~~lAe~v~~~L  156 (199)
                      |+++||+|+|+||||+||+++++++|.+++.|+||+++.|+++.+... +.++|  .+.++||+|++||+.+|+.+.++|
T Consensus         1 ~~~~mN~V~L~G~l~~dpe~r~t~~G~~v~~f~vAv~~~~~~~~~~~~-~~g~~--~~~t~w~~v~~~g~~~a~~~~~~l   77 (115)
T d3ulla_           1 LERSLNRVHLLGRVGQDPVLRQVEGKNPVTIFSLATNEMWRSGDSEVY-QLGDV--SQKTTWHRISVFRPGLRDVAYQYV   77 (115)
T ss_dssp             CCCCEEEEEEEEEECSCCEEECCTTSCCEEEEEEEEEEEECC----------CC--EEEEEEEEEEECSTTHHHHHHHHC
T ss_pred             CCCceeEEEEEEECCCCCEEEEeCCCCEEEEEEEEccccccccccccc-ccccc--eeeeeeeeeeeeecccchhhhhhc
Confidence            568999999999999999999999999999999999999987643211 11244  347999999999866899999999


Q ss_pred             CCCCEEEEEEEeEeeeeeCCCCCeEEEEEEEEEEeCCcEEec
Q 029088          157 VPGSTIYVEGNLEQKVFNDPITGLVRRIREIAIRRNGTYLIF  198 (199)
Q Consensus       157 ~KG~~V~VeGrL~~~~~~d~~dG~~r~~~eI~v~~~g~l~fl  198 (199)
                      +||++|+|+|+|++++|+|+ ||++++.++|+|+   +|+||
T Consensus        78 ~KG~~V~V~Grl~~~~~~dk-dG~~r~~~~v~a~---~i~~L  115 (115)
T d3ulla_          78 KKGSRIYLEGKIDYGEYMDK-NNVRRQATTIIAD---NIIFL  115 (115)
T ss_dssp             CTTCEEEEEEEEECCCEESS-SSEECCCEEEEEE---EEECC
T ss_pred             cCCCEEEEEEEEeeeeEECC-CCCEEEEEEEEEE---EEEeC
Confidence            99999999999999999998 9999999999999   89887
>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]} 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
>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
>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure