Citrus Sinensis ID: 032330

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---
MATAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNVE
ccccccccccccEEEEEEcccccccccEEEEEEEEcccEEEEccccccccccccccccccEEEEEEEcccccEEEEEEEcccccccccccEEEEEccEEEEEEcEEEEEEcccEEEEEcccccEEEccccccccEEEEEEEEc
ccccccccccccEEEEEcccccccccEEEEEEEEEcEEEEccccccccccccccccccccEEEEEEEEccccEEEEEEccccccccccccEEEEEccEEEEEccEEEEEEccccEEEEcccccEEEEcccccEEEEEEEEEcc
matagatakrkpvfikvdqlkpgttghtLTVKVVsskpvqvnkprgarslsslsqpsrppriaeclvgddtgaiyftarndqvdimtpgTTVILRNAKidmfkgsmrlavdkwgrievtepadfevkesnnlsLVEYELVNVE
matagatakrkpvfikvdqlkpgttghtltvkvvsskpvqvnkprgarslsslsqpsrpprIAECLVGDDTGAIYFtarndqvdimtpGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTepadfevkesnnlslveyelvnve
MATAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGArslsslsqpsrpprIAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNVE
************VFIKVDQL*****GHTLTVK*****************************IAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYEL****
*************FIKVDQLKPGTTGHTLTVKVVSSKPV*******************PPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNV*
*********RKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQV*****************PPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNVE
********KRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNK**************RPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNVE
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MATAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNVE
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 ?
Query143 2.2.26 [Sep-21-2011]
O49453153 Uncharacterized protein A yes no 0.951 0.888 0.715 6e-52
>sp|O49453|Y4844_ARATH Uncharacterized protein At4g28440 OS=Arabidopsis thaliana GN=At4g28440 PE=1 SV=1 Back     alignment and function desciption
 Score =  202 bits (513), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 98/137 (71%), Positives = 112/137 (81%), Gaps = 1/137 (0%)

Query: 6   ATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAEC 65
           +T KRKPVF+KV+QLKPGTTGHTLTVKV+ +  V V   R  R  SSLS+PS+P RI EC
Sbjct: 14  STVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIV-VPVTRKTRPASSLSRPSQPSRIVEC 72

Query: 66  LVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFE 125
           L+GD+TG I FTARNDQVD+M PG TVILRN++IDMFKG+MRL VDKWGRIE T  A F 
Sbjct: 73  LIGDETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFT 132

Query: 126 VKESNNLSLVEYELVNV 142
           VKE NNLSLVEYEL+NV
Sbjct: 133 VKEDNNLSLVEYELINV 149

Arabidopsis thaliana (taxid: 3702)

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 ?
Query143
388506946140 unknown [Medicago truncatula] 0.951 0.971 0.748 1e-53
224092922142 predicted protein [Populus trichocarpa] 0.979 0.985 0.75 2e-53
356549894141 PREDICTED: uncharacterized protein At4g2 0.965 0.978 0.781 4e-53
388507556140 unknown [Lotus japonicus] 0.916 0.935 0.783 4e-53
224133442141 predicted protein [Populus trichocarpa] 0.965 0.978 0.751 1e-52
302143333148 unnamed protein product [Vitis vinifera] 0.937 0.905 0.765 2e-52
255553651140 conserved hypothetical protein [Ricinus 0.965 0.985 0.743 2e-52
356543853141 PREDICTED: uncharacterized protein At4g2 0.965 0.978 0.767 2e-52
242055803146 hypothetical protein SORBIDRAFT_03g00044 0.965 0.945 0.736 4e-52
297803236152 hypothetical protein ARALYDRAFT_913675 [ 0.951 0.894 0.729 8e-52
>gi|388506946|gb|AFK41539.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
 Score =  213 bits (543), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 104/139 (74%), Positives = 118/139 (84%), Gaps = 3/139 (2%)

Query: 4   AGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIA 63
           A  TAKRKPVF+KVDQLKPGT GHTLTVKVV+S PV+    RG RS    S+PSR   IA
Sbjct: 2   ATQTAKRKPVFVKVDQLKPGTNGHTLTVKVVNSSPVKTIPNRGGRSAVIASRPSR---IA 58

Query: 64  ECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPAD 123
           EC++GD+T +I FTARN+QVD+M PG T+ILRNAKIDMFKGSMRLAVD+WGRIEVTEPA+
Sbjct: 59  ECVIGDETASIIFTARNEQVDLMNPGATLILRNAKIDMFKGSMRLAVDRWGRIEVTEPAN 118

Query: 124 FEVKESNNLSLVEYELVNV 142
           FEV+E NNLSLVEYELVNV
Sbjct: 119 FEVREDNNLSLVEYELVNV 137

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224092922|ref|XP_002309755.1| predicted protein [Populus trichocarpa] gi|118483079|gb|ABK93449.1| unknown [Populus trichocarpa] gi|222852658|gb|EEE90205.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356549894|ref|XP_003543325.1| PREDICTED: uncharacterized protein At4g28440-like isoform 1 [Glycine max] gi|356549896|ref|XP_003543326.1| PREDICTED: uncharacterized protein At4g28440-like isoform 2 [Glycine max] Back     alignment and taxonomy information
>gi|388507556|gb|AFK41844.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|224133442|ref|XP_002328043.1| predicted protein [Populus trichocarpa] gi|118488667|gb|ABK96145.1| unknown [Populus trichocarpa] gi|222837452|gb|EEE75831.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|302143333|emb|CBI21894.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255553651|ref|XP_002517866.1| conserved hypothetical protein [Ricinus communis] gi|223542848|gb|EEF44384.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|356543853|ref|XP_003540374.1| PREDICTED: uncharacterized protein At4g28440-like [Glycine max] Back     alignment and taxonomy information
>gi|242055803|ref|XP_002457047.1| hypothetical protein SORBIDRAFT_03g000440 [Sorghum bicolor] gi|241929022|gb|EES02167.1| hypothetical protein SORBIDRAFT_03g000440 [Sorghum bicolor] Back     alignment and taxonomy information
>gi|297803236|ref|XP_002869502.1| hypothetical protein ARALYDRAFT_913675 [Arabidopsis lyrata subsp. lyrata] gi|297315338|gb|EFH45761.1| hypothetical protein ARALYDRAFT_913675 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query143
TAIR|locus:2121313153 AT4G28440 "AT4G28440" [Arabido 0.986 0.921 0.640 4.5e-43
TAIR|locus:505006287182 AT2G33845 "AT2G33845" [Arabido 0.895 0.703 0.708 5.7e-43
TAIR|locus:2024239143 AT1G03810 "AT1G03810" [Arabido 0.937 0.937 0.633 1.6e-40
TAIR|locus:2034813137 AT1G23750 "AT1G23750" [Arabido 0.944 0.985 0.605 1.1e-39
TAIR|locus:2019918153 AT1G10590 "AT1G10590" [Arabido 0.958 0.895 0.611 7e-38
TAIR|locus:2121313 AT4G28440 "AT4G28440" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 455 (165.2 bits), Expect = 4.5e-43, P = 4.5e-43
 Identities = 91/142 (64%), Positives = 104/142 (73%)

Query:     1 MATAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGAXXXXXXXXXXXXX 60
             +AT  +T KRKPVF+KV+QLKPGTTGHTLTVKV+ +  V V   R               
Sbjct:     9 VATGTSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIV-VPVTRKTRPASSLSRPSQPS 67

Query:    61 XIAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTE 120
              I ECL+GD+TG I FTARNDQVD+M PG TVILRN++IDMFKG+MRL VDKWGRIE T 
Sbjct:    68 RIVECLIGDETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATG 127

Query:   121 PADFEVKESNNLSLVEYELVNV 142
              A F VKE NNLSLVEYEL+NV
Sbjct:   128 AASFTVKEDNNLSLVEYELINV 149
GO:0003674 "molecular_function" evidence=ND
GO:0008150 "biological_process" evidence=ND
GO:0005829 "cytosol" evidence=IDA
GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=RCA
GO:0009853 "photorespiration" evidence=RCA
GO:0051788 "response to misfolded protein" evidence=RCA
GO:0080129 "proteasome core complex assembly" evidence=RCA
TAIR|locus:505006287 AT2G33845 "AT2G33845" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2024239 AT1G03810 "AT1G03810" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2034813 AT1G23750 "AT1G23750" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2019918 AT1G10590 "AT1G10590" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
O49453Y4844_ARATHNo assigned EC number0.71530.95100.8888yesno

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:
estExt_Genewise1_v1.C_LG_VII0578
SubName- Full=Putative uncharacterized protein; (142 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 ?
Query143
cd0449182 cd04491, SoSSB_OBF, SoSSB_OBF: A subfamily of OB f 1e-14
PRK06461129 PRK06461, PRK06461, single-stranded DNA-binding pr 7e-14
PRK07217 311 PRK07217, PRK07217, replication factor A; Reviewed 0.001
PRK06386 358 PRK06386, PRK06386, replication factor A; Reviewed 0.003
>gnl|CDD|239937 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 
 Score = 64.2 bits (157), Expect = 1e-14
 Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 12/92 (13%)

Query: 28  TLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDI-M 86
           ++  KV+S    +     G              ++   LVGD+TG I FT  +++    +
Sbjct: 1   SVEGKVLSISEPREFTRDG-----------SEGKVQSGLVGDETGTIRFTLWDEKAADDL 49

Query: 87  TPGTTVILRNAKIDMFKGSMRLAVDKWGRIEV 118
            PG  V + NA +  F G + L+V K   IE 
Sbjct: 50  EPGDVVRIENAYVREFNGRLELSVGKNSEIEK 81

SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM. Length = 82
>gnl|CDD|180574 PRK06461, PRK06461, single-stranded DNA-binding protein; Reviewed Back     alignment and domain information
>gnl|CDD|235970 PRK07217, PRK07217, replication factor A; Reviewed Back     alignment and domain information
>gnl|CDD|235790 PRK06386, PRK06386, replication factor A; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 143
KOG3416134 consensus Predicted nucleic acid binding protein [ 99.94
PRK06461129 single-stranded DNA-binding protein; Reviewed 99.94
PRK06386 358 replication factor A; Reviewed 99.86
PRK07217 311 replication factor A; Reviewed 99.86
PRK06386 358 replication factor A; Reviewed 99.85
PRK07218 423 replication factor A; Provisional 99.85
PRK07218 423 replication factor A; Provisional 99.82
PRK08402 355 replication factor A; Reviewed 99.8
PRK07211 485 replication factor A; Reviewed 99.75
PRK15491 374 replication factor A; Provisional 99.75
PRK14699 484 replication factor A; Provisional 99.75
PRK14699 484 replication factor A; Provisional 99.75
PRK12366 637 replication factor A; Reviewed 99.74
cd0449182 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil 99.73
PRK15491374 replication factor A; Provisional 99.68
PRK12366 637 replication factor A; Reviewed 99.59
PRK07211485 replication factor A; Reviewed 99.57
cd04475101 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor 99.26
COG1599 407 RFA1 Single-stranded DNA-binding replication prote 99.26
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 99.25
TIGR00617 608 rpa1 replication factor-a protein 1 (rpa1). This f 99.0
TIGR00617 608 rpa1 replication factor-a protein 1 (rpa1). This f 98.79
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 98.41
cd04497138 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f 98.34
cd0448392 hOBFC1_like hOBFC1_like: A subfamily of OB folds s 97.89
PRK13480 314 3'-5' exoribonuclease YhaM; Provisional 97.74
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 97.73
cd0447895 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor 97.67
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 97.52
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 97.4
cd0448875 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f 97.21
cd04481106 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc 97.07
cd0448086 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of unc 96.77
PF02765146 POT1: Telomeric single stranded DNA binding POT1/C 96.75
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 96.66
COG1599 407 RFA1 Single-stranded DNA-binding replication prote 96.52
cd0448482 polC_OBF polC_OBF: A subfamily of OB folds corresp 94.5
cd04498123 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds simil 94.07
COG4085204 Predicted RNA-binding protein, contains TRAM domai 93.89
PRK10917 681 ATP-dependent DNA helicase RecG; Provisional 93.12
cd0448773 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f 92.77
PRK08402355 replication factor A; Reviewed 92.61
PRK056731135 dnaE DNA polymerase III subunit alpha; Validated 92.34
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 91.97
TIGR00643 630 recG ATP-dependent DNA helicase RecG. 91.89
PRK07373449 DNA polymerase III subunit alpha; Reviewed 91.41
PRK00448 1437 polC DNA polymerase III PolC; Validated 89.27
PF0272195 DUF223: Domain of unknown function DUF223; InterPr 88.24
PF10451256 Stn1: Telomere regulation protein Stn1; InterPro: 87.18
PRK05159 437 aspC aspartyl-tRNA synthetase; Provisional 85.42
cd0448291 RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara 84.39
COG1200 677 RecG RecG-like helicase [DNA replication, recombin 84.07
PF1132584 DUF3127: Domain of unknown function (DUF3127); Int 82.58
cd04494251 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds 82.2
PF08646146 Rep_fac-A_C: Replication factor-A C terminal domai 81.83
PRK073741170 dnaE DNA polymerase III subunit alpha; Validated 81.41
PF1374299 tRNA_anti_2: OB-fold nucleic acid binding domain 80.02
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only] Back     alignment and domain information 
Probab=99.94  E-value=4.1e-27  Score=173.83  Aligned_cols=108  Identities=22%  Similarity=0.406  Sum_probs=100.5

Q ss_pred             eeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCCCCCCCCCCEEEE
Q 032330           15 IKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQVDIMTPGTTVIL   94 (143)
Q Consensus        15 ~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~~~~i~~Gd~v~I   94 (143)
                      +.|+||+|+++|++++++||+.+.++ .++        ||     +.|+.++|||+||+|.+++|||..+.+++||+|++
T Consensus         5 i~ikdi~P~~kN~~v~fIvl~~g~~t-kTk--------dg-----~~v~~~kVaD~TgsI~isvW~e~~~~~~PGDIirL   70 (134)
T KOG3416|consen    5 IFIKDIKPGLKNINVTFIVLEYGRAT-KTK--------DG-----HEVRSCKVADETGSINISVWDEEGCLIQPGDIIRL   70 (134)
T ss_pred             hhHhhcChhhhcceEEEEEEeeceee-ecc--------CC-----CEEEEEEEecccceEEEEEecCcCcccCCccEEEe
Confidence            46899999999999999999999766 333        66     68999999999999999999999999999999999


Q ss_pred             eceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccccce
Q 032330           95 RNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEY  137 (143)
Q Consensus        95 ~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~~ey  137 (143)
                      ++||+++|+|++.|++||.|.++++++|++.|+|++|+| +.|
T Consensus        71 t~Gy~Si~qg~LtL~~GK~Ge~~KiGef~~vf~etpn~S-~~~  112 (134)
T KOG3416|consen   71 TGGYASIFQGCLTLYVGKGGEVQKIGEFCMVFSETPNIS-IQW  112 (134)
T ss_pred             cccchhhhcCceEEEecCCceEeEeeeeEEeeecCCCcc-ccc
Confidence            999999999999999999999999999999999999999 444

>PRK06461 single-stranded DNA-binding protein; Reviewed Back     alignment and domain information
>PRK06386 replication factor A; Reviewed Back     alignment and domain information
>PRK07217 replication factor A; Reviewed Back     alignment and domain information
>PRK06386 replication factor A; Reviewed Back     alignment and domain information
>PRK07218 replication factor A; Provisional Back     alignment and domain information
>PRK07218 replication factor A; Provisional Back     alignment and domain information
>PRK08402 replication factor A; Reviewed 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
>PRK14699 replication factor A; Provisional Back     alignment and domain information
>PRK14699 replication factor A; Provisional Back     alignment and domain information
>PRK12366 replication factor A; 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
>PRK15491 replication factor A; Provisional Back     alignment and domain information
>PRK12366 replication factor A; Reviewed Back     alignment and domain information
>PRK07211 replication factor A; Reviewed 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
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair] 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
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1) Back     alignment and domain information
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1) 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
>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
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1) Back     alignment and domain information
>PRK13480 3'-5' exoribonuclease YhaM; Provisional 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
>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
>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
>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
>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
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70) Back     alignment and domain information
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70) 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
>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
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair] 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
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1) Back     alignment and domain information
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only] Back     alignment and domain information
>PRK10917 ATP-dependent DNA helicase RecG; Provisional 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
>PRK08402 replication factor A; Reviewed Back     alignment and domain information
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated 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
>TIGR00643 recG ATP-dependent DNA helicase RecG Back     alignment and domain information
>PRK07373 DNA polymerase III subunit alpha; Reviewed Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding Back     alignment and domain information
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA Back     alignment and domain information
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional 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
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription] 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
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD Back     alignment and domain information
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing Back     alignment and domain information
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated Back     alignment and domain information
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain 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 ?
Query143
1wjj_A145 Solution Structure Of Hypothetical Protein F20o9.12 6e-44
>pdb|1WJJ|A Chain A, Solution Structure Of Hypothetical Protein F20o9.120 From Arabidopsis Thaliana Length = 145 Back     alignment and structure 
Iteration: 1

 Score =  172 bits (436), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 85/132 (64%), Positives = 96/132 (72%), Gaps = 1/132 (0%)
Query: 7   TAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGAXXXXXXXXXXXXXXIAECL 66
           T KRKPVF+KV+QLKPGTTGHTLTVKV+ +  + V   R                I ECL
Sbjct: 9   TVKRKPVFVKVEQLKPGTTGHTLTVKVIEAN-IVVPVTRKTRPASSLSRPSQPSRIVECL 67
Query: 67  VGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEV 126
           +GD+TG I FTARNDQVD+M PG TVILRN++IDMFKG+MRL VDKWGRIE T  A F V
Sbjct: 68  IGDETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTV 127
Query: 127 KESNNLSLVEYE 138
           KE NNLSLVEYE
Sbjct: 128 KEDNNLSLVEYE 139

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query143
1wjj_A145 Hypothetical protein F20O9.120; DNA-binding protei 1e-50
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 6e-23
2kbn_A109 Conserved protein; nucleic acid binding protein, b 7e-23
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 3e-13
2k50_A115 Replication factor A related protein; uncharacteri 2e-08
3e0e_A97 Replication protein A; structural genomics, PSI-2, 1e-05
3dm3_A105 Replication factor A; probably plays AN essential 1e-05
>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 Length = 145 Back     alignment and structure
 Score =  157 bits (398), Expect = 1e-50
 Identities = 96/135 (71%), Positives = 110/135 (81%), Gaps = 1/135 (0%)

Query: 4   AGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIA 63
           +G+T KRKPVF+KV+QLKPGTTGHTLTVKV+ +  V V   R  R  SSLS+PS+P RI 
Sbjct: 6   SGSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIV-VPVTRKTRPASSLSRPSQPSRIV 64

Query: 64  ECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPAD 123
           ECL+GD+TG I FTARNDQVD+M PG TVILRN++IDMFKG+MRL VDKWGRIE T  A 
Sbjct: 65  ECLIGDETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAAS 124

Query: 124 FEVKESNNLSLVEYE 138
           F VKE NNLSLVEYE
Sbjct: 125 FTVKEDNNLSLVEYE 139
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 Length = 119 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 Length = 109 Back     alignment and structure
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum} Length = 106 Back     alignment and structure
>2k50_A Replication factor A related protein; uncharacterized protein, structural genomics, PSI-2; NMR {Methanothermobacterthermautotrophicus str} Length = 115 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 Length = 97 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} Length = 105 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query143
1wjj_A145 Hypothetical protein F20O9.120; DNA-binding protei 100.0
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 99.93
2kbn_A109 Conserved protein; nucleic acid binding protein, b 99.92
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 99.9
3e0e_A97 Replication protein A; structural genomics, PSI-2, 99.9
3dm3_A105 Replication factor A; probably plays AN essential 99.86
2k50_A115 Replication factor A related protein; uncharacteri 99.71
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 99.53
1jmc_A 246 Protein (replication protein A (RPA)); human ssDNA 99.46
4gop_C 444 Putative uncharacterized protein; OB fold, ssDNA b 99.21
1jmc_A246 Protein (replication protein A (RPA)); human ssDNA 99.02
4gop_C 444 Putative uncharacterized protein; OB fold, ssDNA b 98.98
1xjv_A 294 Protection of telomeres 1; protein-DNA complex, si 97.66
4gop_B136 Putative uncharacterized protein; OB fold, ssDNA b 97.53
3kdf_D132 Replication protein A 32 kDa subunit; wheat GERM c 97.38
1qzg_A187 Protection of telomeres protein 1; protrein-DNA co 97.18
1xjv_A294 Protection of telomeres 1; protein-DNA complex, si 97.12
2pi2_A270 Replication protein A 32 kDa subunit; FULL-length 97.05
1jb7_A 495 Telomere-binding protein alpha subunit; DNA-protei 96.85
4hik_A143 Protection of telomeres protein 1; specificity, pl 96.82
3kf6_A159 Protein STN1; OB fold, chromosomal protein, DNA-bi 95.16
3m4p_A 456 Ehasnrs, asparaginyl-tRNA synthetase, putative; am 92.46
1jb7_A 495 Telomere-binding protein alpha subunit; DNA-protei 91.25
3f2b_A 1041 DNA-directed DNA polymerase III alpha chain; DNA p 89.99
1txy_A104 Primosomal replication protein N; OB fold, dimer, 88.14
3rn5_A208 Interferon-inducible protein AIM2; OB fold, DNA bi 86.42
2v31_A112 Ubiquitin-activating enzyme E1 X; ligase, phosphor 84.9
2xvs_A166 Tetratricopeptide repeat protein 5; antitumor prot 82.63
2oq0_A206 Gamma-interferon-inducible protein IFI-16; OB fold 81.87
>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
Probab=100.00  E-value=2.7e-41  Score=254.95  Aligned_cols=135  Identities=67%  Similarity=1.042  Sum_probs=122.1

Q ss_pred             ccCCCcCCCCceeeeccCCCCCCCceEEEEEEecCcce--eccCCCccccCCCCCC---CCCCeeEEEEEeeCcceEEEE
Q 032330            3 TAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQ--VNKPRGARSLSSLSQP---SRPPRIAECLVGDDTGAIYFT   77 (143)
Q Consensus         3 ~~~~~~~~~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~--~~~~R~~~~~~~DG~~---~~~~~v~~~lVgDeTG~I~lt   77 (143)
                      +..++++++|.|+||+||+|++++++|++|||+++++.  .+++|   .   ||+.   .++++|++|+||||||+|+||
T Consensus         5 ~~~~~~~~kp~~~kI~dL~pg~~~v~l~~kVl~~~~v~~~~~~~R---~---dG~~~~~~r~~~V~~~lVgDeTG~I~ft   78 (145)
T 1wjj_A            5 SSGSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTR---P---ASSLSRPSQPSRIVECLIGDETGCILFT   78 (145)
T ss_dssp             CCCCCCCCCCSSCCSTTCCTTCCCEEEEEEEEEEEECCSSSSCCS---C---SSCCSSCCCCCCCEEEEEECSSCEEEEE
T ss_pred             CCCCccccCccceEHHHcCCCCCceEEEEEEEEcccccccccccc---c---CCccccccCCceEEEEEEEcCCcEEEEE
Confidence            34577999999999999999999999999999999742  03555   3   7741   237899999999999999999


Q ss_pred             EecCCCCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccccceeeeecC
Q 032330           78 ARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYELVNVE  143 (143)
Q Consensus        78 lW~~~~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~~eye~v~~~  143 (143)
                      +|+++++.+++||+|+|+|||+++|+|+|+|++++||+|+++++++|+||+++|||++|||+++++
T Consensus        79 lW~e~~~~l~~Gd~v~i~na~v~~~~G~~~L~vgk~g~Ie~~~e~~~~v~e~~n~S~~e~e~~~~~  144 (145)
T 1wjj_A           79 ARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKEDNNLSLVEYESGPSS  144 (145)
T ss_dssp             ECTTHHHHTCTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSCCCSCCCTTSBTTTSCCSSCCSC
T ss_pred             EecCCcCcCCCCCEEEEeccEEEeECCEEEEEECCCEEEEECCCCcEEEecCCCcCcceEEEeecC
Confidence            999999999999999999999999999999999999999999999999999999999999999875
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum} 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
>1o7i_A SSB, SSO2364, single stranded DNA binding protein; OB fold; 1.2A {Sulfolobus solfataricus} SCOP: b.40.4.3 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
>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
>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
>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
>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded DNA, transcription/DNA complex; 1.73A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A Back     alignment and structure
>4gop_B Putative uncharacterized protein; OB fold, ssDNA binding, DNA binding protein-DNA complex; HET: DNA; 3.10A {Ustilago maydis} Back     alignment and structure
>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
>1qzg_A Protection of telomeres protein 1; protrein-DNA complex, single-stranded telomeric DNA, DNA binding protein/DNA complex; HET: TMP; 1.90A {Schizosaccharomyces pombe} SCOP: b.40.4.3 PDB: 1qzh_A Back     alignment and structure
>1xjv_A Protection of telomeres 1; protein-DNA complex, single-stranded DNA, transcription/DNA complex; 1.73A {Homo sapiens} SCOP: b.40.4.3 b.40.4.3 PDB: 3kjo_A 3kjp_A 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
>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA HYDR sodium ION, quadruplex DNA, DNA-binding protein-DNA complex; 1.86A {Sterkiella nova} SCOP: b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A 1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A 1ph9_A 1ph5_A* 1ph2_A* 1k8g_A Back     alignment and structure
>4hik_A Protection of telomeres protein 1; specificity, plasticity, promiscuity, OB-fold, ssDNA binding stranded telomeric DNA; HET: DNA; 1.64A {Schizosaccharomyces pombe} PDB: 4hid_A* 4him_A* 4hio_A* 4hj5_A* 4hj7_A* 4hj8_A* 4hj9_A* 4hja_A* Back     alignment and structure
>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe} Back     alignment and structure
>3m4p_A Ehasnrs, asparaginyl-tRNA synthetase, putative; aminoacyl-tRNA synthetase, tRNA ligase, AARS, translation, ATP-binding, nucleotide-binding; HET: 4AD; 2.83A {Entamoeba histolytica} PDB: 3m4q_A Back     alignment and structure
>1jb7_A Telomere-binding protein alpha subunit; DNA-protein interactions, DNA HYDR sodium ION, quadruplex DNA, DNA-binding protein-DNA complex; 1.86A {Sterkiella nova} SCOP: b.40.4.3 b.40.4.3 b.40.4.3 PDB: 1kix_A 1otc_A* 2i0q_A 1ph6_A 1ph1_A 1phj_A* 1ph3_A 1pa6_A 1ph4_A 1ph7_A 1ph8_A 1ph9_A 1ph5_A* 1ph2_A* 1k8g_A 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
>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
>3rn5_A Interferon-inducible protein AIM2; OB fold, DNA binding, cytosolic, immune system-DNA complex; HET: DNA; 2.50A {Homo sapiens} PDB: 3rn2_A* Back     alignment and structure
>2v31_A Ubiquitin-activating enzyme E1 X; ligase, phosphorylation, catalytic domain, heteronuclear first catalytic cysteine half-domain, E1 protein; NMR {Mus musculus} Back     alignment and structure
>2xvs_A Tetratricopeptide repeat protein 5; antitumor protein, P53 cofactor, stress-response; 1.80A {Homo sapiens} Back     alignment and structure
>2oq0_A Gamma-interferon-inducible protein IFI-16; OB folds, beta-barrels, structural genomics, PSI-2, protein initiative; 2.00A {Homo sapiens} SCOP: b.40.16.1 b.40.16.1 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 143
d1wjja_145 b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O 5e-48
d1o7ia_115 b.40.4.3 (A:) Archaeal ssDNA-binding protein {Arch 2e-22
d1jmca1116 b.40.4.3 (A:183-298) Replication protein A 70 KDa 0.002
>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 145 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: Hypothetical protein At4g28440 (F20O9.120)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score =  149 bits (378), Expect = 5e-48
 Identities = 96/137 (70%), Positives = 111/137 (81%), Gaps = 1/137 (0%)

Query: 2   ATAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPR 61
            ++G+T KRKPVF+KV+QLKPGTTGHTLTVKV+ +  V V   R  R  SSLS+PS+P R
Sbjct: 4   GSSGSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIV-VPVTRKTRPASSLSRPSQPSR 62

Query: 62  IAECLVGDDTGAIYFTARNDQVDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEP 121
           I ECL+GD+TG I FTARNDQVD+M PG TVILRN++IDMFKG+MRL VDKWGRIE T  
Sbjct: 63  IVECLIGDETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGA 122

Query: 122 ADFEVKESNNLSLVEYE 138
           A F VKE NNLSLVEYE
Sbjct: 123 ASFTVKEDNNLSLVEYE 139
>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} Length = 115 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]} Length = 116 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 ?
Query143
d1wjja_145 Hypothetical protein At4g28440 (F20O9.120) {Thale 100.0
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 99.94
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 99.58
d1jmca2122 Replication protein A 70 KDa subunit (RPA70) {Huma 99.26
d1xjva1140 Protection of telomeres protein 1, Pot1 {Human (Ho 97.82
d1jb7a1169 Telomere end binding protein alpha subunit {Oxytri 97.61
d1qzga_170 Protection of telomeres protein 1, Pot1 {Fission y 97.33
d1xjva2151 Protection of telomeres protein 1, Pot1 {Human (Ho 96.39
d2pi2a1128 Replication protein A 32 KDa subunit (RPA32) fragm 96.23
d1jb7a2124 Telomere end binding protein alpha subunit {Oxytri 96.11
d1gm5a2180 RecG "wedge" domain {Thermotoga maritima [TaxId: 2 95.07
d2oq0a188 Gamma-interferon-inducible protein Ifi-16 {Human ( 95.04
d1e1oa1143 Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g 90.32
d1iyjb4111 OB-fold domains of BRCA2 {Rat (Rattus norvegicus) 89.51
d1n9wa193 Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph 83.97
d1qvca_145 ssDNA-binding protein {Escherichia coli [TaxId: 56 83.03
>d1wjja_ b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O9.120) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} 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: Hypothetical protein At4g28440 (F20O9.120)
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=100.00  E-value=5.3e-36  Score=223.65  Aligned_cols=136  Identities=70%  Similarity=1.090  Sum_probs=117.6

Q ss_pred             ccCCCcCCCCceeeeccCCCCCCCceEEEEEEecCcceeccCCCccccCCCCCCCCCCeeEEEEEeeCcceEEEEEecCC
Q 032330            3 TAGATAKRKPVFIKVDQLKPGTTGHTLTVKVVSSKPVQVNKPRGARSLSSLSQPSRPPRIAECLVGDDTGAIYFTARNDQ   82 (143)
Q Consensus         3 ~~~~~~~~~~~~~kI~dL~p~~~~v~i~~kVl~~~~~~~~~~R~~~~~~~DG~~~~~~~v~~~lVgDeTG~I~ltlW~~~   82 (143)
                      +++.+.+++|+|+||+||+|++++|||+++||++.++. ++.|+...-..-+.+|+..+|++++|||+||+|+|++|+++
T Consensus         5 ~~~~~~~~k~~~~kI~dL~pg~~~vnl~vkVl~~~~~~-~~~r~~~~~~~~~~~g~~~~v~~~~v~DeTG~i~~tlW~~~   83 (145)
T d1wjja_           5 SSGSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIVV-PVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTARNDQ   83 (145)
T ss_dssp             CCCCCCCCCCSSCCSTTCCTTCCCEEEEEEEEEEEECC-SSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEECTTH
T ss_pred             cCCCCCccCCceeEHHHCCCCCCCceEEEEEEEcccce-eecccccccccccccCCCcEEEEEEEEccCCeEEEEEEecc
Confidence            45666889999999999999999999999999999866 45552100000012235678999999999999999999999


Q ss_pred             CCCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCceEEcCCCCccccceee
Q 032330           83 VDIMTPGTTVILRNAKIDMFKGSMRLAVDKWGRIEVTEPADFEVKESNNLSLVEYEL  139 (143)
Q Consensus        83 ~~~i~~Gd~v~I~na~~~~~~g~~~L~ig~~g~I~~~~~~~~~v~e~~n~S~~eye~  139 (143)
                      ++.+++||+|+|+|||+++|+|+|+|++|++|+|+.++++++.+++.+|||++|||.
T Consensus        84 ~~~l~~Gd~v~i~na~v~~~~G~~~L~vg~~g~I~~~~e~~~~v~e~~niS~~e~E~  140 (145)
T d1wjja_          84 VDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKEDNNLSLVEYES  140 (145)
T ss_dssp             HHHTCTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSCCCSCCCTTSBTTTSCCSS
T ss_pred             ccccCcCCEEEEeeEEEEEECCEEEEEECCCEEEEECCCCcccccccCCCceeEEec
Confidence            888999999999999999999999999999999999999999999999999999996
>d1o7ia_ b.40.4.3 (A:) Archaeal ssDNA-binding protein {Archaeon Sulfolobus solfataricus [TaxId: 2287]} 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
>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
>d1xjva1 b.40.4.3 (A:6-145) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jb7a1 b.40.4.3 (A:36-204) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]} Back     information, alignment and structure
>d1qzga_ b.40.4.3 (A:) Protection of telomeres protein 1, Pot1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Back     information, alignment and structure
>d1xjva2 b.40.4.3 (A:149-299) Protection of telomeres protein 1, Pot1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2pi2a1 b.40.4.3 (A:44-171) Replication protein A 32 KDa subunit (RPA32) fragment {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jb7a2 b.40.4.3 (A:205-328) Telomere end binding protein alpha subunit {Oxytricha nova [TaxId: 200597]} Back     information, alignment and structure
>d1gm5a2 b.40.4.9 (A:106-285) RecG "wedge" domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2oq0a1 b.40.16.1 (A:115-202) Gamma-interferon-inducible protein Ifi-16 {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
>d1iyjb4 b.40.4.3 (B:2732-2760,B:2898-2979) OB-fold domains of BRCA2 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]} Back     information, alignment and structure
>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure