Citrus Sinensis ID: 028557

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-------
MALEQTLVSTRNLVFSVSVRRKSPNNIQIPSLSPSQNPLTKQAWFISHRQPLKLRLRCSVDCKDHQYSSQVSYPKPPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVERSSPSMSSYDSESNFMTAGKSYLNK
cHHHHHHHHcccccccccccccccccccccccccccccccHHHHccccccccccEEEEEccccccccccccccccccccccccccccEEEEEEcccccccEEEcccccEEEEEEEEEccccccccEEEEEEEHHHHHHHHHHHccccEEEEEEEEEEEEEEcccccEEEEEEEEEcEEEEEEccccccccccccccccccccccccc
ccHHHHEccccccccccccccccccccccccccccccccccccEEEccccccccEEEEEcccccHHccccccccccccccccHHHccEEEEEEEcccccEEEEcccccEEEEEEEEEcccccccccEEEEEcHHHHHHHHHHHccccEEEEEEEEEEEccccccccccEEEEEEEEEEEEEcccccccccccccccccccccccccc
MALEQTLVSTRNLVFSVSVrrkspnniqipslspsqnpltkqawfishrqplklrlrcsvdckdhqyssqvsypkppeipwdkeltnTVHLIGvvgtpietkhlpsgkvlAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGrlvsdvvesgdgqqqTYYKVVVQQLNFversspsmssydsesnfmtagksylnk
maleqtlvstrnlvfsvsvrrkspnniqipslspsqnpLTKQAWFISHRQPLKLRLRCSVDCKDHqyssqvsypkppeipwdKELTNTVHLIGVVgtpietkhlpsgkvLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVERsspsmssydsesnfmtagksylnk
MALEQTLVSTRNLVFSVSVRRKSPNNIQIPSLSPSQNPLTKQAWFISHRQPLKLRLRCSVDCKDHQYSSQVSYPKPPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGqqqtyykvvvqqLNFVERsspsmssydsesNFMTAGKSYLNK
*****************************************QAWFISHRQPLKLRLRCSVDCKDHQYSSQVSYP*PPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFV**************************
********STRNLVFSVSV*************************************************************WDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQ******************************
********STRNLVFSVSVRRKSPNNIQIPSLSPSQNPLTKQAWFISHRQPLKLRLRCSVDCKDHQYSSQVSYPKPPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVER*************FMTAGKSYLNK
***********NLVFSVSVRRKSPNNIQIPSLSPSQNPLTKQAWFISHRQPLKLRLRCSVDCKDHQYSSQVSYPKPPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVER************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MALEQTLVSTRNLVFSVSVRRKSPNNIQIPSLSPSQNPLTKQAWFISHRQPLKLRLRCSVDCKDHQYSSQVSYPKPPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVERSSPSMSSYDSESNFMTAGKSYLNK
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 ?
Query207 2.2.26 [Sep-21-2011]
Q8GXH3 371 Protein OSB2, chloroplast yes no 0.599 0.334 0.336 1e-12
Q9FYJ2 360 Protein OSB4, chloroplast no no 0.743 0.427 0.244 2e-10
Q8GWJ4 440 Protein OSB3, chloroplast no no 0.531 0.25 0.333 6e-10
P66849174 Single-stranded DNA-bindi yes no 0.570 0.678 0.246 9e-09
P66848174 Single-stranded DNA-bindi yes no 0.570 0.678 0.246 9e-09
P59932169 Single-stranded DNA-bindi yes no 0.454 0.556 0.320 2e-08
Q8Y2B4178 Single-stranded DNA-bindi yes no 0.454 0.528 0.307 2e-08
Q9KUW2177 Single-stranded DNA-bindi yes no 0.458 0.536 0.326 3e-08
Q8DCJ0179 Single-stranded DNA-bindi yes no 0.458 0.530 0.317 4e-08
P59933162 Single-stranded DNA-bindi yes no 0.531 0.679 0.254 8e-08
>sp|Q8GXH3|OSB2_ARATH Protein OSB2, chloroplastic OS=Arabidopsis thaliana GN=OSB2 PE=1 SV=2 Back     alignment and function desciption
 Score = 73.6 bits (179), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/125 (33%), Positives = 71/125 (56%), Gaps = 1/125 (0%)

Query: 68  SSQVSYPKPPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSATQTS-W 126
           +++   P+P EI ++ E+ N V+LIG V  P++ +    GK  A T ++ R ++  +  W
Sbjct: 80  TTENELPRPNEIAYESEVANWVNLIGFVDQPVQFEASSDGKFWAGTVISQRSASDSSGFW 139

Query: 127 INLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVERSSP 186
           I + F  +LA  A+++V K  QI++SG+L  D         Q   +V+VQ LNF++  SP
Sbjct: 140 IPIIFEGDLAKTAARYVSKDDQIHVSGKLFIDSPPPNMTYAQANVQVLVQNLNFIQPMSP 199

Query: 187 SMSSY 191
           S S +
Sbjct: 200 SPSPF 204
Binds preferentially single-stranded DNA. Does not bind to RNA.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9FYJ2|OSB4_ARATH Protein OSB4, chloroplastic OS=Arabidopsis thaliana GN=OSB4 PE=2 SV=1 Back     alignment and function description
>sp|Q8GWJ4|OSB3_ARATH Protein OSB3, chloroplastic/mitochondrial OS=Arabidopsis thaliana GN=OSB3 PE=2 SV=1 Back     alignment and function description
>sp|P66849|SSB_NEIMB Single-stranded DNA-binding protein OS=Neisseria meningitidis serogroup B (strain MC58) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|P66848|SSB_NEIMA Single-stranded DNA-binding protein OS=Neisseria meningitidis serogroup A / serotype 4A (strain Z2491) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|P59932|SSB_RHOBA Single-stranded DNA-binding protein OS=Rhodopirellula baltica (strain SH1) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q8Y2B4|SSB_RALSO Single-stranded DNA-binding protein OS=Ralstonia solanacearum (strain GMI1000) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q9KUW2|SSB_VIBCH Single-stranded DNA-binding protein OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|Q8DCJ0|SSB_VIBVU Single-stranded DNA-binding protein OS=Vibrio vulnificus (strain CMCP6) GN=ssb PE=3 SV=1 Back     alignment and function description
>sp|P59933|SSB_WOLSU Single-stranded DNA-binding protein OS=Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W) 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 ?
Query207
224066309292 predicted protein [Populus trichocarpa] 0.946 0.671 0.602 4e-59
224082730292 predicted protein [Populus trichocarpa] 0.951 0.674 0.591 5e-59
359479595292 PREDICTED: protein OSB2, chloroplastic [ 0.777 0.551 0.68 4e-56
297735490286 unnamed protein product [Vitis vinifera] 0.772 0.559 0.678 6e-56
449458446294 PREDICTED: protein OSB2, chloroplastic-l 0.922 0.649 0.552 2e-53
255559919285 single-stranded DNA-binding protein, ssb 0.927 0.673 0.543 4e-51
357440511291 Single-stranded DNA-binding protein [Med 0.898 0.639 0.519 5e-50
255636182242 unknown [Glycine max] 0.913 0.780 0.519 7e-45
356536581292 PREDICTED: protein OSB2, chloroplastic-l 0.913 0.647 0.519 8e-45
356500150284 PREDICTED: protein OSB2, chloroplastic-l 0.893 0.651 0.509 8e-44
>gi|224066309|ref|XP_002302076.1| predicted protein [Populus trichocarpa] gi|222843802|gb|EEE81349.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 126/209 (60%), Positives = 152/209 (72%), Gaps = 13/209 (6%)

Query: 1   MALEQTLV--STRNLVFSVSVRRKSP-NNIQIPSLSPSQNPLTKQAWFISHRQPLKLRLR 57
           MALEQTL   ST NL F +    K+P  NI+IP+L  S    + +          K  L+
Sbjct: 1   MALEQTLALSSTANLFFPIP---KNPLTNIKIPTLPLSPLSSSSKK------SLPKRSLK 51

Query: 58  CSVDCKDHQYSSQVSYPKPPEIPWDKELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAV 117
           CS+D +D+ YS  V++ KP EI W+KEL N+VHLIG+VG P+E KHLPSGKV+AWTRLAV
Sbjct: 52  CSIDFRDNHYSQTVTHAKPAEIQWNKELCNSVHLIGIVGIPVEIKHLPSGKVVAWTRLAV 111

Query: 118 RKSATQTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQ 177
           +KSAT TSWINLTFWDELA V SQHVEKGQQIY+SGRL+SD VE+ DG+ QTYYKVVVQQ
Sbjct: 112 KKSATDTSWINLTFWDELAQVVSQHVEKGQQIYVSGRLISDSVENDDGKLQTYYKVVVQQ 171

Query: 178 LNFVERSSPSMSSYDSESNFMTAGKSYLN 206
           LNF+ERSSP+   YD   N M AG+ + N
Sbjct: 172 LNFIERSSPT-GLYDRGFNNMEAGRKFGN 199

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224082730|ref|XP_002306816.1| predicted protein [Populus trichocarpa] gi|222856265|gb|EEE93812.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359479595|ref|XP_002275197.2| PREDICTED: protein OSB2, chloroplastic [Vitis vinifera] Back     alignment and taxonomy information
>gi|297735490|emb|CBI17930.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449458446|ref|XP_004146958.1| PREDICTED: protein OSB2, chloroplastic-like [Cucumis sativus] gi|449527159|ref|XP_004170580.1| PREDICTED: protein OSB2, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|255559919|ref|XP_002520978.1| single-stranded DNA-binding protein, ssb, putative [Ricinus communis] gi|223539815|gb|EEF41395.1| single-stranded DNA-binding protein, ssb, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|357440511|ref|XP_003590533.1| Single-stranded DNA-binding protein [Medicago truncatula] gi|355479581|gb|AES60784.1| Single-stranded DNA-binding protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|255636182|gb|ACU18433.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|356536581|ref|XP_003536815.1| PREDICTED: protein OSB2, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|356500150|ref|XP_003518896.1| PREDICTED: protein OSB2, chloroplastic-like [Glycine max] 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 ?
Query207
TAIR|locus:2015721 360 OSB4 "organellar single-strand 0.637 0.366 0.290 4.6e-12
TAIR|locus:2119767 371 PTAC9 "plastid transcriptional 0.405 0.226 0.390 7.8e-10
TAIR|locus:505006672 442 OSB3 "organellar single-strand 0.516 0.242 0.305 2.2e-08
TIGR_CMR|GSU_2151139 GSU_2151 "single-strand bindin 0.381 0.568 0.333 4.8e-07
TIGR_CMR|GSU_3117146 GSU_3117 "single-strand bindin 0.381 0.541 0.298 3.8e-06
UNIPROTKB|Q9KUW2177 ssb "Single-stranded DNA-bindi 0.333 0.389 0.346 5.4e-06
TIGR_CMR|VC_0397177 VC_0397 "single-strand binding 0.333 0.389 0.346 5.4e-06
TIGR_CMR|DET_1045135 DET_1045 "single-strand bindin 0.468 0.718 0.257 6.6e-06
UNIPROTKB|P0AGE0178 ssb "ssDNA-binding protein" [E 0.333 0.387 0.371 8.6e-06
TIGR_CMR|CBU_0271158 CBU_0271 "single-strand bindin 0.333 0.436 0.333 0.00042
TAIR|locus:2015721 OSB4 "organellar single-stranded DNA binding protein 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 168 (64.2 bits), Expect = 4.6e-12, P = 4.6e-12
 Identities = 43/148 (29%), Positives = 80/148 (54%)

Query:    31 SLSPSQNPLTKQAWFISHRQPLKL-------RLRCSVDCKDHQYSSQVSYPKPPEIPWDK 83
             S+ PS N   +++W +S +Q L         R R        + SS+  +P+P E+P+  
Sbjct:    11 SIRPSLNSTARKSWVLSSQQFLSTSSTESSSRTRGGGGGNRAEKSSE-EWPRPMEVPYQP 69

Query:    84 ELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVR-----KSATQTS---WINLTFWDEL 135
             ++ N++ LIG V  P++      GK  A T ++       KS + +S   WI + F  +L
Sbjct:    70 KIANSIDLIGYVHQPVQFDSTLDGKFWAGTVISHEPSSDSKSESDSSSNFWIPVLFEGDL 129

Query:   136 AHVASQHVEKGQQIYISGRLVSDVVESG 163
             AH A+ +++K  +++I+G+++ DV++SG
Sbjct:   130 AHTANSYLKKNDRVHITGQILGDVIQSG 157
GO:0003697 "single-stranded DNA binding" evidence=IEA
GO:0008150 "biological_process" evidence=ND
GO:0009507 "chloroplast" evidence=ISM
TAIR|locus:2119767 PTAC9 "plastid transcriptionally active 9" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:505006672 OSB3 "organellar single-stranded DNA binding protein 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_2151 GSU_2151 "single-strand binding protein" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_3117 GSU_3117 "single-strand binding protein" [Geobacter sulfurreducens PCA (taxid:243231)] Back     alignment and assigned GO terms
UNIPROTKB|Q9KUW2 ssb "Single-stranded DNA-binding protein" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_0397 VC_0397 "single-strand binding protein" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|DET_1045 DET_1045 "single-strand binding protein" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
UNIPROTKB|P0AGE0 ssb "ssDNA-binding protein" [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_0271 CBU_0271 "single-strand binding protein" [Coxiella burnetii RSA 493 (taxid:227377)] 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:
eugene3.00051251
hypothetical protein (292 aa)
(Populus trichocarpa)
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 ?
Query207
cd04496100 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds 7e-19
pfam00436104 pfam00436, SSB, Single-strand binding protein fami 4e-16
TIGR00621164 TIGR00621, ssb, single stranded DNA-binding protei 8e-15
COG0629167 COG0629, Ssb, Single-stranded DNA-binding protein 7e-14
PRK06958182 PRK06958, PRK06958, single-stranded DNA-binding pr 2e-12
PRK07459121 PRK07459, PRK07459, single-stranded DNA-binding pr 2e-10
PRK08486182 PRK08486, PRK08486, single-stranded DNA-binding pr 5e-08
PRK09010177 PRK09010, PRK09010, single-stranded DNA-binding pr 2e-07
PRK08763164 PRK08763, PRK08763, single-stranded DNA-binding pr 5e-07
PRK05733172 PRK05733, PRK05733, single-stranded DNA-binding pr 2e-06
PRK13732175 PRK13732, PRK13732, single-stranded DNA-binding pr 5e-06
PRK06863168 PRK06863, PRK06863, single-stranded DNA-binding pr 9e-06
PRK06341166 PRK06341, PRK06341, single-stranded DNA-binding pr 9e-06
PRK06751173 PRK06751, PRK06751, single-stranded DNA-binding pr 1e-04
PRK06293161 PRK06293, PRK06293, single-stranded DNA-binding pr 0.001
PRK06752112 PRK06752, PRK06752, single-stranded DNA-binding pr 0.001
PRK06642152 PRK06642, PRK06642, single-stranded DNA-binding pr 0.001
PRK07275162 PRK07275, PRK07275, single-stranded DNA-binding pr 0.003
>gnl|CDD|239942 cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB) Back     alignment and domain information 
 Score = 77.7 bits (192), Expect = 7e-19
 Identities = 32/99 (32%), Positives = 54/99 (54%), Gaps = 7/99 (7%)

Query: 89  VHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSAT-------QTSWINLTFWDELAHVASQ 141
           V LIG +G   E ++ PSG  +A   LAV +          +T WI +  + +LA  A++
Sbjct: 1   VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAK 60

Query: 142 HVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNF 180
           +++KG  +Y+ GRL +   E  DGQ++   +VV  ++ F
Sbjct: 61  YLKKGDLVYVEGRLRTRSWEDKDGQKRYGTEVVADRIEF 99

SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart at forks that have stalled at sites of DNA damage. It also plays a role in the assembly of primosome during replication initiation at the bacteriophage phiX174 origin. PriB physically interacts with SSB and binds ssDNA with high affinity. Length = 100
>gnl|CDD|215919 pfam00436, SSB, Single-strand binding protein family Back     alignment and domain information
>gnl|CDD|233057 TIGR00621, ssb, single stranded DNA-binding protein (ssb) 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
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|180986 PRK07459, PRK07459, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|236275 PRK08486, PRK08486, 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|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|184284 PRK13732, PRK13732, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|136097 PRK06863, PRK06863, 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|168659 PRK06751, PRK06751, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|180517 PRK06293, PRK06293, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|168660 PRK06752, PRK06752, single-stranded DNA-binding protein; Validated Back     alignment and domain information
>gnl|CDD|135984 PRK06642, PRK06642, single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>gnl|CDD|180915 PRK07275, PRK07275, single-stranded DNA-binding protein; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 207
PRK06752112 single-stranded DNA-binding protein; Validated 99.97
PRK07459121 single-stranded DNA-binding protein; Provisional 99.97
PRK07275162 single-stranded DNA-binding protein; Provisional 99.97
PRK06751173 single-stranded DNA-binding protein; Provisional 99.96
PRK07274131 single-stranded DNA-binding protein; Provisional 99.96
PRK08486182 single-stranded DNA-binding protein; Provisional 99.96
PRK08763164 single-stranded DNA-binding protein; Provisional 99.96
PRK06293161 single-stranded DNA-binding protein; Provisional 99.96
PRK06958182 single-stranded DNA-binding protein; Provisional 99.96
PRK06642152 single-stranded DNA-binding protein; Provisional 99.96
PRK08182148 single-stranded DNA-binding protein; Provisional 99.95
PRK06863168 single-stranded DNA-binding protein; Provisional 99.95
TIGR00621164 ssb single stranded DNA-binding protein (ssb). Thi 99.95
PRK13732175 single-stranded DNA-binding protein; Provisional 99.95
PRK09010177 single-stranded DNA-binding protein; Provisional 99.95
PRK06341166 single-stranded DNA-binding protein; Provisional 99.95
PRK05733172 single-stranded DNA-binding protein; Provisional 99.95
PF00436104 SSB: Single-strand binding protein family; InterPr 99.94
PRK05813219 single-stranded DNA-binding protein; Provisional 99.93
PRK07772186 single-stranded DNA-binding protein; Provisional 99.92
PRK02801101 primosomal replication protein N; Provisional 99.92
COG0629167 Ssb Single-stranded DNA-binding protein [DNA repli 99.91
cd04496100 SSB_OBF SSB_OBF: A subfamily of OB folds similar t 99.89
PRK05853161 hypothetical protein; Validated 99.88
PRK05813219 single-stranded DNA-binding protein; Provisional 99.82
KOG1653175 consensus Single-stranded DNA-binding protein [Rep 99.71
COG2965103 PriB Primosomal replication protein N [DNA replica 98.74
PRK00036107 primosomal replication protein N; Reviewed 98.71
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 97.93
cd0448482 polC_OBF polC_OBF: A subfamily of OB folds corresp 97.17
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 97.1
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 96.9
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 96.81
cd0448773 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f 96.77
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 96.71
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 96.59
cd0448291 RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara 96.03
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 95.99
PRK07211 485 replication factor A; Reviewed 95.79
PF1374299 tRNA_anti_2: OB-fold nucleic acid binding domain 95.54
PF1132584 DUF3127: Domain of unknown function (DUF3127); Int 94.82
COG3390196 Uncharacterized protein conserved in archaea [Func 94.21
PRK06461129 single-stranded DNA-binding protein; Reviewed 94.07
PRK13480 314 3'-5' exoribonuclease YhaM; Provisional 94.04
PRK07373449 DNA polymerase III subunit alpha; Reviewed 93.84
cd0449182 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil 93.81
cd04320102 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r 93.68
PF11506104 DUF3217: Protein of unknown function (DUF3217); In 93.57
cd04475101 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor 93.33
PRK15491 374 replication factor A; Provisional 93.07
cd0448875 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f 92.97
PRK07211 485 replication factor A; Reviewed 92.9
PRK15491374 replication factor A; Provisional 92.73
PRK00286 438 xseA exodeoxyribonuclease VII large subunit; Revie 92.59
PRK056731135 dnaE DNA polymerase III subunit alpha; Validated 92.53
TIGR00237 432 xseA exodeoxyribonuclease VII, large subunit. This 92.5
cd0410085 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, ant 92.35
cd04317135 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod 92.18
PRK14699 484 replication factor A; Provisional 91.95
cd0432384 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, a 91.6
PRK12366 637 replication factor A; Reviewed 91.19
PRK00448 1437 polC DNA polymerase III PolC; Validated 91.16
PRK08402 355 replication factor A; Reviewed 91.12
TIGR01405 1213 polC_Gram_pos DNA polymerase III, alpha chain, Gra 90.87
PRK068261151 dnaE DNA polymerase III DnaE; Reviewed 90.1
PRK073741170 dnaE DNA polymerase III subunit alpha; Validated 89.71
PRK069201107 dnaE DNA polymerase III DnaE; Reviewed 89.66
PRK12366 637 replication factor A; Reviewed 89.17
COG1570 440 XseA Exonuclease VII, large subunit [DNA replicati 89.09
cd04316108 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a 88.6
cd04497138 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f 88.17
PRK14699 484 replication factor A; Provisional 87.3
cd04322108 LysRS_N LysRS_N: N-terminal, anticodon recognition 86.82
TIGR00617 608 rpa1 replication factor-a protein 1 (rpa1). This f 85.78
PRK072791034 dnaE DNA polymerase III DnaE; Reviewed 85.66
PF02765146 POT1: Telomeric single stranded DNA binding POT1/C 85.33
PRK056721046 dnaE2 error-prone DNA polymerase; Validated 84.75
cd0432186 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, a 83.44
cd0447895 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor 83.32
KOG3416134 consensus Predicted nucleic acid binding protein [ 82.39
cd04319103 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticod 81.97
TIGR00458 428 aspS_arch aspartyl-tRNA synthetase, archaeal type. 81.89
PLN02903 652 aminoacyl-tRNA ligase 81.81
PF12101137 DUF3577: Protein of unknown function (DUF3577); In 81.8
>PRK06752 single-stranded DNA-binding protein; Validated Back     alignment and domain information 
Probab=99.97  E-value=3.3e-30  Score=198.90  Aligned_cols=103  Identities=26%  Similarity=0.383  Sum_probs=97.8

Q ss_pred             CccEEEEEEEECCCceEEEcCCCcEEEEEEEEEecCCC------CCeEEEEEEEchHHHHHHHhcCCCCEEEEEEEeeee
Q 028557           85 LTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSAT------QTSWINLTFWDELAHVASQHVEKGQQIYISGRLVSD  158 (207)
Q Consensus        85 ~mN~V~LiGrL~~dPeir~t~nG~~va~f~LAv~r~~~------~t~wi~V~awgk~Ae~~~~~LkKGd~V~VeGrL~~~  158 (207)
                      |||+|+|+|||++||+++++++|.++++|+||+++.+.      +++||+|++||++|+.+.++|+||++|.|+|+|+++
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            79999999999999999999999999999999998652      589999999999999999999999999999999999


Q ss_pred             eeEcCCCcEEEEEEEEEEEEEEeeCCCCC
Q 028557          159 VVESGDGQQQTYYKVVVQQLNFVERSSPS  187 (207)
Q Consensus       159 ~~~dkdG~~~~~~eIva~~I~~L~~k~~~  187 (207)
                      .|+|+||++++.++|+|++|.||+++.+.
T Consensus        81 ~~~~~~G~~~~~~ei~a~~i~~l~~~~~~  109 (112)
T PRK06752         81 NYEDDQGKRIYITEVVIESITFLERRREG  109 (112)
T ss_pred             ccCCCCCcEEEEEEEEEEEEEECCCCCcc
Confidence            99999999999999999999999977644

>PRK07459 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07275 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06751 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07274 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08486 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08763 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06293 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06958 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06642 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK08182 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06863 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>TIGR00621 ssb single stranded DNA-binding protein (ssb) Back     alignment and domain information
>PRK13732 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK09010 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK06341 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK05733 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids Back     alignment and domain information
>PRK05813 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK07772 single-stranded DNA-binding protein; Provisional Back     alignment and domain information
>PRK02801 primosomal replication protein N; Provisional Back     alignment and domain information
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair] 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
>PRK05853 hypothetical protein; Validated 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
>COG2965 PriB Primosomal replication protein N [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00036 primosomal replication protein N; Reviewed 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
>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
>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
>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
>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
>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
>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
>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
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain 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
>COG3390 Uncharacterized protein conserved in archaea [Function unknown] Back     alignment and domain information
>PRK06461 single-stranded DNA-binding protein; Reviewed Back     alignment and domain information
>PRK13480 3'-5' exoribonuclease YhaM; Provisional Back     alignment and domain information
>PRK07373 DNA polymerase III subunit alpha; Reviewed 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
>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
>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
>PRK15491 replication factor A; Provisional 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
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed Back     alignment and domain information
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated Back     alignment and domain information
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit 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
>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
>PRK14699 replication factor A; Provisional 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
>PRK12366 replication factor A; Reviewed Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PRK08402 replication factor A; Reviewed Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type Back     alignment and domain information
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed Back     alignment and domain information
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated Back     alignment and domain information
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed Back     alignment and domain information
>PRK12366 replication factor A; Reviewed Back     alignment and domain information
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair] 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
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP) Back     alignment and domain information
>PRK14699 replication factor A; Provisional 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
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1) Back     alignment and domain information
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed Back     alignment and domain information
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold [] Back     alignment and domain information
>PRK05672 dnaE2 error-prone DNA polymerase; Validated 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
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32) Back     alignment and domain information
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only] Back     alignment and domain information
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS) Back     alignment and domain information
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type Back     alignment and domain information
>PLN02903 aminoacyl-tRNA ligase Back     alignment and domain information
>PF12101 DUF3577: Protein of unknown function (DUF3577); InterPro: IPR021960 This family of proteins is functionally uncharacterised 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 ?
Query207
1eqq_A178 Single Stranded Dna Binding Protein And Ssdna Compl 6e-07
1sru_A113 Crystal Structure Of Full Length E. Coli Ssb Protei 1e-06
1eyg_A116 Crystal Structure Of Chymotryptic Fragment Of E. Co 2e-06
1qvc_A145 Crystal Structure Analysis Of Single Stranded Dna B 2e-06
1kaw_A135 Structure Of Single Stranded Dna Binding Protein (S 2e-06
3tqy_A158 Structure Of A Single-Stranded Dna-Binding Protein 6e-05
3pgz_A193 Crystal Structure Of A Single Strand Binding Protei 7e-05
2vw9_A134 Single Stranded Dna Binding Protein Complex From He 5e-04
>pdb|1EQQ|A Chain A, Single Stranded Dna Binding Protein And Ssdna Complex Length = 178 Back     alignment and structure 
Iteration: 1

 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 9/78 (11%)
Query: 87  NTVHLIGVVGTPIETKHLPSGKVLA---------WTRLAVRKSATQTSWINLTFWDELAH 137
           N V L+G +G   E +++P+G  +A         W   A  +   QT W  +  + +LA 
Sbjct: 7   NKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAE 66
Query: 138 VASQHVEKGQQIYISGRL 155
           VAS+++ KG Q+YI G+L
Sbjct: 67  VASEYLRKGSQVYIEGQL 84
>pdb|1SRU|A Chain A, Crystal Structure Of Full Length E. Coli Ssb Protein Length = 113 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|1QVC|A Chain A, Crystal Structure Analysis Of Single Stranded Dna Binding Protein (Ssb) From E.Coli Length = 145 Back     alignment and structure
>pdb|1KAW|A Chain A, Structure Of Single Stranded Dna Binding Protein (Ssb) Length = 135 Back     alignment and structure
>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|2VW9|A Chain A, Single Stranded Dna Binding Protein Complex From Helicobacter Pylori Length = 134 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 ?
Query207
2vw9_A134 Single-stranded DNA binding protein; DNA replicati 9e-18
3vdy_A116 SSB, single-stranded DNA-binding protein SSBB; OB 2e-17
1z9f_A153 Single-strand binding protein; TM0604, single stra 2e-17
2fxq_A264 Single-strand binding protein; strand beta-sheet e 1e-16
2fxq_A 264 Single-strand binding protein; strand beta-sheet e 3e-14
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 2e-15
3eiv_A199 Single-stranded DNA-binding protein 2; DNA damage, 1e-14
3afp_A168 Single-stranded DNA-binding protein; OB-fold, quat 1e-14
3tqy_A158 Single-stranded DNA-binding protein; DNA replicati 4e-14
1se8_A 301 Single-strand binding protein; DNA binding protein 7e-14
1se8_A301 Single-strand binding protein; DNA binding protein 2e-13
1qvc_A145 Single stranded DNA binding protein monomer; beta- 6e-12
1eqq_A178 Single stranded DNA binding protein; beta barrel, 6e-12
3ull_A132 DNA binding protein; DNA replication, mitochondrio 2e-10
3ulp_A124 Single-strand binding protein; OB-fold, DNA bindin 3e-10
3pgz_A193 Single-stranded DNA-binding protein; ssgcid, singl 4e-10
3lgj_A169 Single-stranded DNA-binding protein; niaid, CAT sc 6e-10
>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
 Score = 75.1 bits (185), Expect = 9e-18
 Identities = 27/125 (21%), Positives = 56/125 (44%), Gaps = 8/125 (6%)

Query: 87  NTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSAT--------QTSWINLTFWDELAHV 138
           N V ++G +   +E K+LPSG   A   LA  +           +  +I+   +   A +
Sbjct: 3   NKVIMVGRLTRNVELKYLPSGSAAATIGLATSRRFKKQDGTLGEEVCFIDARLFGRTAEI 62

Query: 139 ASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVERSSPSMSSYDSESNFM 198
           A+Q++ KG  + I GRL  +      G++ + + +    L F+++ S +  +   + + M
Sbjct: 63  ANQYLSKGSSVLIEGRLTYESWMDQTGKKNSRHTITADSLQFMDKKSDNPQANAMQDSIM 122

Query: 199 TAGKS 203
               +
Sbjct: 123 HENSN 127
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis} Length = 116 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
>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
>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
>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
>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii} Length = 158 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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query207
3vdy_A116 SSB, single-stranded DNA-binding protein SSBB; OB 99.97
2vw9_A134 Single-stranded DNA binding protein; DNA replicati 99.97
3tqy_A158 Single-stranded DNA-binding protein; DNA replicati 99.96
3ulp_A124 Single-strand binding protein; OB-fold, DNA bindin 99.96
3ull_A132 DNA binding protein; DNA replication, mitochondrio 99.96
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 99.96
1z9f_A153 Single-strand binding protein; TM0604, single stra 99.96
1qvc_A145 Single stranded DNA binding protein monomer; beta- 99.96
3lgj_A169 Single-stranded DNA-binding protein; niaid, CAT sc 99.95
3pgz_A193 Single-stranded DNA-binding protein; ssgcid, singl 99.95
3k7u_C148 MP18 RNA editing complex protein; OB-fold, RNA-edi 99.95
3afp_A168 Single-stranded DNA-binding protein; OB-fold, quat 99.94
4dam_A128 Single-stranded DNA-binding protein 1; OB-fold; 1. 99.94
1txy_A104 Primosomal replication protein N; OB fold, dimer, 99.94
1eqq_A178 Single stranded DNA binding protein; beta barrel, 99.94
4gs3_A107 Single-stranded DNA-binding protein; primosome, ol 99.94
2fxq_A264 Single-strand binding protein; strand beta-sheet e 99.94
3eiv_A199 Single-stranded DNA-binding protein 2; DNA damage, 99.93
1v1q_A134 Primosomal replication protein N; primosome, DNA r 99.93
1se8_A 301 Single-strand binding protein; DNA binding protein 99.93
3k81_C164 MP18 RNA editing complex protein; krepa6, single d 99.93
1se8_A301 Single-strand binding protein; DNA binding protein 99.93
2fxq_A 264 Single-strand binding protein; strand beta-sheet e 99.92
4dni_A257 Fusion protein of RNA-editing complex proteins MP 99.89
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 99.82
3stb_C148 RNA-editing complex protein MP42; editosome, nanob 99.81
4dni_A 257 Fusion protein of RNA-editing complex proteins MP 99.78
4dka_C105 RNA-editing complex protein MP81; krepa1, VHH, sin 97.64
3e0e_A97 Replication protein A; structural genomics, PSI-2, 96.87
2k50_A115 Replication factor A related protein; uncharacteri 96.66
3dm3_A105 Replication factor A; probably plays AN essential 96.43
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 95.9
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 95.56
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 95.47
3f2b_A 1041 DNA-directed DNA polymerase III alpha chain; DNA p 94.98
2hql_A110 Hypothetical protein Mg376 homolog; structural gen 93.59
3au7_A402 TIAS, putative uncharacterized protein; ATP hydrol 91.64
3kdf_D132 Replication protein A 32 kDa subunit; wheat GERM c 91.32
4gop_B136 Putative uncharacterized protein; OB fold, ssDNA b 89.21
1jmc_A 246 Protein (replication protein A (RPA)); human ssDNA 89.17
1eov_A 487 ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA sy 88.64
2hpi_A1220 DNA polymerase III alpha subunit; POL-beta-like nu 88.59
2kbn_A109 Conserved protein; nucleic acid binding protein, b 88.55
4gop_C 444 Putative uncharacterized protein; OB fold, ssDNA b 87.7
3kf8_A220 Protein STN1; OB fold; 2.40A {Candida tropicalis m 87.21
1wjj_A145 Hypothetical protein F20O9.120; DNA-binding protei 83.79
3bju_A 521 Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, 83.27
2vl6_A268 SSO MCM N-TER, minichromosome maintenance protein 82.28
2pi2_A270 Replication protein A 32 kDa subunit; FULL-length 82.11
2xgt_A 435 Asparaginyl-tRNA synthetase, cytoplasmic; ligase, 80.98
>3vdy_A SSB, single-stranded DNA-binding protein SSBB; OB fold; 2.80A {Bacillus subtilis} Back     alignment and structure
Probab=99.97  E-value=4.5e-30  Score=197.62  Aligned_cols=104  Identities=22%  Similarity=0.390  Sum_probs=91.5

Q ss_pred             CCccEEEEEEEECCCceEEEcCCCcEEEEEEEEEecCCC------CCeEEEEEEEchHHHHHHHhcCCCCEEEEEEEeee
Q 028557           84 ELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSAT------QTSWINLTFWDELAHVASQHVEKGQQIYISGRLVS  157 (207)
Q Consensus        84 ~~mN~V~LiGrL~~dPeir~t~nG~~va~f~LAv~r~~~------~t~wi~V~awgk~Ae~~~~~LkKGd~V~VeGrL~~  157 (207)
                      .|||+|+|+|+|++||++|++++|.++++|+||+++.+.      +++||+|++||++|+.+.++|+||++|+|+|+|++
T Consensus         3 ~mmN~v~l~G~l~~dpe~r~t~~G~~v~~f~la~~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G~l~~   82 (116)
T 3vdy_A            3 HMFNQVMLVGRLTKDPDLRYTSAGAAVAHVTLAVNRSFKNASGEIEADYVNCTLWRKTAENTALYCQKGSLVGVSGRIQT   82 (116)
T ss_dssp             CCCCCEEEEEEESSCCEEEECTTSCEEEEEEEEEECSSCCSSSCCCEEEEEEEEEHHHHHHHHHHCCTTCEEEEEEEEEE
T ss_pred             ceEeEEEEEEEEccCcEEEECCCCCEEEEEEEEEeccccCCCCccccEEEEEEEECHHHHHHHHhCCCCCEEEEEEEEEe
Confidence            599999999999999999999999999999999998652      68999999999999999999999999999999999


Q ss_pred             eeeEcCCCcEEEEEEEEEEEEEEeeCCCCC
Q 028557          158 DVVESGDGQQQTYYKVVVQQLNFVERSSPS  187 (207)
Q Consensus       158 ~~~~dkdG~~~~~~eIva~~I~~L~~k~~~  187 (207)
                      +.|+|+||++++.++|+|++|+||++++..
T Consensus        83 ~~~~d~dG~~~~~~ev~a~~i~~l~~~~~~  112 (116)
T 3vdy_A           83 RSYENEEGVNVYVTEVLADTVRFMDPKPRE  112 (116)
T ss_dssp             EEEC----CCEEEEEEEEEEEEECC-----
T ss_pred             eEEECCCCCEEEEEEEEEEEEEEccCCCcc
Confidence            999999999999999999999999877643
>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
>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase; 2.60A {Coxiella burnetii} 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
>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
>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
>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
>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
>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
>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
>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
>4dam_A Single-stranded DNA-binding protein 1; OB-fold; 1.70A {Streptomyces coelicolor} 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
>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
>4gs3_A Single-stranded DNA-binding protein; primosome, oligonucleotide/oligosaccharide binding domain, D binding protein; 1.09A {Thermoanaerobacter tengcongensis} 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
>3eiv_A Single-stranded DNA-binding protein 2; DNA damage, DNA repair, DNA replication, phosphoprotein; 2.14A {Streptomyces coelicolor} 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
>3k81_C MP18 RNA editing complex protein; krepa6, single domain antibody, immune system, RNA BIND protein; 3.40A {Trypanosoma brucei} Back     alignment and structure
>1se8_A Single-strand binding protein; DNA binding protein; 1.80A {Deinococcus radiodurans} SCOP: b.40.4.3 Back     alignment and structure
>2fxq_A Single-strand binding protein; strand beta-sheet extended loops, DNA binding protein; 1.85A {Thermus aquaticus} PDB: 2ihe_A 2cwa_A 2ihf_A Back     alignment and structure
>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
>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
>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
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 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
>1ynx_A Replication factor-A protein 1; canonical OB fold, DNA binding protein; NMR {Saccharomyces cerevisiae} 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
>2hql_A Hypothetical protein Mg376 homolog; structural genomics, conserved hypothetical protein, GI:1673959, MPN554, OB fold; 2.00A {Mycoplasma pneumoniae} Back     alignment and structure
>3au7_A TIAS, putative uncharacterized protein; ATP hydrolysis, RNA binding protein; 2.60A {Archaeoglobus fulgidus} PDB: 3amt_A* 3amu_A* Back     alignment and structure
>3kdf_D Replication protein A 32 kDa subunit; wheat GERM cell free, protein complex, center for eukaryotic structural genomics, PSI; HET: MSE; 1.98A {Homo sapiens} SCOP: b.40.4.3 PDB: 2pqa_A 1quq_A 1l1o_B Back     alignment and structure
>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} Back     alignment and structure
>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
>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
>2hpi_A DNA polymerase III alpha subunit; POL-beta-like nucleotidyltransferase fold, transferase; HET: DNA; 3.00A {Thermus aquaticus} PDB: 2hpm_A* 3e0d_A* Back     alignment and structure
>2kbn_A Conserved protein; nucleic acid binding protein, beta barrel, structural genomics, PSI-2, protein structure initiative; NMR {Methanosarcina mazei} PDB: 2ken_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
>3kf8_A Protein STN1; OB fold; 2.40A {Candida tropicalis mya-3404} Back     alignment and structure
>1wjj_A Hypothetical protein F20O9.120; DNA-binding protein-related, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.40.4.3 Back     alignment and structure
>3bju_A Lysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP- binding, cytoplasm, ligase, nucleotide-binding, phosphoprotein, polymorphism; HET: LYS ATP; 2.31A {Homo sapiens} Back     alignment and structure
>2vl6_A SSO MCM N-TER, minichromosome maintenance protein MCM; helicase, hydrolase, zinc-finger, ATP-binding, DNA-BIND ssDNA binding; 2.8A {Sulfolobus solfataricus} Back     alignment and structure
>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A Back     alignment and structure
>2xgt_A Asparaginyl-tRNA synthetase, cytoplasmic; ligase, ATP-binding, protein biosynthesis; HET: NSS; 1.90A {Brugia malayi} PDB: 2xti_A* 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 207
d1se8a_231 b.40.4.3 (A:) ssDNA-binding protein {Deinococcus r 6e-17
d1se8a_231 b.40.4.3 (A:) ssDNA-binding protein {Deinococcus r 3e-14
d1ue1a_118 b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium 7e-14
d1v1qa_111 b.40.4.3 (A:) Primosomal replication protein N, Pr 3e-13
d1qvca_145 b.40.4.3 (A:) ssDNA-binding protein {Escherichia c 6e-13
d3ulla_115 b.40.4.3 (A:) ssDNA-binding protein {Human (Homo s 3e-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 = 74.2 bits (182), Expect = 6e-17
 Identities = 16/119 (13%), Positives = 42/119 (35%), Gaps = 9/119 (7%)

Query: 87  NTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSAT--------QTSWINLTFWDELA-H 137
           N V+LIG +    E ++  +G  +    +A                 +  ++   + A  
Sbjct: 4   NHVYLIGALARDPELRYTGNGMAVFEATVAGEDRVIGNDGRERNLPWYHRVSILGKPAEW 63

Query: 138 VASQHVEKGQQIYISGRLVSDVVESGDGQQQTYYKVVVQQLNFVERSSPSMSSYDSESN 196
            A ++++ G  + + G L     E+ +G +++   V   ++  +      +        
Sbjct: 64  QAERNLKGGDAVVVEGTLEYRQWEAPEGGKRSAVNVKALRMEQLGTQPELIQDAGGGVR 122
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Length = 231 Back     information, alignment and structure
>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]} Length = 118 Back     information, alignment and structure
>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]} Length = 111 Back     information, alignment and structure
>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]} Length = 145 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query207
d1qvca_145 ssDNA-binding protein {Escherichia coli [TaxId: 56 99.96
d3ulla_115 ssDNA-binding protein {Human (Homo sapiens), mitoc 99.96
d1ue1a_118 ssDNA-binding protein {Mycobacterium tuberculosis 99.94
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.93
d1se8a_231 ssDNA-binding protein {Deinococcus radiodurans [Ta 99.93
d1v1qa_111 Primosomal replication protein N, PriB {Escherichi 99.9
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 95.9
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 94.76
d1eova1134 Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S 94.46
d1b8aa1103 Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococ 92.03
d1wjja_145 Hypothetical protein At4g28440 (F20O9.120) {Thale 90.27
d1c0aa1106 Aspartyl-tRNA synthetase (AspRS) {Escherichia coli 86.53
d1l0wa1104 Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph 85.17
d1jmca2122 Replication protein A 70 KDa subunit (RPA70) {Huma 82.52
d1e1oa1143 Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g 81.74
>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=99.96  E-value=9.7e-29  Score=195.16  Aligned_cols=104  Identities=31%  Similarity=0.462  Sum_probs=95.4

Q ss_pred             cCCccEEEEEEEECCCceEEEcCCCcEEEEEEEEEecCC---------CCCeEEEEEEEchHHHHHHHhcCCCCEEEEEE
Q 028557           83 KELTNTVHLIGVVGTPIETKHLPSGKVLAWTRLAVRKSA---------TQTSWINLTFWDELAHVASQHVEKGQQIYISG  153 (207)
Q Consensus        83 ~~~mN~V~LiGrL~~dPeir~t~nG~~va~f~LAv~r~~---------~~t~wi~V~awgk~Ae~~~~~LkKGd~V~VeG  153 (207)
                      ...||+|+|+|||++||++|++++|..+++|+||+++++         ++++||+|++||++|+.+.++|+|||+|+|+|
T Consensus         2 ~~~mN~v~LiG~l~~dpe~r~~~~G~~v~~f~va~~~~~~~~~~~~~~~~t~w~~v~~~g~~Ae~~~~~l~KG~~V~V~G   81 (145)
T d1qvca_           2 SRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEG   81 (145)
T ss_dssp             CCCEEEEEEEEEESSCCEEECCSSSCCEEEEEEEECCCCSCCSSSSCCCCCEEEEEEEETHHHHHHHHHCCTTCEEEEEE
T ss_pred             CCcceEEEEEEECCCCCEEEECCCCCEEEEEEEEecccccccccccccccceEEeeEEecchhhhHhhhcccCCEEEEEE
Confidence            357999999999999999999999999999999999763         36899999999999999999999999999999


Q ss_pred             EeeeeeeEcCCCcEEEEEEEEEE---EEEEeeCCCC
Q 028557          154 RLVSDVVESGDGQQQTYYKVVVQ---QLNFVERSSP  186 (207)
Q Consensus       154 rL~~~~~~dkdG~~~~~~eIva~---~I~~L~~k~~  186 (207)
                      +|+++.|+|+||++++.++|+|+   .|.+|+.+..
T Consensus        82 ~l~~~~~~~kdG~~r~~~ei~~~~~~~l~~l~~r~~  117 (145)
T d1qvca_          82 QLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQG  117 (145)
T ss_dssp             EEEEEEECSSSSCEEEEEEEECTTCEEEECCCCSCC
T ss_pred             EEEEeeeECCCCCEEEEEEEEEecCCcEEECcCccC
Confidence            99999999999999999999996   6777765543
>d3ulla_ b.40.4.3 (A:) ssDNA-binding protein {Human (Homo sapiens), mitochondria [TaxId: 9606]} Back     information, alignment and structure
>d1ue1a_ b.40.4.3 (A:) ssDNA-binding protein {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1se8a_ b.40.4.3 (A:) ssDNA-binding protein {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>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
>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} 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
>d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]} Back     information, alignment and structure
>d1jmca2 b.40.4.3 (A:299-420) Replication protein A 70 KDa subunit (RPA70) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1e1oa1 b.40.4.1 (A:11-153) Lysyl-tRNA synthetase (LysRS) {Escherichia coli, gene lysU [TaxId: 562]} Back     information, alignment and structure