Citrus Sinensis ID: 034973

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-------
MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRVVSHHPPIPETPSLKDVEPSSVNEVTKVKKDTEERKQNVGRKNRN
ccccHHHHHccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHccccc
ccccHHHHHccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccHHHHHcccccccccccccc
mdasmedlagcpgiverKVKCLYdtfhepfkrvvshhppipetpslkdvepssvnevtkVKKDTEERkqnvgrknrn
mdasmedlagcpgiveRKVKCLYDTFHEPFkrvvshhppipetpslkdvepssvnevtkvkkdteerkqnvgrknrn
MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRVVSHHPPIPETPSLKDVEPSSVNEVTKVKKDTEERKQNVGRKNRN
********AGCPGIVERKVKCLYDTFHEPFKRVV*******************************************
**********CPGIVERKVKCLYDTFHEPFK**********************************************
********AGCPGIVERKVKCLYDTFHEPFKRVVSHHPPIPETPSLK******************************
*****EDLAGCPGIVERKVKCLYDTFHEPFKR*********************************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooo
iiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRVVSHHPPIPETPSLKDVEPSSVNEVTKVKKDTEERKQNVGRKNRN
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 ?
Query77 2.2.26 [Sep-21-2011]
Q9MA98410 DNA excision repair prote yes no 0.636 0.119 0.703 8e-14
>sp|Q9MA98|ERCC1_ARATH DNA excision repair protein ERCC-1 OS=Arabidopsis thaliana GN=ERCC1 PE=2 SV=1 Back     alignment and function desciption
 Score = 75.5 bits (184), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 38/54 (70%), Positives = 40/54 (74%), Gaps = 5/54 (9%)

Query: 1   MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRVVSHH-----PPIPETPSLKDV 49
           +DASMEDLA CPGI ERKVK LYDTFHEPFKR  S +     PPIPE P  KDV
Sbjct: 289 IDASMEDLARCPGIGERKVKRLYDTFHEPFKRATSSYPSVVEPPIPEAPVEKDV 342
Seems to be involved in nucleotide excision repair (NER) of damaged DNA (dark repair mechanism). The UVH1/RAD1-ERCC1/RAD10 complex may act as an endonuclease making DNA incision 5' to the lesion site. In vitro, is implicated in double strand breaks (DSBs) repair and is required for homologous recombination in the presence of non-homologous overhangs. In vitro, is involved in chromosomal recombination between tandem repeats in both direct and inverted orientations. May mediate the induction of a DNA-damage sensitive cell-cycle checkpoint during the G2 phase.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

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 ?
Query77
255542562 392 excision repair cross-complementing 1 er 0.792 0.155 0.774 8e-18
224130994 382 predicted protein [Populus trichocarpa] 0.714 0.143 0.8 9e-18
449520473 412 PREDICTED: DNA excision repair protein E 0.727 0.135 0.732 9e-16
449441216 391 PREDICTED: DNA excision repair protein E 0.727 0.143 0.732 9e-16
359487720 398 PREDICTED: DNA excision repair protein E 0.688 0.133 0.735 1e-13
15229933 410 DNA excision repair protein ERCC-1 [Arab 0.636 0.119 0.703 4e-12
326512966 388 predicted protein [Hordeum vulgare subsp 0.909 0.180 0.547 1e-10
297829042 407 hypothetical protein ARALYDRAFT_477808 [ 0.636 0.120 0.648 1e-10
357441595 401 DNA excision repair protein ERCC-1 [Medi 0.558 0.107 0.767 3e-10
356533598 398 PREDICTED: DNA excision repair protein E 0.558 0.108 0.767 3e-10
>gi|255542562|ref|XP_002512344.1| excision repair cross-complementing 1 ercc1, putative [Ricinus communis] gi|223548305|gb|EEF49796.1| excision repair cross-complementing 1 ercc1, putative [Ricinus communis] Back     alignment and taxonomy information
 Score = 94.4 bits (233), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 52/62 (83%), Gaps = 1/62 (1%)

Query: 1   MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRVVSHHPPIPETPSLKDVEPSSVNEVTKV 60
           MDASMEDLA CPGI ERKVK LYDTFHEPFKRVVS HP +PET S KD EP+ V+EVT+V
Sbjct: 266 MDASMEDLARCPGIGERKVKRLYDTFHEPFKRVVSSHPAVPET-SQKDSEPALVDEVTEV 324

Query: 61  KK 62
            K
Sbjct: 325 GK 326

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224130994|ref|XP_002328427.1| predicted protein [Populus trichocarpa] gi|222838142|gb|EEE76507.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449520473|ref|XP_004167258.1| PREDICTED: DNA excision repair protein ERCC-1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449441216|ref|XP_004138378.1| PREDICTED: DNA excision repair protein ERCC-1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|359487720|ref|XP_002281063.2| PREDICTED: DNA excision repair protein ERCC-1-like [Vitis vinifera] gi|296088298|emb|CBI36743.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|15229933|ref|NP_187172.1| DNA excision repair protein ERCC-1 [Arabidopsis thaliana] gi|55976606|sp|Q9MA98.1|ERCC1_ARATH RecName: Full=DNA excision repair protein ERCC-1; Short=AtERCC1; Short=AtRAD10; AltName: Full=Ultraviolet hypersensitive 7 gi|6729031|gb|AAF27027.1|AC009177_17 putative nucleotide repair protein [Arabidopsis thaliana] gi|9800490|gb|AAF99316.1|AF276082_1 ERCC1 [Arabidopsis thaliana] gi|15215614|gb|AAK91352.1| AT3g05210/T12H1_18 [Arabidopsis thaliana] gi|21435979|gb|AAM51569.1| AT3g05210/T12H1_18 [Arabidopsis thaliana] gi|21618171|gb|AAM67221.1| putative nucleotide repair protein [Arabidopsis thaliana] gi|332640684|gb|AEE74205.1| DNA excision repair protein ERCC-1 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|326512966|dbj|BAK03390.1| predicted protein [Hordeum vulgare subsp. vulgare] Back     alignment and taxonomy information
>gi|297829042|ref|XP_002882403.1| hypothetical protein ARALYDRAFT_477808 [Arabidopsis lyrata subsp. lyrata] gi|297328243|gb|EFH58662.1| hypothetical protein ARALYDRAFT_477808 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|357441595|ref|XP_003591075.1| DNA excision repair protein ERCC-1 [Medicago truncatula] gi|355480123|gb|AES61326.1| DNA excision repair protein ERCC-1 [Medicago truncatula] Back     alignment and taxonomy information
>gi|356533598|ref|XP_003535349.1| PREDICTED: DNA excision repair protein ERCC-1-like [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query77
TAIR|locus:2096329410 ERCC1 [Arabidopsis thaliana (t 0.896 0.168 0.573 1.9e-14
UNIPROTKB|Q1LZ75294 ERCC1 "DNA excision repair pro 0.402 0.105 0.548 0.00052
UNIPROTKB|B3KRR0225 ERCC1 "cDNA FLJ34720 fis, clon 0.402 0.137 0.548 0.00066
UNIPROTKB|Q9QYP5293 ERCC1 "ERCC1 protein" [Cricetu 0.428 0.112 0.515 0.00085
TAIR|locus:2096329 ERCC1 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 191 (72.3 bits), Expect = 1.9e-14, P = 1.9e-14
 Identities = 43/75 (57%), Positives = 49/75 (65%)

Query:     1 MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRVVSHHP-----PIPETPSLKDVEPSS-V 54
             +DASMEDLA CPGI ERKVK LYDTFHEPFKR  S +P     PIPE P  KDV     V
Sbjct:   289 IDASMEDLARCPGIGERKVKRLYDTFHEPFKRATSSYPSVVEPPIPEAPVEKDVNSEEPV 348

Query:    55 NEVTKVKKDTEERKQ 69
              E     +D+ +RK+
Sbjct:   349 EEDEDFVEDSRKRKK 363
GO:0003677 "DNA binding" evidence=IEA
GO:0003684 "damaged DNA binding" evidence=IEA
GO:0004519 "endonuclease activity" evidence=IEA
GO:0005634 "nucleus" evidence=ISM;IEA
GO:0006281 "DNA repair" evidence=IEA
GO:0006284 "base-excision repair" evidence=ISS
GO:0010332 "response to gamma radiation" evidence=IMP
GO:0000724 "double-strand break repair via homologous recombination" evidence=IMP
GO:0006294 "nucleotide-excision repair, preincision complex assembly" evidence=IMP
GO:0017108 "5'-flap endonuclease activity" evidence=IMP
GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA
GO:0010213 "non-photoreactive DNA repair" evidence=IMP
GO:0010224 "response to UV-B" evidence=IMP
UNIPROTKB|Q1LZ75 ERCC1 "DNA excision repair protein ERCC-1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|B3KRR0 ERCC1 "cDNA FLJ34720 fis, clone MESAN2005724, highly similar to DNA EXCISION REPAIR PROTEIN ERCC-1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q9QYP5 ERCC1 "ERCC1 protein" [Cricetulus griseus (taxid:10029)] 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) ?
Q9MA98ERCC1_ARATH3, ., 1, ., -, ., -0.70370.63630.1195yesno

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:
gw1.70.559.1
hypothetical protein (329 aa)
(Populus trichocarpa)
Predicted Functional Partners:
eugene3.00290111
hypothetical protein (982 aa)
    ••• 0.882
eugene3.00020503
hypothetical protein (758 aa)
   • •• 0.639
fgenesh4_pg.C_LG_I002797
hypothetical protein (1088 aa)
    ••• 0.603
fgenesh4_pg.C_LG_I000900
hypothetical protein (803 aa)
     •• 0.566
eugene3.00120511
hypothetical protein (944 aa)
    • • 0.478
estExt_fgenesh4_pg.C_LG_IV0538
hypothetical protein (449 aa)
     •• 0.472
estExt_Genewise1_v1.C_LG_IV2251
hypothetical protein (909 aa)
     •• 0.468
gw1.XVII.631.1
annotation not avaliable (1425 aa)
     •• 0.440
gw1.IV.3592.1
hypothetical protein (871 aa)
     •• 0.409
gw1.XIII.413.1
annotation not avaliable (325 aa)
    • • 0.408

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 77
KOG2841254 consensus Structure-specific endonuclease ERCC1-XP 99.01
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 97.96
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 97.83
PRK02515132 psbU photosystem II complex extrinsic protein prec 97.29
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 97.14
TIGR01259120 comE comEA protein. This model describes the ComEA 96.97
COG1555149 ComEA DNA uptake protein and related DNA-binding p 96.25
PF1283665 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE 96.21
PRK13766773 Hef nuclease; Provisional 96.16
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 96.05
PRK12766 232 50S ribosomal protein L32e; Provisional 95.69
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 95.6
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recomb 95.04
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 94.98
COG5241224 RAD10 Nucleotide excision repair endonuclease NEF1 94.93
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 94.83
PRK13482352 DNA integrity scanning protein DisA; Provisional 94.74
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 94.65
smart00483 334 POLXc DNA polymerase X family. includes vertebrate 94.49
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 94.03
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 93.49
PRK08609 570 hypothetical protein; Provisional 93.07
PRK00254720 ski2-like helicase; Provisional 93.01
PRK14666694 uvrC excinuclease ABC subunit C; Provisional 92.76
PRK14670574 uvrC excinuclease ABC subunit C; Provisional 92.59
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 92.59
PF0057068 HRDC: HRDC domain Bloom syndrome. Werner syndrome. 92.44
PRK00558598 uvrC excinuclease ABC subunit C; Validated 92.43
PRK00024224 hypothetical protein; Reviewed 92.23
cd00141 307 NT_POLXc Nucleotidyltransferase (NT) domain of fam 92.22
TIGR00608218 radc DNA repair protein radc. This family is based 92.12
PF14635104 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PS 92.01
TIGR01259120 comE comEA protein. This model describes the ComEA 91.97
PRK08097562 ligB NAD-dependent DNA ligase LigB; Reviewed 91.52
PF0311866 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha 91.18
smart0027936 HhH2 Helix-hairpin-helix class 2 (Pol1 family) mot 91.17
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 90.14
PRK14351689 ligA NAD-dependent DNA ligase LigA; Provisional 89.65
PRK12766 232 50S ribosomal protein L32e; Provisional 89.26
TIGR00615 195 recR recombination protein RecR. This family is ba 88.69
PF1283665 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE 88.32
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain 88.26
PRK14350669 ligA NAD-dependent DNA ligase LigA; Provisional 88.26
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 famil 88.01
TIGR03252177 uncharacterized HhH-GPD family protein. This model 87.93
COG1796 326 POL4 DNA polymerase IV (family X) [DNA replication 86.45
PRK00076 196 recR recombination protein RecR; Reviewed 86.41
PRK14669624 uvrC excinuclease ABC subunit C; Provisional 85.88
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 85.78
TIGR00596814 rad1 DNA repair protein (rad1). This family is bas 85.55
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 85.43
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 85.3
PRK14667567 uvrC excinuclease ABC subunit C; Provisional 84.94
COG2003224 RadC DNA repair proteins [DNA replication, recombi 84.89
COG0353 198 RecR Recombinational DNA repair protein (RecF path 84.34
PRK13844 200 recombination protein RecR; Provisional 84.3
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 84.2
smart0034181 HRDC Helicase and RNase D C-terminal. Hypothetical 84.18
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 83.71
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 83.65
TIGR0195450 nusA_Cterm_rpt transcription termination factor Nu 83.4
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 83.01
PF1471668 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU 82.91
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 82.18
PRK14668577 uvrC excinuclease ABC subunit C; Provisional 81.84
COG4277404 Predicted DNA-binding protein with the Helix-hairp 80.66
PRK14668577 uvrC excinuclease ABC subunit C; Provisional 80.62
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair] Back     alignment and domain information 
Probab=99.01  E-value=1.6e-10  Score=88.69  Aligned_cols=32  Identities=38%  Similarity=0.613  Sum_probs=30.5

Q ss_pred             CCCChhHHhcCCCchHHHHHHHHHHhcccccc
Q 034973            1 MDASMEDLAGCPGIVERKVKCLYDTFHEPFKR   32 (77)
Q Consensus         1 i~AS~E~Ls~CPG~G~~KarrL~~afhePF~k   32 (77)
                      ++||+++|+.|||+||.||++||++||+||.+
T Consensus       222 ~~AS~~ele~~~G~G~~kak~l~~~l~~pf~~  253 (254)
T KOG2841|consen  222 SNASEGELEQCPGLGPAKAKRLHKFLHQPFLS  253 (254)
T ss_pred             HhcCHhHHHhCcCcCHHHHHHHHHHHhccccC
Confidence            47999999999999999999999999999975

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ] Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional Back     alignment and domain information
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>PRK14666 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK14670 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains Back     alignment and domain information
>PF00570 HRDC: HRDC domain Bloom syndrome Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>PRK00024 hypothetical protein; Reviewed Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>TIGR00608 radc DNA repair protein radc Back     alignment and domain information
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals Back     alignment and domain information
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>TIGR00615 recR recombination protein RecR Back     alignment and domain information
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>TIGR03252 uncharacterized HhH-GPD family protein Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>PRK14669 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>TIGR00596 rad1 DNA repair protein (rad1) Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14667 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13844 recombination protein RecR; Provisional Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>smart00341 HRDC Helicase and RNase D C-terminal Back     alignment and domain information
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication Back     alignment and domain information
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14668 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only] Back     alignment and domain information
>PRK14668 uvrC excinuclease ABC subunit C; Provisional 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 ?
Query77
2a1j_B91 Crystal Structure Of The Complex Between The C-Term 4e-04
1z00_A89 Solution Structure Of The C-Terminal Domain Of Ercc 4e-04
>pdb|2A1J|B Chain B, Crystal Structure Of The Complex Between The C-Terminal Domains Of Human Xpf And Ercc1 Length = 91 Back     alignment and structure 
Iteration: 1

 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/31 (54%), Positives = 22/31 (70%)
Query: 3  ASMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33
          AS EDLA CPG+  +K + L+D  HEPF +V
Sbjct: 61 ASREDLALCPGLGPQKARRLFDVLHEPFLKV 91
>pdb|1Z00|A Chain A, Solution Structure Of The C-Terminal Domain Of Ercc1 Complexed With The C-Terminal Domain Of Xpf Length = 89 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 ?
Query77
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 1e-10
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 8e-10
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Length = 91 Back     alignment and structure
 Score = 51.3 bits (123), Expect = 1e-10
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 1  MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRV 33
          + AS EDLA CPG+  +K + L+D  HEPF +V
Sbjct: 59 IAASREDLALCPGLGPQKARRLFDVLHEPFLKV 91
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Length = 89 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query77
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 97.93
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 97.91
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 97.88
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 97.72
3arc_U97 Photosystem II 12 kDa extrinsic protein; PSII, mem 97.52
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 97.29
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 97.29
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 97.11
2duy_A75 Competence protein comea-related protein; helix-ha 96.88
2i5h_A205 Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s 96.2
2duy_A75 Competence protein comea-related protein; helix-ha 95.85
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA bindi 95.83
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 95.39
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 95.25
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 95.2
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 95.11
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 95.03
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 94.84
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 94.27
3sgi_A615 DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub 93.84
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucle 93.53
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 93.51
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA bindi 93.35
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 93.03
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 92.71
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 92.59
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 92.57
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, tran 92.52
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 92.07
2rhf_A77 DNA helicase RECQ; HRDC, D. radiodurans, ATP-bindi 91.9
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 91.76
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein- 91.21
2e1f_A103 Werner syndrome ATP-dependent helicase; HRDC domai 91.19
1b22_A114 DNA repair protein RAD51; DNA binding, riken struc 91.04
1wud_A89 ATP-dependent DNA helicase RECQ; DNA-binding domai 90.76
1jms_A 381 Terminal deoxynucleotidyltransferase; polymerase; 90.76
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, trans 90.61
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein- 90.45
3bzc_A 785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 90.29
2kv2_A85 Bloom syndrome protein; HRDC domain, disease mutat 89.77
2bcq_A 335 DNA polymerase lambda; misalignment, extrahelical, 89.69
3vdp_A 212 Recombination protein RECR; zinc finger, DNA repai 89.19
1vdd_A 228 Recombination protein RECR; helix-hairpin-helix, z 88.2
3psf_A 1030 Transcription elongation factor SPT6; nucleus; 2.5 86.24
2rrd_A101 BLM HRDC domain, HRDC domain from bloom syndrome p 86.24
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 86.23
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 85.28
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 84.35
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 84.15
2dgz_A113 Werner syndrome protein variant; HRDC domain, stru 83.69
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 83.43
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 83.18
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial 82.64
3b0x_A 575 DNA polymerase beta family (X family); structural 82.43
2bcq_A 335 DNA polymerase lambda; misalignment, extrahelical, 81.92
2kp7_A87 Crossover junction endonuclease MUS81; helix-hairp 80.81
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
Probab=97.93  E-value=4.1e-06  Score=48.75  Aligned_cols=32  Identities=25%  Similarity=0.334  Sum_probs=28.9

Q ss_pred             CCChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973            2 DASMEDLAGCPGIVERKVKCLYDTFHEPFKRV   33 (77)
Q Consensus         2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~k~   33 (77)
                      .|+.++|..+||||+++|..|+..|++||...
T Consensus        42 ~a~~~~L~~i~Gig~~~a~~i~~~~~~~~~~~   73 (75)
T 1x2i_A           42 TASVAELMKVEGIGEKIAKEIRRVITAPYIED   73 (75)
T ss_dssp             HCCHHHHTTSTTCCHHHHHHHHHHHHSCCCC-
T ss_pred             hCCHHHHhcCCCCCHHHHHHHHHHHhCccccc
Confidence            47899999999999999999999999999754
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Back     alignment and structure
>3arc_U Photosystem II 12 kDa extrinsic protein; PSII, membrane-protein complex, transmembrane alpha-helix, E transport, photosynthesis; HET: OEX CLA PHO BCR PL9 SQD LMG UNL LMT HTG DGD LHG HEM; 1.90A {Thermosynechococcus vulcanus} PDB: 3bz1_U* 2axt_U* 3bz2_U* 3kzi_U* 3prq_U* 3prr_U* 3a0b_U* 3a0h_U* Back     alignment and structure
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7 Back     alignment and structure
>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1 Back     alignment and structure
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus} SCOP: a.60.2.7 Back     alignment and structure
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Back     alignment and structure
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Back     alignment and structure
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} Back     alignment and structure
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli} Back     alignment and structure
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA BIND oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans} Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Back     alignment and structure
>2e1f_A Werner syndrome ATP-dependent helicase; HRDC domain, hydrolase; 2.00A {Homo sapiens} SCOP: a.60.8.1 PDB: 2e1e_A Back     alignment and structure
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Back     alignment and structure
>1wud_A ATP-dependent DNA helicase RECQ; DNA-binding domain, HRDC, hydrolase; 2.20A {Escherichia coli} SCOP: a.60.8.1 Back     alignment and structure
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Back     alignment and structure
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A Back     alignment and structure
>2kv2_A Bloom syndrome protein; HRDC domain, disease mutation, DNA replicati binding, nucleotide-binding, nucleus, gene regulation; NMR {Homo sapiens} Back     alignment and structure
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Back     alignment and structure
>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D Back     alignment and structure
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Back     alignment and structure
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Back     alignment and structure
>2rrd_A BLM HRDC domain, HRDC domain from bloom syndrome protein; DNA helicase, RECQ family, HRDC DOMA binding protein; NMR {Homo sapiens} Back     alignment and structure
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Back     alignment and structure
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Back     alignment and structure
>2dgz_A Werner syndrome protein variant; HRDC domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.60.8.1 Back     alignment and structure
>4glx_A DNA ligase; inhibitor, ligase-ligase inhibitor-DNA complex; HET: DNA 0XS; 1.90A {Escherichia coli} Back     alignment and structure
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B Back     alignment and structure
>3b0x_A DNA polymerase beta family (X family); structural genomics, riken structural genomics/proteomics in RSGI, polxc, PHP, DRP lyase; HET: DNA DGT; 1.36A {Thermus thermophilus} PDB: 3au2_A* 3au6_A* 3auo_A* 3b0y_A* Back     alignment and structure
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Back     alignment and structure
>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} 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 77
d2a1ja162 a.60.2.5 (A:837-898) DNA repair endonuclease XPF { 7e-05
d2bgwa170 a.60.2.5 (A:160-229) DNA repair endonuclease XPF { 2e-04
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Length = 62 Back     information, alignment and structure

class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.7 bits (80), Expect = 7e-05
 Identities = 11/34 (32%), Positives = 13/34 (38%), Gaps = 1/34 (2%)

Query: 1  MDASMEDLAGCPGIVERKVKCLYDTFHEPFKRVV 34
             S ++L    G      K LYD  H  F  VV
Sbjct: 30 AALSQDELTSILGN-AANAKQLYDFIHTSFAEVV 62
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Length = 70 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 ?
Query77
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 98.85
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 98.51
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 98.43
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 98.18
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 98.08
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 97.48
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 97.14
d3bzka190 Transcriptional accessory factor Tex {Pseudomonas 96.81
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 96.6
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 96.5
d2duya165 Uncharacterized protein TTHA1967 {Thermus thermoph 96.36
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [Ta 96.27
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human 96.07
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 95.74
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 95.61
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 95.02
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 94.89
d1wuda177 HRDC domain from RecQ helicase {Escherichia coli [ 94.7
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 94.66
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 94.6
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 93.64
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 93.42
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 93.12
d2e1fa194 Werner syndrome ATP-dependent helicase, WRN {Human 93.09
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 91.32
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 90.82
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [Ta 90.4
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 89.89
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 89.83
d1xo1a1105 T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726] 89.63
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 89.34
d1vdda_ 199 Recombination protein RecR {Deinococcus radioduran 89.14
d1doqa_69 C-terminal domain of RNA polymerase alpha subunit 87.94
d2i5ha1180 Hypothetical protein AF1531 {Archaeoglobus fulgidu 86.83
d2p6ra2198 Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22 85.58
d1lb2b_72 C-terminal domain of RNA polymerase alpha subunit 85.3
d1rrqa1221 Catalytic domain of MutY {Bacillus stearothermophi 84.67
d2duya165 Uncharacterized protein TTHA1967 {Thermus thermoph 84.3
d1z3eb167 C-terminal domain of RNA polymerase alpha subunit 84.24
d1rxwa1105 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc 84.19
d1kg2a_224 Catalytic domain of MutY {Escherichia coli [TaxId: 83.75
d2bcqa176 DNA polymerase lambda {Human (Homo sapiens) [TaxId 83.46
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 83.09
d1a77a1108 Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met 80.79
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium 80.77
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=4.2e-10  Score=68.16  Aligned_cols=32  Identities=53%  Similarity=0.905  Sum_probs=30.3

Q ss_pred             CCChhHHhcCCCchHHHHHHHHHHhccccccc
Q 034973            2 DASMEDLAGCPGIVERKVKCLYDTFHEPFKRV   33 (77)
Q Consensus         2 ~AS~E~Ls~CPG~G~~KarrL~~afhePF~k~   33 (77)
                      +|+.++|..+||||+++|++|++.||+||.+.
T Consensus        47 ~A~~eeL~~i~GiG~~~A~~i~~~f~~pf~~~   78 (78)
T d2a1jb1          47 AASREDLALCPGLGPQKARRLFDVLHEPFLKV   78 (78)
T ss_dssp             SCCHHHHHTSSSCCSHHHHHHHHHHHSCSCCC
T ss_pred             hhhHHHHHHhhhhhHHHHHHHHHHHcCccccC
Confidence            69999999999999999999999999999863
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1wuda1 a.60.8.1 (A:530-606) HRDC domain from RecQ helicase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2e1fa1 a.60.8.1 (A:1142-1235) Werner syndrome ATP-dependent helicase, WRN {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1xo1a1 a.60.7.1 (A:186-290) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2i5ha1 e.71.1.1 (A:16-195) Hypothetical protein AF1531 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d2p6ra2 a.289.1.2 (A:489-686) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1rxwa1 a.60.7.1 (A:220-324) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1a77a1 a.60.7.1 (A:209-316) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Back     information, alignment and structure