Citrus Sinensis ID: 031443

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-------16
MATRTTKQQQKAQKQQQGSSSDTNAKVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNVVEE
cccHHHHHHHHccccccccccccccccccccccEEEEEccccccccccEEEEEEEEccccccccccccccccccEEEEEEEEccccEEEEEEEcccccccccccEEEEEccEEEEEccEEEEEEcccccEEEcccccEEEcccccccccEEEEEEEEcc
cccccccccccccccccccccccccccccccccEEEEEcccccccccEEEEEEEEEcEEEccccccccccccccEEEEEEEEccccEEEEEEccccccccccccEEEEEccEEEEEccEEEEEEccccEEEEcccccEEEEccccccEEEEEEEEEEcc
MATRTTKQQQKAqkqqqgsssdtnakvvekrkpvftkvdqlkpgtnghnltvnvlksepvlpknraaspqlRQTRIAEclvgddtgtILFTarndqvdlmkpgtTVILRNAKIDMFKGSMRIAVdkwgrieatepakfvvkednnlSLVEYELVNVVEE
matrttkqqqkaqkqqqgsssdtnakvvekrkpvftkvdqlkpgtnghnltvnvlksepvlpknraaspqlrqTRIAECLVGDDTGTILFtarndqvdlmkpgTTVILRnakidmfkGSMRIAVDKWGRIEAtepakfvvkednnlslveyelvnvvee
MATRTTkqqqkaqkqqqGSSSDTNAKVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDnnlslveyelvnvvee
***************************************************V********************QTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNV***
***********************************TKVDQLKPGTNGHNLTVNVLKSEP**************TRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNVV**
*************************KVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNVVEE
******************************RKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRA*SPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNVVEE
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MATRTTKQQQKAQKQQQGSSSDTNAKVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNVVEE
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 ?
Query159 2.2.26 [Sep-21-2011]
O49453153 Uncharacterized protein A no no 0.798 0.830 0.706 9e-49
>sp|O49453|Y4844_ARATH Uncharacterized protein At4g28440 OS=Arabidopsis thaliana GN=At4g28440 PE=1 SV=1 Back     alignment and function desciption
 Score =  192 bits (487), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 94/133 (70%), Positives = 107/133 (80%), Gaps = 6/133 (4%)

Query: 30  KRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLP---KNRAASPQLRQT---RIAECLVGD 83
           KRKPVF KV+QLKPGT GH LTV V+++  V+P   K R AS   R +   RI ECL+GD
Sbjct: 17  KRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGD 76

Query: 84  DTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKED 143
           +TG ILFTARNDQVDLMKPG TVILRN++IDMFKG+MR+ VDKWGRIEAT  A F VKED
Sbjct: 77  ETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKED 136

Query: 144 NNLSLVEYELVNV 156
           NNLSLVEYEL+NV
Sbjct: 137 NNLSLVEYELINV 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 ?
Query159
255536741150 conserved hypothetical protein [Ricinus 0.918 0.973 0.753 1e-57
118484382153 unknown [Populus trichocarpa] 0.962 1.0 0.723 1e-57
302143333148 unnamed protein product [Vitis vinifera] 0.849 0.912 0.785 7e-57
225446441166 PREDICTED: uncharacterized protein At4g2 0.836 0.801 0.789 2e-56
224128240134 predicted protein [Populus trichocarpa] 0.792 0.940 0.825 4e-56
225443616149 PREDICTED: uncharacterized protein At4g2 0.811 0.865 0.821 5e-56
297740422130 unnamed protein product [Vitis vinifera] 0.811 0.992 0.821 8e-56
225452474137 PREDICTED: uncharacterized protein At4g2 0.811 0.941 0.813 9e-56
147778578149 hypothetical protein VITISV_005066 [Viti 0.811 0.865 0.813 2e-55
403318295137 hypothetical protein [Camellia sinensis] 0.811 0.941 0.798 4e-55
>gi|255536741|ref|XP_002509437.1| conserved hypothetical protein [Ricinus communis] gi|223549336|gb|EEF50824.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
 Score =  227 bits (579), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 113/150 (75%), Positives = 123/150 (82%), Gaps = 4/150 (2%)

Query: 12  AQKQQQGSSSDTNAKVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRA--ASP 69
           A  QQQ + ++ N   +EKRKPVF KVDQLKPGTNGH L   VL S+ VL K RA  +S 
Sbjct: 2   ATNQQQAAKTNNNK--IEKRKPVFVKVDQLKPGTNGHTLIAKVLASDTVLHKGRATASSN 59

Query: 70  QLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGR 129
           +LR TRIAECL+GD+TGTILFTARNDQVDLMKP TTVILRNAKIDMFKGSMR+AVDKWGR
Sbjct: 60  RLRNTRIAECLIGDETGTILFTARNDQVDLMKPETTVILRNAKIDMFKGSMRLAVDKWGR 119

Query: 130 IEATEPAKFVVKEDNNLSLVEYELVNVVEE 159
           IE TEPAKF VKEDNNLSLVEYELV V  E
Sbjct: 120 IEVTEPAKFAVKEDNNLSLVEYELVTVAAE 149

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|118484382|gb|ABK94068.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|302143333|emb|CBI21894.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225446441|ref|XP_002276699.1| PREDICTED: uncharacterized protein At4g28440-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|224128240|ref|XP_002329115.1| predicted protein [Populus trichocarpa] gi|222869784|gb|EEF06915.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225443616|ref|XP_002279414.1| PREDICTED: uncharacterized protein At4g28440 [Vitis vinifera] Back     alignment and taxonomy information
>gi|297740422|emb|CBI30604.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225452474|ref|XP_002278536.1| PREDICTED: uncharacterized protein At4g28440 [Vitis vinifera] Back     alignment and taxonomy information
>gi|147778578|emb|CAN60304.1| hypothetical protein VITISV_005066 [Vitis vinifera] Back     alignment and taxonomy information
>gi|403318295|gb|AFR36911.1| hypothetical protein [Camellia sinensis] 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 ?
Query159
TAIR|locus:2034813137 AT1G23750 "AT1G23750" [Arabido 0.710 0.824 0.707 4.6e-41
TAIR|locus:505006287182 AT2G33845 "AT2G33845" [Arabido 0.723 0.631 0.741 1.1e-39
TAIR|locus:2024239143 AT1G03810 "AT1G03810" [Arabido 0.767 0.853 0.656 4.3e-38
TAIR|locus:2121313153 AT4G28440 "AT4G28440" [Arabido 0.792 0.823 0.628 8.9e-38
TAIR|locus:2019918153 AT1G10590 "AT1G10590" [Arabido 0.710 0.738 0.646 3.5e-36
TAIR|locus:2034813 AT1G23750 "AT1G23750" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 436 (158.5 bits), Expect = 4.6e-41, P = 4.6e-41
 Identities = 80/113 (70%), Positives = 96/113 (84%)

Query:    31 RKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILF 90
             +KP FTKVDQL+PGT+GHN+ V ++ ++ VL K RA  PQ RQ RI+EC+VGD+TG I+F
Sbjct:    10 KKPAFTKVDQLRPGTSGHNVNVKIVSTKMVLQKGRADGPQARQLRISECIVGDETGVIVF 69

Query:    91 TARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKED 143
             TARNDQVDLMK G+TV LRNAKIDM+KGSMR+AVDKWGR+E TEPA F VKED
Sbjct:    70 TARNDQVDLMKEGSTVTLRNAKIDMYKGSMRLAVDKWGRVEVTEPASFKVKED 122
GO:0008150 "biological_process" evidence=ND
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:2121313 AT4G28440 "AT4G28440" [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

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:
GSVIVG00018634001
SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (148 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query159
cd0449182 cd04491, SoSSB_OBF, SoSSB_OBF: A subfamily of OB f 2e-17
PRK06461129 PRK06461, PRK06461, single-stranded DNA-binding pr 5e-13
PRK07218 423 PRK07218, PRK07218, replication factor A; Provisio 0.001
PRK07217 311 PRK07217, PRK07217, replication factor A; Reviewed 0.002
PRK06386 358 PRK06386, PRK06386, replication factor A; Reviewed 0.002
>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 = 71.9 bits (177), Expect = 2e-17
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 5/84 (5%)

Query: 49  NLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQV-DLMKPGTTVI 107
           ++   VL         R  S      ++   LVGD+TGTI FT  +++  D ++PG  V 
Sbjct: 1   SVEGKVLSISEPREFTRDGSE----GKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVR 56

Query: 108 LRNAKIDMFKGSMRIAVDKWGRIE 131
           + NA +  F G + ++V K   IE
Sbjct: 57  IENAYVREFNGRLELSVGKNSEIE 80

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|180890 PRK07218, PRK07218, replication factor A; Provisional 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 159
PRK06461129 single-stranded DNA-binding protein; Reviewed 99.94
KOG3416134 consensus Predicted nucleic acid binding protein [ 99.94
PRK06386 358 replication factor A; Reviewed 99.87
PRK07218 423 replication factor A; Provisional 99.87
PRK07217 311 replication factor A; Reviewed 99.85
PRK06386 358 replication factor A; Reviewed 99.85
PRK08402 355 replication factor A; Reviewed 99.85
PRK07218 423 replication factor A; Provisional 99.83
PRK15491 374 replication factor A; Provisional 99.82
PRK14699 484 replication factor A; Provisional 99.81
PRK07211 485 replication factor A; Reviewed 99.81
PRK14699 484 replication factor A; Provisional 99.81
PRK12366 637 replication factor A; Reviewed 99.79
cd0449182 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds simil 99.77
PRK15491374 replication factor A; Provisional 99.76
PRK07211 485 replication factor A; Reviewed 99.72
PRK12366 637 replication factor A; Reviewed 99.66
COG1599 407 RFA1 Single-stranded DNA-binding replication prote 99.38
cd04475101 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds cor 99.38
cd04474104 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds cor 99.36
TIGR00617 608 rpa1 replication factor-a protein 1 (rpa1). This f 99.06
TIGR00617 608 rpa1 replication factor-a protein 1 (rpa1). This f 98.9
PF0133675 tRNA_anti-codon: OB-fold nucleic acid binding doma 98.41
cd04497138 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB f 98.33
cd0448392 hOBFC1_like hOBFC1_like: A subfamily of OB folds s 97.91
cd0447895 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds cor 97.87
cd0352475 RPA2_OBF_family RPA2_OBF_family: A family of oligo 97.75
cd0449283 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB fol 97.68
PRK13480 314 3'-5' exoribonuclease YhaM; Provisional 97.68
cd04481106 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of unc 97.41
COG1599 407 RFA1 Single-stranded DNA-binding replication prote 97.23
cd0448875 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB f 97.22
cd0448584 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresp 97.14
PF02765146 POT1: Telomeric single stranded DNA binding POT1/C 97.03
cd0448086 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of unc 96.96
cd0448978 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB fol 96.57
COG4085204 Predicted RNA-binding protein, contains TRAM domai 94.35
PRK10917 681 ATP-dependent DNA helicase RecG; Provisional 94.14
cd04498123 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds simil 93.8
cd0448482 polC_OBF polC_OBF: A subfamily of OB folds corresp 93.04
TIGR00643 630 recG ATP-dependent DNA helicase RecG. 93.02
PRK08402355 replication factor A; Reviewed 92.84
cd0448773 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB f 92.13
cd0449079 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds 91.14
PRK056731135 dnaE DNA polymerase III subunit alpha; Validated 90.53
PF02760170 HIN: HIN-200/IF120x domain; InterPro: IPR004021 Th 90.35
PRK07373449 DNA polymerase III subunit alpha; Reviewed 90.22
PRK05159 437 aspC aspartyl-tRNA synthetase; Provisional 90.08
COG5235258 RFA2 Single-stranded DNA-binding replication prote 88.71
PLN02850 530 aspartate-tRNA ligase 88.31
PF0272195 DUF223: Domain of unknown function DUF223; InterPr 88.27
cd04316108 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, a 87.6
COG1200 677 RecG RecG-like helicase [DNA replication, recombin 86.75
PF1132584 DUF3127: Domain of unknown function (DUF3127); Int 86.56
cd04317135 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticod 86.52
cd04322108 LysRS_N LysRS_N: N-terminal, anticodon recognition 85.73
PRK00448 1437 polC DNA polymerase III PolC; Validated 85.47
cd04494251 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds 84.98
PF10451256 Stn1: Telomere regulation protein Stn1; InterPro: 84.85
cd0448291 RPA2_OBF_like RPA2_OBF_like: A subgroup of unchara 84.28
PTZ00401 550 aspartyl-tRNA synthetase; Provisional 84.28
PF1374299 tRNA_anti_2: OB-fold nucleic acid binding domain 83.95
cd04320102 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon r 83.95
PRK02983 1094 lysS lysyl-tRNA synthetase; Provisional 82.59
PF08646146 Rep_fac-A_C: Replication factor-A C terminal domai 82.56
TIGR00499 496 lysS_bact lysyl-tRNA synthetase, eukaryotic and no 82.4
PRK00484 491 lysS lysyl-tRNA synthetase; Reviewed 81.23
KOG3108265 consensus Single-stranded DNA-binding replication 80.51
PF04076103 BOF: Bacterial OB fold (BOF) protein; InterPro: IP 80.33
PRK12445 505 lysyl-tRNA synthetase; Reviewed 80.15
cd01491286 Ube1_repeat1 Ubiquitin activating enzyme (E1), rep 80.05
>PRK06461 single-stranded DNA-binding protein; Reviewed Back     alignment and domain information 
Probab=99.94  E-value=9.6e-27  Score=176.65  Aligned_cols=114  Identities=29%  Similarity=0.452  Sum_probs=105.4

Q ss_pred             ceeecccCCCCCCCceEEEEEEecCcccccccCCCCCCCcceEEEEEEeeCceeEEEEEecCCcCCCCCCCEEEEeceEE
Q 031443           34 VFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQLRQTRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKI  113 (159)
Q Consensus        34 ~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~~~~~~V~~~lVgDeTG~I~ltlWde~~~~i~~Gdvv~I~na~v  113 (159)
                      .++||+||.|++.+++++++|+++++++++.+++    +...+.+++|+|+||+|+|++|+++++.+++||+|+|.||++
T Consensus         3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~----~~~~v~~~~l~D~TG~I~~tlW~~~a~~l~~GdvV~I~na~v   78 (129)
T PRK06461          3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKG----GPRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWT   78 (129)
T ss_pred             CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCC----CceEEEEEEEECCCCEEEEEEeCCccccCCCCCEEEEECcEE
Confidence            3789999999999999999999999988877653    347899999999999999999999988999999999999999


Q ss_pred             ceeCCeEEEEeCCceeEEEcCCCcEEEccCCCccccceee
Q 031443          114 DMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYEL  153 (159)
Q Consensus       114 ~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~ieye~  153 (159)
                      ++|+|+++|+++++|.|.++++.  +|+..++||+.+||.
T Consensus        79 ~~f~G~lqL~i~~~~~i~~~~~~--~v~~~~~i~~~~~~~  116 (129)
T PRK06461         79 TLYRGKVQLNVGKYGSISESDDE--EVPEAEEIPEETPEA  116 (129)
T ss_pred             eeeCCEEEEEECCCEEEEECCcc--ccCCCCccCccCccc
Confidence            99999999999999999999765  899999999999996

>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only] 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
>PRK07217 replication factor A; Reviewed Back     alignment and domain information
>PRK06386 replication factor A; Reviewed Back     alignment and domain information
>PRK08402 replication factor A; Reviewed Back     alignment and domain information
>PRK07218 replication factor A; Provisional 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
>PRK07211 replication factor A; Reviewed 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
>PRK07211 replication factor A; Reviewed Back     alignment and domain information
>PRK12366 replication factor A; Reviewed 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
>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
>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
>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
>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
>PRK13480 3'-5' exoribonuclease YhaM; Provisional 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>TIGR00643 recG ATP-dependent DNA helicase RecG Back     alignment and domain information
>PRK08402 replication factor A; Reviewed 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
>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
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated Back     alignment and domain information
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function Back     alignment and domain information
>PRK07373 DNA polymerase III subunit alpha; Reviewed Back     alignment and domain information
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional Back     alignment and domain information
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PLN02850 aspartate-tRNA ligase 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
>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
>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
>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
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS) Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>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
>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
>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
>PTZ00401 aspartyl-tRNA synthetase; Provisional Back     alignment and domain information
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain 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
>PRK02983 lysS lysyl-tRNA synthetase; Provisional 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
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial Back     alignment and domain information
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed Back     alignment and domain information
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair] Back     alignment and domain information
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif) Back     alignment and domain information
>PRK12445 lysyl-tRNA synthetase; Reviewed Back     alignment and domain information
>cd01491 Ube1_repeat1 Ubiquitin activating enzyme (E1), repeat 1 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 ?
Query159
1wjj_A145 Solution Structure Of Hypothetical Protein F20o9.12 1e-41
1o7i_A119 Crystal Structure Of A Single Stranded Dna Binding 2e-04
>pdb|1WJJ|A Chain A, Solution Structure Of Hypothetical Protein F20o9.120 From Arabidopsis Thaliana Length = 145 Back     alignment and structure 
Iteration: 1

 Score =  164 bits (416), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 82/120 (68%), Positives = 94/120 (78%), Gaps = 6/120 (5%)
Query: 30  KRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLP---KNRAASPQLRQT---RIAECLVGD 83
           KRKPVF KV+QLKPGT GH LTV V+++  V+P   K R AS   R +   RI ECL+GD
Sbjct: 11  KRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGD 70
Query: 84  DTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKED 143
           +TG ILFTARNDQVDLMKPG TVILRN++IDMFKG+MR+ VDKWGRIEAT  A F VKED
Sbjct: 71  ETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKED 130
>pdb|1O7I|A Chain A, Crystal Structure Of A Single Stranded Dna Binding Protein Length = 119 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 ?
Query159
1wjj_A145 Hypothetical protein F20O9.120; DNA-binding protei 7e-49
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 4e-24
2kbn_A109 Conserved protein; nucleic acid binding protein, b 2e-20
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 8e-12
2k50_A115 Replication factor A related protein; uncharacteri 1e-07
3e0e_A97 Replication protein A; structural genomics, PSI-2, 1e-06
3dm3_A105 Replication factor A; probably plays AN essential 2e-06
>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 =  153 bits (388), Expect = 7e-49
 Identities = 89/139 (64%), Positives = 104/139 (74%), Gaps = 6/139 (4%)

Query: 20  SSDTNAKVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASP------QLRQ 73
            S  ++    KRKPVF KV+QLKPGT GH LTV V+++  V+P  R   P        + 
Sbjct: 1   GSSGSSGSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQP 60

Query: 74  TRIAECLVGDDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEAT 133
           +RI ECL+GD+TG ILFTARNDQVDLMKPG TVILRN++IDMFKG+MR+ VDKWGRIEAT
Sbjct: 61  SRIVECLIGDETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEAT 120

Query: 134 EPAKFVVKEDNNLSLVEYE 152
             A F VKEDNNLSLVEYE
Sbjct: 121 GAASFTVKEDNNLSLVEYE 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 ?
Query159
1wjj_A145 Hypothetical protein F20O9.120; DNA-binding protei 100.0
2k75_A106 Uncharacterized protein TA0387; closed beta barrel 99.93
3e0e_A97 Replication protein A; structural genomics, PSI-2, 99.92
2kbn_A109 Conserved protein; nucleic acid binding protein, b 99.92
1o7i_A119 SSB, SSO2364, single stranded DNA binding protein; 99.91
3dm3_A105 Replication factor A; probably plays AN essential 99.89
2k50_A115 Replication factor A related protein; uncharacteri 99.76
1ynx_A114 Replication factor-A protein 1; canonical OB fold, 99.61
1jmc_A 246 Protein (replication protein A (RPA)); human ssDNA 99.54
4gop_C 444 Putative uncharacterized protein; OB fold, ssDNA b 99.3
1jmc_A246 Protein (replication protein A (RPA)); human ssDNA 99.15
4gop_C 444 Putative uncharacterized protein; OB fold, ssDNA b 99.12
4gop_B136 Putative uncharacterized protein; OB fold, ssDNA b 97.84
3kdf_D132 Replication protein A 32 kDa subunit; wheat GERM c 97.74
1xjv_A 294 Protection of telomeres 1; protein-DNA complex, si 97.69
2pi2_A270 Replication protein A 32 kDa subunit; FULL-length 97.4
1qzg_A187 Protection of telomeres protein 1; protrein-DNA co 97.29
4hik_A143 Protection of telomeres protein 1; specificity, pl 97.16
1xjv_A294 Protection of telomeres 1; protein-DNA complex, si 97.07
1jb7_A 495 Telomere-binding protein alpha subunit; DNA-protei 97.06
3kf6_A159 Protein STN1; OB fold, chromosomal protein, DNA-bi 96.23
1jb7_A 495 Telomere-binding protein alpha subunit; DNA-protei 92.53
3m4p_A 456 Ehasnrs, asparaginyl-tRNA synthetase, putative; am 90.94
2xvs_A166 Tetratricopeptide repeat protein 5; antitumor prot 88.87
3nem_A 438 Aspartyl-tRNA synthetase; rossmann fold, OB fold, 87.47
1txy_A104 Primosomal replication protein N; OB fold, dimer, 87.18
3rlo_A204 Gamma-interferon-inducible protein 16; HIN200/OB f 87.11
3f2b_A 1041 DNA-directed DNA polymerase III alpha chain; DNA p 86.15
1n9w_A 422 Aspartyl-tRNA synthetase 2; biosynthetic protein; 85.95
3rn5_A208 Interferon-inducible protein AIM2; OB fold, DNA bi 84.19
3rn5_A208 Interferon-inducible protein AIM2; OB fold, DNA bi 83.42
3au7_A402 TIAS, putative uncharacterized protein; ATP hydrol 83.42
2v31_A112 Ubiquitin-activating enzyme E1 X; ligase, phosphor 82.84
3koj_A108 Uncharacterized protein YCF41; single-strand bindi 80.23
>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=1.6e-42  Score=267.57  Aligned_cols=133  Identities=67%  Similarity=1.009  Sum_probs=125.5

Q ss_pred             cccccCCCceeecccCCCCCCCceEEEEEEecCccc---ccccCCCCC---CCcceEEEEEEeeCceeEEEEEecCCcCC
Q 031443           26 KVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVL---PKNRAASPQ---LRQTRIAECLVGDDTGTILFTARNDQVDL   99 (159)
Q Consensus        26 ~~~~l~~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~---~~~R~DG~~---~~~~~V~~~lVgDeTG~I~ltlWde~~~~   99 (159)
                      .++++++|.|+||+||+|++++++++++||++++++   +++|+||++   .++++|++++||||||+|+||+|+++++.
T Consensus         7 ~~~~~~kp~~~kI~dL~pg~~~v~l~~kVl~~~~v~~~~~~~R~dG~~~~~~r~~~V~~~lVgDeTG~I~ftlW~e~~~~   86 (145)
T 1wjj_A            7 GSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTARNDQVDL   86 (145)
T ss_dssp             CCCCCCCCSSCCSTTCCTTCCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEECTTHHHH
T ss_pred             CCccccCccceEHHHcCCCCCceEEEEEEEEcccccccccccccCCccccccCCceEEEEEEEcCCcEEEEEEecCCcCc
Confidence            467899999999999999999999999999999988   889999861   23699999999999999999999999889


Q ss_pred             CCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCcEEEccCCCccccceeeeeeec
Q 031443          100 MKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELVNVVE  158 (159)
Q Consensus       100 i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~ieye~v~~~~  158 (159)
                      +++||+|+|+|||+++|+|+|+|++|+||+|+++++++|+||+.+|||++|||+++|++
T Consensus        87 l~~Gd~v~i~na~v~~~~G~~~L~vgk~g~Ie~~~e~~~~v~e~~n~S~~e~e~~~~~~  145 (145)
T 1wjj_A           87 MKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKEDNNLSLVEYESGPSSG  145 (145)
T ss_dssp             TCTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSCCCSCCCTTSBTTTSCCSSCCSCC
T ss_pred             CCCCCEEEEeccEEEeECCEEEEEECCCEEEEECCCCcEEEecCCCcCcceEEEeecCC
Confidence            99999999999999999999999999999999999999999999999999999999875
>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold, structural genomics, PSI-2, protein structure initiative; NMR {Thermoplasma acidophilum} 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
>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
>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
>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
>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
>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
>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
>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
>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
>3kf6_A Protein STN1; OB fold, chromosomal protein, DNA-binding, nucleus, telomere; 1.65A {Schizosaccharomyces pombe} 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
>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
>2xvs_A Tetratricopeptide repeat protein 5; antitumor protein, P53 cofactor, stress-response; 1.80A {Homo sapiens} Back     alignment and structure
>3nem_A Aspartyl-tRNA synthetase; rossmann fold, OB fold, ligase; HET: AMO ATP; 1.89A {Thermococcus kodakarensis} PDB: 3nel_A* 3nen_A 1b8a_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
>3rlo_A Gamma-interferon-inducible protein 16; HIN200/OB fold/DNA binding, DNA binding/cytosolic DNA sensor cytosol, DNA binding protein; 1.80A {Homo sapiens} PDB: 3rnu_A* 3b6y_A 3rln_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
>1n9w_A Aspartyl-tRNA synthetase 2; biosynthetic protein; 2.30A {Thermus thermophilus} SCOP: b.40.4.1 d.104.1.1 PDB: 3kfu_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
>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
>3au7_A TIAS, putative uncharacterized protein; ATP hydrolysis, RNA binding protein; 2.60A {Archaeoglobus fulgidus} PDB: 3amt_A* 3amu_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
>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

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 159
d1wjja_145 b.40.4.3 (A:) Hypothetical protein At4g28440 (F20O 4e-44
d1o7ia_115 b.40.4.3 (A:) Archaeal ssDNA-binding protein {Arch 8e-25
d1jmca1116 b.40.4.3 (A:183-298) Replication protein A 70 KDa 0.001
>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 =  140 bits (354), Expect = 4e-44
 Identities = 88/130 (67%), Positives = 101/130 (77%), Gaps = 6/130 (4%)

Query: 29  EKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQ------LRQTRIAECLVG 82
            KRKPVF KV+QLKPGT GH LTV V+++  V+P  R   P        + +RI ECL+G
Sbjct: 10  VKRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIG 69

Query: 83  DDTGTILFTARNDQVDLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKE 142
           D+TG ILFTARNDQVDLMKPG TVILRN++IDMFKG+MR+ VDKWGRIEAT  A F VKE
Sbjct: 70  DETGCILFTARNDQVDLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKE 129

Query: 143 DNNLSLVEYE 152
           DNNLSLVEYE
Sbjct: 130 DNNLSLVEYE 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 ?
Query159
d1wjja_145 Hypothetical protein At4g28440 (F20O9.120) {Thale 100.0
d1o7ia_115 Archaeal ssDNA-binding protein {Archaeon Sulfolobu 99.95
d1jmca1116 Replication protein A 70 KDa subunit (RPA70) {Huma 99.66
d1jmca2122 Replication protein A 70 KDa subunit (RPA70) {Huma 99.34
d1xjva1140 Protection of telomeres protein 1, Pot1 {Human (Ho 97.99
d1jb7a1169 Telomere end binding protein alpha subunit {Oxytri 97.67
d1qzga_170 Protection of telomeres protein 1, Pot1 {Fission y 97.21
d1xjva2151 Protection of telomeres protein 1, Pot1 {Human (Ho 97.21
d2pi2a1128 Replication protein A 32 KDa subunit (RPA32) fragm 96.97
d1jb7a2124 Telomere end binding protein alpha subunit {Oxytri 96.52
d1gm5a2180 RecG "wedge" domain {Thermotoga maritima [TaxId: 2 95.33
d2oq0a188 Gamma-interferon-inducible protein Ifi-16 {Human ( 94.24
d1e1oa1143 Lysyl-tRNA synthetase (LysRS) {Escherichia coli, g 94.18
d1n9wa193 Aspartyl-tRNA synthetase (AspRS) {Thermus thermoph 91.3
d1iyjb4111 OB-fold domains of BRCA2 {Rat (Rattus norvegicus) 89.97
d2oq0a2103 Gamma-interferon-inducible protein Ifi-16 {Human ( 89.74
d1qvca_145 ssDNA-binding protein {Escherichia coli [TaxId: 56 86.16
d1v1qa_111 Primosomal replication protein N, PriB {Escherichi 83.65
d1eova1134 Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (S 82.96
>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=7.2e-36  Score=227.98  Aligned_cols=131  Identities=67%  Similarity=1.058  Sum_probs=120.0

Q ss_pred             cccccccCCCceeecccCCCCCCCceEEEEEEecCcccccccCCCCC------CCcceEEEEEEeeCceeEEEEEecCCc
Q 031443           24 NAKVVEKRKPVFTKVDQLKPGTNGHNLTVNVLKSEPVLPKNRAASPQ------LRQTRIAECLVGDDTGTILFTARNDQV   97 (159)
Q Consensus        24 ~~~~~~l~~~~~~kI~dL~P~~~~vnv~~kVL~i~~~~~~~R~DG~~------~~~~~V~~~lVgDeTG~I~ltlWde~~   97 (159)
                      .......++|.|+||+||+|+++++||+++||++.++++|.|.+++.      |.+.+|++++|||+||+|+|+||++++
T Consensus         5 ~~~~~~~~k~~~~kI~dL~pg~~~vnl~vkVl~~~~~~~~~r~~~~~~~~~~~g~~~~v~~~~v~DeTG~i~~tlW~~~~   84 (145)
T d1wjja_           5 SSGSTVKRKPVFVKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRPASSLSRPSQPSRIVECLIGDETGCILFTARNDQV   84 (145)
T ss_dssp             CCCCCCCCCCSSCCSTTCCTTCCCEEEEEEEEEEEECCSSSSCCSCSSCCSSCCCCCCCEEEEEECSSCEEEEEECTTHH
T ss_pred             cCCCCCccCCceeEHHHCCCCCCCceEEEEEEEcccceeecccccccccccccCCCcEEEEEEEEccCCeEEEEEEeccc
Confidence            34455667889999999999999999999999999999999877644      345689999999999999999999988


Q ss_pred             CCCCCCCEEEEeceEEceeCCeEEEEeCCceeEEEcCCCcEEEccCCCccccceeee
Q 031443           98 DLMKPGTTVILRNAKIDMFKGSMRIAVDKWGRIEATEPAKFVVKEDNNLSLVEYELV  154 (159)
Q Consensus        98 ~~i~~Gdvv~I~na~v~~~~G~~~L~vgk~g~I~~~~~~~~~vne~~N~S~ieye~v  154 (159)
                      +.+++||+|+|+|||+++|+|+|+|++|++|+|++++++.+.+++.+|||++|||.-
T Consensus        85 ~~l~~Gd~v~i~na~v~~~~G~~~L~vg~~g~I~~~~e~~~~v~e~~niS~~e~E~~  141 (145)
T d1wjja_          85 DLMKPGATVILRNSRIDMFKGTMRLGVDKWGRIEATGAASFTVKEDNNLSLVEYESG  141 (145)
T ss_dssp             HHTCTTCEEEEEEEEEEEETTEEEEEECTTCCBCCCSCCCSCCCTTSBTTTSCCSSC
T ss_pred             cccCcCCEEEEeeEEEEEECCEEEEEECCCEEEEECCCCcccccccCCCceeEEecC
Confidence            889999999999999999999999999999999999999999999999999999964
>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
>d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]} 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
>d2oq0a2 b.40.16.1 (A:12-114) Gamma-interferon-inducible protein Ifi-16 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1qvca_ b.40.4.3 (A:) ssDNA-binding protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v1qa_ b.40.4.3 (A:) Primosomal replication protein N, PriB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1eova1 b.40.4.1 (A:71-204) Aspartyl-tRNA synthetase (AspRS) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure