Citrus Sinensis ID: 041647

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210------
MALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSRHPPIPETPSLKDVEPSSVNESALSAAFANYADKMGEKKNSSSQKQETETRIPENRSSILAKEAMAAELTHSLTMHIYRLLCPPHLDDVGGVLAITISMDSLKLHS
ccccccccccccccccccHHHcccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHcccccccHHHHHHccHHHHHHcccccHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEEEcccccccc
cccHHHHEEEHEcccccHHHHHHHccccccccHHHcccccHHHHHHHHHcccccHHHHHHHHHHHHcHcccHHHHHHccHHHHHHcccccHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEcccccccc
MALTHALTSVwsvnktdvvnlgstsgihndpEQLLRARVSLVLYLNTKRRSAKSFQRQNnllfktqsapvslSHIMDASMEdlarcpgiverKVKCLydtfhepfkpvvsrhppipetpslkdvepssvneSALSAAFANYADKmgekknsssqkqetetripenrsSILAKEAMAAELTHSLTMHIYRllcpphlddvgGVLAITISMDSLKLHS
malthaltsvwsvnktDVVNLGstsgihndpeqLLRARVSLVLYLNTKRrsaksfqrqnnllfktqsapvsLSHIMDASMEDLARCPGIVERKVKCLYDTFHEpfkpvvsrhppipetpslkdvepsSVNESALSAAFANYADKMgekknsssqkqetetripenrssiLAKEAMAAELTHSLTMHIYRLLCPPHLDDVGGVLAITISMDSLKLHS
MALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSRHPPIPETPSLKDVEPSSVNESALSAAFANYADKMGEKKNSSSQKQETETRIPENRSSILAKEAMAAELTHSLTMHIYRLLCPPHLDDVGGVLAITISMDSLKLHS
*****ALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKR**********NLLFKTQ*APVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPV******************************************************************MAAELTHSLTMHIYRLLCPPHLDDVGGVLAITISM*******
****HALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFH**************************************************************************AELTHSLTMHIYRLLCPPHLDDVGGVLAITISMDSLKL**
MALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSRHPPIPETPS**********ESALSAAFANYADKM******************ENRSSILAKEAMAAELTHSLTMHIYRLLCPPHLDDVGGVLAITISMDSLKLHS
MALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVS********************************************************SSILAKEAMAAELTHSLTMHIYRLLCPPHLDDVGGVLAITISMDS*****
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
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MALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSRHPPIPETPSLKDVEPSSVNESALSAAFANYADKMGEKKNSSSQKQETETRIPENRSSILAKEAMAAELTHSLTMHIYRLLCPPHLDDVGGVLAITISMDSLKLHS
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 ?
Query216 2.2.26 [Sep-21-2011]
Q9MA98410 DNA excision repair prote yes no 0.458 0.241 0.395 8e-22
Q1LZ75294 DNA excision repair prote yes no 0.162 0.119 0.514 0.0004
P07992297 DNA excision repair prote yes no 0.162 0.117 0.514 0.0009
>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 =  103 bits (257), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 68/172 (39%), Positives = 79/172 (45%), Gaps = 73/172 (42%)

Query: 3   LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLL 62
           L H+LTS+  VNK+DVV LGST G                                    
Sbjct: 260 LNHSLTSIRHVNKSDVVTLGSTFG------------------------------------ 283

Query: 63  FKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSRH-----PPIPE 117
                   SL+HI+DASMEDLARCPGI ERKVK LYDTFHEPFK   S +     PPIPE
Sbjct: 284 --------SLAHIIDASMEDLARCPGIGERKVKRLYDTFHEPFKRATSSYPSVVEPPIPE 335

Query: 118 TPSLKDV------------------------EPSSVNESALSAAFANYADKM 145
            P  KDV                        EP    ++ALSA FA Y+D++
Sbjct: 336 APVEKDVNSEEPVEEDEDFVEDSRKRKKKEPEPEKTVKTALSAVFARYSDRL 387
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: -
>sp|Q1LZ75|ERCC1_BOVIN DNA excision repair protein ERCC-1 OS=Bos taurus GN=ERCC1 PE=2 SV=1 Back     alignment and function description
>sp|P07992|ERCC1_HUMAN DNA excision repair protein ERCC-1 OS=Homo sapiens GN=ERCC1 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query216
449441216 391 PREDICTED: DNA excision repair protein E 0.537 0.296 0.441 4e-26
224130994 382 predicted protein [Populus trichocarpa] 0.537 0.303 0.443 1e-25
449520473 412 PREDICTED: DNA excision repair protein E 0.537 0.281 0.416 1e-25
359487720 398 PREDICTED: DNA excision repair protein E 0.560 0.304 0.426 2e-25
255542562 392 excision repair cross-complementing 1 er 0.523 0.288 0.428 6e-24
356574927264 PREDICTED: LOW QUALITY PROTEIN: DNA exci 0.564 0.462 0.411 6e-21
15229933 410 DNA excision repair protein ERCC-1 [Arab 0.458 0.241 0.395 4e-20
356533598 398 PREDICTED: DNA excision repair protein E 0.564 0.306 0.367 8e-20
357441595 401 DNA excision repair protein ERCC-1 [Medi 0.537 0.289 0.373 4e-18
297829042 407 hypothetical protein ARALYDRAFT_477808 [ 0.458 0.243 0.394 5e-18
>gi|449441216|ref|XP_004138378.1| PREDICTED: DNA excision repair protein ERCC-1-like [Cucumis sativus] Back     alignment and taxonomy information
 Score =  124 bits (310), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 83/188 (44%), Positives = 91/188 (48%), Gaps = 72/188 (38%)

Query: 3   LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLL 62
           LTH LTSV  VNKTDVV LG+T G                                    
Sbjct: 247 LTHVLTSVRHVNKTDVVTLGTTFG------------------------------------ 270

Query: 63  FKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSRHPPIPETPSLK 122
                   SLSHIMDASMEDLARCPGI ERKV+ LYDTFHEPFK VVS HP +PETP+  
Sbjct: 271 --------SLSHIMDASMEDLARCPGIGERKVRRLYDTFHEPFKRVVSTHPAVPETPTQI 322

Query: 123 DVEPSSVNE-------------------------SALSAAFANYADKMGEKKNSSSQKQE 157
             +P S NE                         SALSAAFA YADK+ +   S S  QE
Sbjct: 323 STKPRSSNEEQDVDGKRIEEDGSQHKKEPKLNVKSALSAAFAKYADKIAK---SGSIPQE 379

Query: 158 TETRIPEN 165
            E   PE+
Sbjct: 380 KEKGEPES 387

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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|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|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
>gi|356574927|ref|XP_003555594.1| PREDICTED: LOW QUALITY PROTEIN: DNA excision repair protein ERCC-1-like [Glycine max] 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|356533598|ref|XP_003535349.1| PREDICTED: DNA excision repair protein ERCC-1-like [Glycine max] 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|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

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 ?
Query216
TAIR|locus:2096329410 ERCC1 [Arabidopsis thaliana (t 0.597 0.314 0.428 1.3e-24
ZFIN|ZDB-GENE-040426-2606342 ercc1 "excision repair cross-c 0.162 0.102 0.485 0.00084
TAIR|locus:2096329 ERCC1 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 223 (83.6 bits), Expect = 1.3e-24, Sum P(2) = 1.3e-24
 Identities = 60/140 (42%), Positives = 77/140 (55%)

Query:     2 ALTHALTSVWSVNKTDVVNLGSTSGIH-NDPEQLLRARVSLVLYLNTKRRSAKSFQRQNN 60
             AL H  T + + + T+      T  ++ N P  L++ ++    YL+    S  S +  N 
Sbjct:   214 ALLHDCTLLCAWSMTECARYLETIKVYENKPADLIQGQMDTD-YLSRLNHSLTSIRHVNK 272

Query:    61 LLFKTQSAPV-SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPVVSRHP-----P 114
                 T  +   SL+HI+DASMEDLARCPGI ERKVK LYDTFHEPFK   S +P     P
Sbjct:   273 SDVVTLGSTFGSLAHIIDASMEDLARCPGIGERKVKRLYDTFHEPFKRATSSYPSVVEPP 332

Query:   115 IPETPSLKDV---EPSSVNE 131
             IPE P  KDV   EP   +E
Sbjct:   333 IPEAPVEKDVNSEEPVEEDE 352
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
ZFIN|ZDB-GENE-040426-2606 ercc1 "excision repair cross-complementing rodent repair deficiency, complementation group 1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

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 216
KOG2841254 consensus Structure-specific endonuclease ERCC1-XP 99.71
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 99.0
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 98.58
PRK14670574 uvrC excinuclease ABC subunit C; Provisional 98.23
PRK13482352 DNA integrity scanning protein DisA; Provisional 98.22
PRK12766232 50S ribosomal protein L32e; Provisional 98.13
PRK13766773 Hef nuclease; Provisional 98.11
PRK00558598 uvrC excinuclease ABC subunit C; Validated 98.03
PRK14666694 uvrC excinuclease ABC subunit C; Provisional 97.96
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recomb 97.93
PRK14669624 uvrC excinuclease ABC subunit C; Provisional 97.87
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 97.72
PRK14672691 uvrC excinuclease ABC subunit C; Provisional 97.67
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 97.66
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 97.64
COG5241224 RAD10 Nucleotide excision repair endonuclease NEF1 97.57
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 97.52
TIGR00596814 rad1 DNA repair protein (rad1). This family is bas 97.49
PRK00254720 ski2-like helicase; Provisional 97.34
PRK14351689 ligA NAD-dependent DNA ligase LigA; Provisional 97.26
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain 96.5
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 96.18
PRK14350669 ligA NAD-dependent DNA ligase LigA; Provisional 96.1
COG1623349 Predicted nucleic-acid-binding protein (contains t 96.08
PRK00024224 hypothetical protein; Reviewed 96.04
TIGR00608218 radc DNA repair protein radc. This family is based 95.97
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 95.9
TIGR01259120 comE comEA protein. This model describes the ComEA 95.87
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 95.83
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 95.79
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 95.78
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 95.74
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 95.61
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 95.46
PRK08097562 ligB NAD-dependent DNA ligase LigB; Reviewed 95.43
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 95.42
TIGR01259120 comE comEA protein. This model describes the ComEA 95.23
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 95.08
TIGR02236 310 recomb_radA DNA repair and recombination protein R 94.69
COG2003224 RadC DNA repair proteins [DNA replication, recombi 94.39
PRK02515132 psbU photosystem II complex extrinsic protein prec 94.35
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 93.98
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 93.2
PF0311866 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha cha 92.89
PRK04301 317 radA DNA repair and recombination protein RadA; Va 92.87
PRK14667567 uvrC excinuclease ABC subunit C; Provisional 92.42
COG1555149 ComEA DNA uptake protein and related DNA-binding p 91.5
PF1283665 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE 91.45
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 91.11
TIGR01448 720 recD_rel helicase, putative, RecD/TraA family. Thi 90.9
KOG0442892 consensus Structure-specific endonuclease ERCC1-XP 90.27
TIGR0195450 nusA_Cterm_rpt transcription termination factor Nu 89.63
PRK14668577 uvrC excinuclease ABC subunit C; Provisional 87.63
PRK08609 570 hypothetical protein; Provisional 87.34
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 87.28
PRK01172674 ski2-like helicase; Provisional 82.49
smart00483 334 POLXc DNA polymerase X family. includes vertebrate 81.69
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair] Back     alignment and domain information 
Probab=99.71  E-value=5.3e-18  Score=148.52  Aligned_cols=62  Identities=40%  Similarity=0.522  Sum_probs=59.9

Q ss_pred             cccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHh
Q 041647            2 ALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASME   81 (216)
Q Consensus         2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~E   81 (216)
                      ++.++||+|+||||||++.||.+||                                            ||++|.+||++
T Consensus       192 ~~~~~Lt~i~~VnKtda~~LL~~Fg--------------------------------------------sLq~~~~AS~~  227 (254)
T KOG2841|consen  192 SLLGFLTTIPGVNKTDAQLLLQKFG--------------------------------------------SLQQISNASEG  227 (254)
T ss_pred             HHHHHHHhCCCCCcccHHHHHHhcc--------------------------------------------cHHHHHhcCHh
Confidence            4678999999999999999999999                                            99999999999


Q ss_pred             hhccCCCCcHHHHHHHHHHhcCCCCC
Q 041647           82 DLARCPGIVERKVKCLYDTFHEPFKP  107 (216)
Q Consensus        82 dLA~cPGig~~Kvk~L~d~fhePF~~  107 (216)
                      ||++|||+|++||++||++||+||.+
T Consensus       228 ele~~~G~G~~kak~l~~~l~~pf~~  253 (254)
T KOG2841|consen  228 ELEQCPGLGPAKAKRLHKFLHQPFLS  253 (254)
T ss_pred             HHHhCcCcCHHHHHHHHHHHhccccC
Confidence            99999999999999999999999986

>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B 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
>PRK14670 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>PRK14666 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK14669 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>PRK14672 uvrC excinuclease ABC subunit C; Provisional 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
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>TIGR00596 rad1 DNA repair protein (rad1) Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional 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
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only] Back     alignment and domain information
>PRK00024 hypothetical protein; Reviewed Back     alignment and domain information
>TIGR00608 radc DNA repair protein radc Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14602 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
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA Back     alignment and domain information
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 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
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>PRK14667 uvrC excinuclease ABC subunit C; Provisional 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
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>TIGR01448 recD_rel helicase, putative, RecD/TraA family Back     alignment and domain information
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair] Back     alignment and domain information
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication Back     alignment and domain information
>PRK14668 uvrC excinuclease ABC subunit C; Provisional Back     alignment and domain information
>PRK08609 hypothetical protein; 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
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family 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 ?
Query216
1z00_A89 Solution Structure Of The C-Terminal Domain Of Ercc 9e-05
2a1j_B91 Crystal Structure Of The Complex Between The C-Term 9e-05
>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 
Iteration: 1

 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 25/38 (65%)
Query: 71  SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPV 108
           SL  ++ AS EDLA CPG+  +K + L+D  HEPF  V
Sbjct: 41  SLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKV 78
>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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query216
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 5e-12
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 4e-11
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 1e-04
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 2e-04
>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 = 58.7 bits (142), Expect = 5e-12
 Identities = 32/106 (30%), Positives = 41/106 (38%), Gaps = 44/106 (41%)

Query: 3   LTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLL 62
           +T  LT+V SVNKTD   L +T G                                    
Sbjct: 30  VTECLTTVKSVNKTDSQTLLTTFG------------------------------------ 53

Query: 63  FKTQSAPVSLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFKPV 108
                   SL  ++ AS EDLA CPG+  +K + L+D  HEPF  V
Sbjct: 54  --------SLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKV 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
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Length = 75 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 Length = 219 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query216
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 99.2
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 99.13
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 99.09
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 99.04
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 98.9
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 98.85
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 98.72
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 98.15
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 98.04
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 98.04
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 97.91
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 97.71
3sgi_A615 DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tub 97.53
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 97.47
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein- 97.35
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 97.14
2duy_A75 Competence protein comea-related protein; helix-ha 97.02
4gfj_A685 Topoisomerase V; helix-hairpin-helix, DNA repair e 96.6
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA bindi 96.28
1wcn_A70 Transcription elongation protein NUSA; RNA-binding 95.99
3arc_U97 Photosystem II 12 kDa extrinsic protein; PSII, mem 95.87
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 95.2
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucle 95.11
2w9m_A 578 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 95.04
2duy_A75 Competence protein comea-related protein; helix-ha 95.0
3b0x_A 575 DNA polymerase beta family (X family); structural 94.4
1b22_A114 DNA repair protein RAD51; DNA binding, riken struc 94.21
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA bindi 93.66
1u9l_A70 Transcription elongation protein NUSA; escherichia 93.38
3arc_U97 Photosystem II 12 kDa extrinsic protein; PSII, mem 92.89
2i5h_A205 Hypothetical protein AF1531; PFAM:DUF655, PSI-2, s 89.93
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse 89.76
1wud_A89 ATP-dependent DNA helicase RECQ; DNA-binding domai 89.62
2ziu_A311 MUS81 protein; helix-hairpin-helix, alternative sp 88.68
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 88.48
2h56_A233 DNA-3-methyladenine glycosidase; 10174367, EC 3.2. 86.2
2e1f_A103 Werner syndrome ATP-dependent helicase; HRDC domai 86.07
4b21_A232 Probable DNA-3-methyladenine glycosylase 2; hydrol 85.81
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 85.58
2i1q_A 322 DNA repair and recombination protein RADA; ATPase, 85.19
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 84.59
2kv2_A85 Bloom syndrome protein; HRDC domain, disease mutat 83.66
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 83.51
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 83.18
2rhf_A77 DNA helicase RECQ; HRDC, D. radiodurans, ATP-bindi 82.88
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial 82.22
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 81.03
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, tran 81.0
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fo 80.74
3s6i_A228 DNA-3-methyladenine glycosylase 1; DNA glycosylase 80.18
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 80.14
>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
Probab=99.20  E-value=5.7e-12  Score=86.50  Aligned_cols=60  Identities=23%  Similarity=0.303  Sum_probs=56.4

Q ss_pred             cccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHhhh
Q 041647            4 THALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASMEDL   83 (216)
Q Consensus         4 t~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~EdL   83 (216)
                      .+.|++|+||++++...|+.+||                                            |+++|..||.|||
T Consensus         3 ~s~L~~IpGIG~kr~~~LL~~Fg--------------------------------------------s~~~i~~As~eeL   38 (63)
T 2a1j_A            3 QDFLLKMPGVNAKNCRSLMHHVK--------------------------------------------NIAELAALSQDEL   38 (63)
T ss_dssp             CHHHHTSTTCCHHHHHHHHHHCS--------------------------------------------SHHHHHTCCHHHH
T ss_pred             HhHHHcCCCCCHHHHHHHHHHcC--------------------------------------------CHHHHHHCCHHHH
Confidence            46789999999999999999999                                            9999999999999


Q ss_pred             ccCCCCcHHH-HHHHHHHhcCCCCCCC
Q 041647           84 ARCPGIVERK-VKCLYDTFHEPFKPVV  109 (216)
Q Consensus        84 A~cPGig~~K-vk~L~d~fhePF~~~~  109 (216)
                      +.+  ||..+ |+.||+.||+||.+.|
T Consensus        39 ~~v--ig~~~~A~~I~~~l~~~~~~~~   63 (63)
T 2a1j_A           39 TSI--LGNAANAKQLYDFIHTSFAEVV   63 (63)
T ss_dssp             HHH--HSCHHHHHHHHHHHHCCCCCCC
T ss_pred             HHH--cCchHHHHHHHHHHhccccccC
Confidence            999  88999 9999999999998753
>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
>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
>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
>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
>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
>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
>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
>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
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} 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
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis} 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
>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
>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
>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
>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19} 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
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B 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
>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
>2w9m_A Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} 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
>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
>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
>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
>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_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
>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
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A 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
>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_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
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc genomics, PSI-2, protein structure initiative, joint center structural genomics; 2.55A {Bacillus halodurans} 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
>4b21_A Probable DNA-3-methyladenine glycosylase 2; hydrolase-DNA complex, helix-hairpin-helix; HET: BGC 3DR; 1.45A {Schizosaccharomyces pombe} PDB: 4b22_A* 4b23_A* 4b24_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
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A* 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
>2kv2_A Bloom syndrome protein; HRDC domain, disease mutation, DNA replicati binding, nucleotide-binding, nucleus, gene regulation; NMR {Homo sapiens} 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
>2rhf_A DNA helicase RECQ; HRDC, D. radiodurans, ATP-binding, hydrolase nucleotide-binding; HET: DNA; 1.10A {Deinococcus radiodurans} 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
>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
>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
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Back     alignment and structure
>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair, helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF); HET: 3DR; 2.28A {Schizosaccharomyces pombe} 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

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 216
d2bgwa170 a.60.2.5 (A:160-229) DNA repair endonuclease XPF { 2e-05
d2a1ja162 a.60.2.5 (A:837-898) DNA repair endonuclease XPF { 5e-05
d1x2ia168 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF201 0.001
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Length = 70 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: Aeropyrum pernix [TaxId: 56636]

 Score = 39.4 bits (92), Expect = 2e-05
 Identities = 9/36 (25%), Positives = 18/36 (50%)

Query: 71  SLSHIMDASMEDLARCPGIVERKVKCLYDTFHEPFK 106
           SL     AS  ++++  GI E++ + +      P+K
Sbjct: 35  SLERFFTASKAEISKVEGIGEKRAEEIKKILMTPYK 70
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Length = 62 Back     information, alignment and structure
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 68 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 ?
Query216
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 99.63
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 99.38
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 99.36
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 99.34
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 99.32
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 98.64
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 98.52
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 98.3
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 97.28
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 96.72
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human 96.66
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 96.57
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 96.44
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 95.62
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [Ta 93.23
d3bzka190 Transcriptional accessory factor Tex {Pseudomonas 92.53
d2duya165 Uncharacterized protein TTHA1967 {Thermus thermoph 91.78
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 90.61
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 90.4
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 90.15
d1doqa_69 C-terminal domain of RNA polymerase alpha subunit 88.94
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 88.85
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 88.58
d1lb2b_72 C-terminal domain of RNA polymerase alpha subunit 88.56
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 86.87
d1wuda177 HRDC domain from RecQ helicase {Escherichia coli [ 86.74
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 86.62
d1z3eb167 C-terminal domain of RNA polymerase alpha subunit 86.57
d2noha1190 8-oxoguanine glycosylase {Human (Homo sapiens) [Ta 85.68
d2csba355 Topoisomerase V {Methanopyrus kandleri [TaxId: 232 85.59
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 84.56
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 82.71
d2e1fa194 Werner syndrome ATP-dependent helicase, WRN {Human 82.01
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [Ta 80.55
>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=99.63  E-value=6.5e-17  Score=112.86  Aligned_cols=63  Identities=51%  Similarity=0.722  Sum_probs=60.4

Q ss_pred             cccccccccCCcChhhHHHHHhhcCCCCChHHHHHHHHHHHHhhhhhccchhhhhhhhhhhhccccchhcHHHHHhCCHh
Q 041647            2 ALTHALTSVWSVNKTDVVNLGSTSGIHNDPEQLLRARVSLVLYLNTKRRSAKSFQRQNNLLFKTQSAPVSLSHIMDASME   81 (216)
Q Consensus         2 ~lt~aLTsV~sVNKTDv~nLlstfG~~~dpeql~~~~~~l~~~l~t~rr~a~~~~~~nn~~~~~~s~~~SL~~Im~AS~E   81 (216)
                      ++.++|++|+||+++++..|+.+||                                            |+++|++|+.|
T Consensus        16 ~~~~~L~~I~gIg~~~a~~L~~~F~--------------------------------------------s~~~i~~A~~e   51 (78)
T d2a1jb1          16 RVTECLTTVKSVNKTDSQTLLTTFG--------------------------------------------SLEQLIAASRE   51 (78)
T ss_dssp             HHHHHHTTSTTCCHHHHHHHHHHHS--------------------------------------------SHHHHHSCCHH
T ss_pred             HHHHHhcCCCCcCHHHHHHHHHHhC--------------------------------------------CcHHHHhhhHH
Confidence            4678899999999999999999999                                            99999999999


Q ss_pred             hhccCCCCcHHHHHHHHHHhcCCCCCC
Q 041647           82 DLARCPGIVERKVKCLYDTFHEPFKPV  108 (216)
Q Consensus        82 dLA~cPGig~~Kvk~L~d~fhePF~~~  108 (216)
                      ||+.|||||+.||+.|++.||+||.++
T Consensus        52 eL~~i~GiG~~~A~~i~~~f~~pf~~~   78 (78)
T d2a1jb1          52 DLALCPGLGPQKARRLFDVLHEPFLKV   78 (78)
T ss_dssp             HHHTSSSCCSHHHHHHHHHHHSCSCCC
T ss_pred             HHHHhhhhhHHHHHHHHHHHcCccccC
Confidence            999999999999999999999999875
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} 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
>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} 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
>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
>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
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} 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
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} 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
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} 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
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} 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
>d3bzka1 a.60.2.6 (A:474-563) Transcriptional accessory factor Tex {Pseudomonas aeruginosa [TaxId: 287]} 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
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} 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
>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
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} 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
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d1wuda1 a.60.8.1 (A:530-606) HRDC domain from RecQ helicase {Escherichia coli [TaxId: 562]} 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
>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
>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2csba3 a.60.2.4 (A:410-464) Topoisomerase V {Methanopyrus kandleri [TaxId: 2320]} 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
>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
>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure