Citrus Sinensis ID: 045823

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-------220-------230---
KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPGIGERKHVVSSHPPIPETPSQKDVEPSSVNEVTEVEKDAEDVNKRRKKELELTVKSALSAAFSKYADKMGKKKNTLSAEVGETSASNSGAKNSDSGKRDS
cccccccccccccEEEccccccEEEcccEEEEEEEEEEEEcccHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHccccccccccccHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccc
cccHHHHHHccccccHccccccEEEccccEEEEEEEEHccccHHHHHHHEEEEcccccHHHHHHHccccHHHHHHHHHHHHHHHcccHHHHHHHccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccccccEEEEcccccccccccHccccccccccccccccccHHccccccccccHHHHHHHHHHHHHHHHHHHcccccHHHHccccccccccccccccccccc
kgnpllkhITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFStfgtsscleswsnfsQEECGRYLETIKvyenkpadltqgqmdTDYLSRLTHALTSvrsvnktdvvnlgstfgedlshcpgigerkhvvsshppipetpsqkdvepssvnevteveKDAEDVNKRRKKELELTVKSALSAAFSKYADKMGKKKNTLSaevgetsasnsgaknsdsgkrds
kgnpllkhITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALtsvrsvnktDVVNLGSTFGEDLSHCPGIGERKHVVSSHPPipetpsqkdvepssvnevtevekdaedvnkrrkkeleltvKSALSAAFSKYADKMGKKKNTLsaevgetsasnsgaknsdsgkrds
KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPGIGERKHVVSSHPPIPETPSQKDVEPSSVNEVTEVEKDAEDVNKRRKKELELTVKSALSAAFSKYADKMGKKKNTLSAEVGETSASNSGAKNSDSGKRDS
****LLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPG***************************************************************************************************
KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADL*******DYLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPGIGERKHVVSSHP***************************************************************************************
KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPGIGERK************************************NKRRKKELELTVKSALSAAFSKYADKMGKKKN**************************
*GNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPGIGERKHVVSSH****************************************************************************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLNLLFDNVLLWVFSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPGIGERKHVVSSHPPIPETPSQKDVEPSSVNEVTEVEKDAEDVNKRRKKELELTVKSALSAAFSKYADKMGKKKNTLSAEVGETSASNSGAKNSDSGKRDS
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 ?
Query233 2.2.26 [Sep-21-2011]
Q9MA98410 DNA excision repair prote yes no 0.849 0.482 0.498 3e-53
P07992297 DNA excision repair prote no no 0.583 0.457 0.378 5e-25
Q1LZ75294 DNA excision repair prote yes no 0.583 0.462 0.384 8e-25
P07903298 DNA excision repair prote yes no 0.583 0.456 0.372 6e-24
Q06182252 Mating-type switching pro yes no 0.527 0.488 0.344 6e-16
>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 =  208 bits (529), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 130/261 (49%), Positives = 152/261 (58%), Gaps = 63/261 (24%)

Query: 1   KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLN---LLF------------ 45
           KGNPLLKHI  V+W F+D++ DY+LGQNSCALYL L  + L+   L F            
Sbjct: 133 KGNPLLKHIRNVKWVFSDIIPDYVLGQNSCALYLSLRYHLLHPDYLYFRIRELQKNFKLS 192

Query: 46  ---------DNV--LLWVFSTFGTSSC--LESWSNFSQEECGRYLETIKVYENKPADLTQ 92
                    D V  LL V  T     C  L +WS     EC RYLETIKVYENKPADL Q
Sbjct: 193 VVLCHVDVEDTVKPLLEVTKTALLHDCTLLCAWS---MTECARYLETIKVYENKPADLIQ 249

Query: 93  GQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGER---- 138
           GQMDTDYLSRL H+LTS+R VNK+DVV LGSTFG          EDL+ CPGIGER    
Sbjct: 250 GQMDTDYLSRLNHSLTSIRHVNKSDVVTLGSTFGSLAHIIDASMEDLARCPGIGERKVKR 309

Query: 139 ---------KHVVSSH-----PPIPETPSQKDVEPSSVNEVTEVEKDAEDVNKRRKKELE 184
                    K   SS+     PPIPE P +KDV  +S   V E E   ED  KR+KKE E
Sbjct: 310 LYDTFHEPFKRATSSYPSVVEPPIPEAPVEKDV--NSEEPVEEDEDFVEDSRKRKKKEPE 367

Query: 185 L--TVKSALSAAFSKYADKMG 203
              TVK+ALSA F++Y+D++ 
Sbjct: 368 PEKTVKTALSAVFARYSDRLS 388
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|P07992|ERCC1_HUMAN DNA excision repair protein ERCC-1 OS=Homo sapiens GN=ERCC1 PE=1 SV=1 Back     alignment and function description
>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|P07903|ERCC1_MOUSE DNA excision repair protein ERCC-1 OS=Mus musculus GN=Ercc1 PE=2 SV=2 Back     alignment and function description
>sp|Q06182|SWI10_SCHPO Mating-type switching protein swi10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=swi10 PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query233
255542562 392 excision repair cross-complementing 1 er 0.969 0.576 0.551 3e-65
224130994 382 predicted protein [Populus trichocarpa] 0.922 0.562 0.553 9e-62
449441216 391 PREDICTED: DNA excision repair protein E 0.935 0.557 0.521 4e-59
356533598 398 PREDICTED: DNA excision repair protein E 0.918 0.537 0.516 5e-59
359487720 398 PREDICTED: DNA excision repair protein E 0.969 0.567 0.531 7e-59
449520473 412 PREDICTED: DNA excision repair protein E 0.862 0.487 0.535 4e-58
357441595 401 DNA excision repair protein ERCC-1 [Medi 0.866 0.503 0.490 6e-54
356574927264 PREDICTED: LOW QUALITY PROTEIN: DNA exci 0.815 0.719 0.515 3e-52
15229933 410 DNA excision repair protein ERCC-1 [Arab 0.849 0.482 0.498 1e-51
297829042 407 hypothetical protein ARALYDRAFT_477808 [ 0.849 0.486 0.501 1e-47
>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 =  253 bits (647), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 156/283 (55%), Positives = 176/283 (62%), Gaps = 57/283 (20%)

Query: 1   KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFL--NLLFDNV---------- 48
           KGNPLLKHI  VRWAFADVVCDYLLGQN C+LYL L  + L  + L+  +          
Sbjct: 110 KGNPLLKHIRNVRWAFADVVCDYLLGQNCCSLYLSLRYHLLHPDYLYYRIRELQKNYKLR 169

Query: 49  --------------LLWVFSTFGTSSC--LESWSNFSQEECGRYLETIKVYENKPADLTQ 92
                         LL V  T     C  L +WS    EECGRYLETIK+YENKPADL Q
Sbjct: 170 VVLCHVDVEDVVKPLLEVTKTALLHDCTLLCAWS---LEECGRYLETIKMYENKPADLIQ 226

Query: 93  GQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGER---- 138
           GQMDTDYLSRLTHALT++R VNKTDVV LGSTFG          EDL+ CPGIGER    
Sbjct: 227 GQMDTDYLSRLTHALTTIRHVNKTDVVTLGSTFGSLSNIMDASMEDLARCPGIGERKVKR 286

Query: 139 ---------KHVVSSHPPIPETPSQKDVEPSSVNEVTEVEKDAEDVNKRRKKELELTVKS 189
                    K VVSSHP +PET SQKD EP+ V+EVTEV K   D +K RKKE ELTVKS
Sbjct: 287 LYDTFHEPFKRVVSSHPAVPET-SQKDSEPALVDEVTEVGKGEYDESKWRKKEPELTVKS 345

Query: 190 ALSAAFSKYADKMGKKKNTLSAE-VGETSAS-NSGAKNSDSGK 230
           ALSAAFSKYA+   K+ +    E  GETS S  +G  N + G+
Sbjct: 346 ALSAAFSKYANTFVKRTDKSEGENAGETSCSVETGTDNRNPGE 388

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|449441216|ref|XP_004138378.1| PREDICTED: DNA excision repair protein ERCC-1-like [Cucumis sativus] 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|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|449520473|ref|XP_004167258.1| PREDICTED: DNA excision repair protein ERCC-1-like [Cucumis sativus] 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|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|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 ?
Query233
TAIR|locus:2096329410 ERCC1 [Arabidopsis thaliana (t 0.442 0.251 0.584 2.2e-40
UNIPROTKB|B3KRR0225 ERCC1 "cDNA FLJ34720 fis, clon 0.309 0.32 0.512 3.1e-26
UNIPROTKB|K7ES46209 ERCC1 "DNA excision repair pro 0.309 0.344 0.512 3.1e-26
UNIPROTKB|P07992297 ERCC1 "DNA excision repair pro 0.309 0.242 0.512 3.1e-26
UNIPROTKB|Q6UIQ5251 ERCC1 "Excision repair protein 0.309 0.286 0.512 3.1e-26
UNIPROTKB|Q1LZ75294 ERCC1 "DNA excision repair pro 0.309 0.244 0.524 5.1e-26
UNIPROTKB|F1PPD0323 ERCC1 "Uncharacterized protein 0.309 0.222 0.512 1.5e-25
MGI|MGI:95412298 Ercc1 "excision repair cross-c 0.309 0.241 0.512 2.9e-25
UNIPROTKB|Q9QYP5293 ERCC1 "ERCC1 protein" [Cricetu 0.309 0.245 0.512 4.6e-25
RGD|1306992298 Ercc1 "excision repair cross-c 0.309 0.241 0.512 6e-25
TAIR|locus:2096329 ERCC1 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 294 (108.6 bits), Expect = 2.2e-40, Sum P(2) = 2.2e-40
 Identities = 69/118 (58%), Positives = 77/118 (65%)

Query:    68 FSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG- 126
             +S  EC RYLETIKVYENKPADL QGQMDTDYLSRL H+LTS+R VNK+DVV LGSTFG 
Sbjct:   225 WSMTECARYLETIKVYENKPADLIQGQMDTDYLSRLNHSLTSIRHVNKSDVVTLGSTFGS 284

Query:   127 ---------EDLSHCPGIGERK--HVVSS-HPPIPE-TPSQKDVEPSSVNEVTEVEKD 171
                      EDL+ CPGIGERK   +  + H P    T S   V    + E   VEKD
Sbjct:   285 LAHIIDASMEDLARCPGIGERKVKRLYDTFHEPFKRATSSYPSVVEPPIPEAP-VEKD 341
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|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|K7ES46 ERCC1 "DNA excision repair protein ERCC-1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|P07992 ERCC1 "DNA excision repair protein ERCC-1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q6UIQ5 ERCC1 "Excision repair protein" [Pan troglodytes (taxid:9598)] Back     alignment and assigned GO terms
UNIPROTKB|Q1LZ75 ERCC1 "DNA excision repair protein ERCC-1" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1PPD0 ERCC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:95412 Ercc1 "excision repair cross-complementing rodent repair deficiency, complementation group 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|Q9QYP5 ERCC1 "ERCC1 protein" [Cricetulus griseus (taxid:10029)] Back     alignment and assigned GO terms
RGD|1306992 Ercc1 "excision repair cross-complementing rodent repair deficiency, complementation group 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query233
pfam0383468 pfam03834, Rad10, Binding domain of DNA repair pro 3e-10
TIGR00597112 TIGR00597, rad10, DNA repair protein rad10 6e-08
COG5241224 COG5241, RAD10, Nucleotide excision repair endonuc 6e-07
>gnl|CDD|190768 pfam03834, Rad10, Binding domain of DNA repair protein Ercc1 (rad10/Swi10) Back     alignment and domain information 
 Score = 54.5 bits (132), Expect = 3e-10
 Identities = 19/36 (52%), Positives = 27/36 (75%)

Query: 1  KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRL 36
          KGNPLLKH+  V W ++D+V DY++G+  C L+L L
Sbjct: 10 KGNPLLKHLKNVPWEYSDIVPDYVVGKTRCVLFLSL 45

Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex. Length = 68
>gnl|CDD|129685 TIGR00597, rad10, DNA repair protein rad10 Back     alignment and domain information
>gnl|CDD|227566 COG5241, RAD10, Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 233
KOG2841254 consensus Structure-specific endonuclease ERCC1-XP 100.0
TIGR00597112 rad10 DNA repair protein rad10. All proteins in th 100.0
COG5241224 RAD10 Nucleotide excision repair endonuclease NEF1 99.96
PF0383469 Rad10: Binding domain of DNA repair protein Ercc1 99.88
PRK13766773 Hef nuclease; Provisional 98.62
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recomb 97.11
TIGR00596814 rad1 DNA repair protein (rad1). This family is bas 96.61
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 96.6
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 96.48
COG5241224 RAD10 Nucleotide excision repair endonuclease NEF1 95.84
PRK13482352 DNA integrity scanning protein DisA; Provisional 95.22
KOG0442892 consensus Structure-specific endonuclease ERCC1-XP 87.74
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 87.4
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 86.92
PRK12766232 50S ribosomal protein L32e; Provisional 86.9
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 86.43
COG1796 326 POL4 DNA polymerase IV (family X) [DNA replication 86.42
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 85.83
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 85.19
TIGR01259120 comE comEA protein. This model describes the ComEA 84.73
PRK14666694 uvrC excinuclease ABC subunit C; Provisional 84.54
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 83.23
PRK00558598 uvrC excinuclease ABC subunit C; Validated 83.19
PRK02515132 psbU photosystem II complex extrinsic protein prec 82.54
PF1283665 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE 81.14
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair] Back     alignment and domain information 
Probab=100.00  E-value=3e-52  Score=370.22  Aligned_cols=147  Identities=44%  Similarity=0.710  Sum_probs=140.6

Q ss_pred             CCCccccccccCceeec-ccccceeecCceeEEEEeehhHHH---------hhhhHHH-----------------HHHHH
Q 045823            1 KGNPLLKHITYVRWAFA-DVVCDYLLGQNSCALYLRLCIYFL---------NLLFDNV-----------------LLWVF   53 (233)
Q Consensus         1 kGNPLLk~IrnVpwEy~-dIvpDYviG~t~cvLFLSLKYH~L---------q~L~k~y-----------------L~ELt   53 (233)
                      ||||||+|||||+|+|+ ||+|||++|+++||||||||||.|         +.|+++|                 |+||+
T Consensus        65 kGNplLk~vrnv~w~f~ddi~PDf~lg~~~cvLyLSl~yH~l~pdYi~~Ri~~l~k~yk~~VLl~~vd~~e~~~~l~el~  144 (254)
T KOG2841|consen   65 KGNPLLKHVRNVKWEFGDDIIPDFVLGRGCCVLYLSLKYHKLHPDYIYRRIRKLGKNYKLRVLLVHVDMEEPYKPLLELT  144 (254)
T ss_pred             ccChHHHHHhcCCeEecCCCCcceEecCceEEEEeehHhhhcCcHHHHHHHHHhcccccceEEEEEecCcchHHHHHHHH
Confidence            79999999999999998 899999999999999999999999         3455565                 99999


Q ss_pred             HHHhhccc--ccccCCCCHHHHHHHHHHHHhhcCCCcccccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh-----
Q 045823           54 STFGTSSC--LESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG-----  126 (233)
Q Consensus        54 ~~c~~~~~--IlAW~~~S~EEAArYLEt~K~yEnk~~d~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG-----  126 (233)
                      ++|++++|  +|||   |.||||+|||+||.||++|+|+|+++.+.||++++..+||+||+||||||.+||.+||     
T Consensus       145 k~~~l~~~Tl~lA~---s~EeaaryIE~~k~~ek~p~dli~~~~~~d~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~  221 (254)
T KOG2841|consen  145 KTCDLNDVTLVLAW---SMEEAARYIETYKEYEKKPIDLIMERKDRDLLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQI  221 (254)
T ss_pred             HHHHhhceeeeeec---cHHHHHHHHHHHHHhhcCCchhhhhcccccHHHHHHHHHHhCCCCCcccHHHHHHhcccHHHH
Confidence            99999999  9999   9999999999999999999999999999999999999999999999999999999999     


Q ss_pred             -----hhccCCCCCcchh----hhhcCCCCCCC
Q 045823          127 -----EDLSHCPGIGERK----HVVSSHPPIPE  150 (233)
Q Consensus       127 -----EeLs~cPGiG~kK----~~v~~~PFi~~  150 (233)
                           ++|+.|||+||.|    +.+|++||..+
T Consensus       222 ~~AS~~ele~~~G~G~~kak~l~~~l~~pf~~~  254 (254)
T KOG2841|consen  222 SNASEGELEQCPGLGPAKAKRLHKFLHQPFLSN  254 (254)
T ss_pred             HhcCHhHHHhCcCcCHHHHHHHHHHHhccccCC
Confidence                 9999999999999    78999999753

>TIGR00597 rad10 DNA repair protein rad10 Back     alignment and domain information
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs) Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00596 rad1 DNA repair protein (rad1) Back     alignment and domain information
>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
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional 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
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>PRK14666 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
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional 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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query233
2a1i_A146 Crystal Structure Of The Central Domain Of Human Er 1e-11
2jpd_A135 Solution Structure Of The Ercc1 Central Domain Leng 4e-10
2a1j_B91 Crystal Structure Of The Complex Between The C-Term 4e-09
1z00_A89 Solution Structure Of The C-Terminal Domain Of Ercc 3e-08
2jnw_A133 Solution Structure Of A Ercc1-Xpa Heterodimer Lengt 5e-07
>pdb|2A1I|A Chain A, Crystal Structure Of The Central Domain Of Human Ercc1 Length = 146 Back     alignment and structure 
Iteration: 1

 Score = 66.2 bits (160), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 42/123 (34%), Positives = 58/123 (47%), Gaps = 31/123 (25%)
Query: 1   KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFL--------------NLLFD 46
           +GNP+LK +  V W F DV+ DY+LGQ++CAL+L L  + L              N    
Sbjct: 27  RGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALR 86
Query: 47  NVLLWV--------------FSTFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQ 92
            +L+ V                     + + +W   S EE GRYLET K YE KPADL  
Sbjct: 87  VLLVQVDVKDPQQALKELAKMCILADCTLILAW---SPEEAGRYLETYKAYEQKPADLLM 143
Query: 93  GQM 95
            ++
Sbjct: 144 EKL 146
>pdb|2JPD|A Chain A, Solution Structure Of The Ercc1 Central Domain Length = 135 Back     alignment and structure
>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
>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
>pdb|2JNW|A Chain A, Solution Structure Of A Ercc1-Xpa Heterodimer Length = 133 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 ?
Query233
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 3e-21
2a1i_A146 DNA excision repair protein ERCC-1; XPF, central d 3e-20
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 5e-17
3lvg_D190 LCB, clathrin light chain B; SELF assembly, coated 2e-05
>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 = 83.3 bits (206), Expect = 3e-21
 Identities = 29/69 (42%), Positives = 42/69 (60%), Gaps = 10/69 (14%)

Query: 81  KVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLS 130
             +   PADL   +++ D++SR+T  LT+V+SVNKTD   L +TFG          EDL+
Sbjct: 8   HHHSQDPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLA 67

Query: 131 HCPGIGERK 139
            CPG+G +K
Sbjct: 68  LCPGLGPQK 76
>2a1i_A DNA excision repair protein ERCC-1; XPF, central domain, DNA repair, endonuclease, DNA binding protein; HET: DNA; 1.90A {Homo sapiens} SCOP: c.52.1.20 PDB: 2jnw_A* 2jpd_A* Length = 146 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 Length = 89 Back     alignment and structure
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query233
2a1i_A146 DNA excision repair protein ERCC-1; XPF, central d 100.0
2bgw_A219 XPF endonuclease; hydrolase, structure specific en 99.8
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 98.62
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 98.61
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 98.16
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 96.59
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 95.82
2duy_A75 Competence protein comea-related protein; helix-ha 92.55
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 91.14
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-bindin 90.25
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 89.64
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA bindi 88.42
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 87.46
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 87.25
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucle 86.13
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 85.74
3arc_U97 Photosystem II 12 kDa extrinsic protein; PSII, mem 84.54
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 81.9
>2a1i_A DNA excision repair protein ERCC-1; XPF, central domain, DNA repair, endonuclease, DNA binding protein; HET: DNA; 1.90A {Homo sapiens} SCOP: c.52.1.20 PDB: 2jnw_A* 2jpd_A* Back     alignment and structure
Probab=100.00  E-value=3.8e-40  Score=273.73  Aligned_cols=91  Identities=47%  Similarity=0.784  Sum_probs=86.4

Q ss_pred             CCCccccccccCceeecccccceeecCceeEEEEeehhHHH---------hhhhHHH-----------------HHHHHH
Q 045823            1 KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFL---------NLLFDNV-----------------LLWVFS   54 (233)
Q Consensus         1 kGNPLLk~IrnVpwEy~dIvpDYviG~t~cvLFLSLKYH~L---------q~L~k~y-----------------L~ELt~   54 (233)
                      ||||||++||||||||+||+|||++|+++||||||||||+|         +.|+++|                 |+|||+
T Consensus        27 kGNPlL~~irnv~we~~dI~~Dyvvg~~tcvLFLSLkYH~L~PeYI~~Ri~~L~~~y~lrVLL~~VDv~d~~~~L~eL~~  106 (146)
T 2a1i_A           27 RGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAK  106 (146)
T ss_dssp             TTCGGGGGCCSSCEEECCCSSSEEEETTEEEEEEEHHHHHHSTTHHHHHHHHHTTSSSEEEEEEECCSSSCHHHHHHHHH
T ss_pred             cCChHHHHHhcCCeEecCcCCCEEecCeeEEEEEecHHhccCHHHHHHHHHHhccccceEEEEEEEeCCChHHHHHHHHH
Confidence            79999999999999999999999999999999999999999         4555666                 999999


Q ss_pred             HHhhccc--ccccCCCCHHHHHHHHHHHHhhcCCCcccccCC
Q 045823           55 TFGTSSC--LESWSNFSQEECGRYLETIKVYENKPADLTQGQ   94 (233)
Q Consensus        55 ~c~~~~~--IlAW~~~S~EEAArYLEt~K~yEnk~~d~Ik~k   94 (233)
                      +|+.+||  ||||   |+||||||||+||+||++|+|.|+++
T Consensus       107 ~c~~~~~TLiLaw---S~eEaa~Yle~~k~~e~k~~d~i~~~  145 (146)
T 2a1i_A          107 MCILADCTLILAW---SPEEAGRYLETYKAYEQKPADLLMEK  145 (146)
T ss_dssp             HHHHHTCEEEEES---SHHHHHHHHHHHHTCCSSCCCHHHHH
T ss_pred             HHHHcCCEEEEEC---CHHHHHHHHHHHHHhccCChhHhhcC
Confidence            9999999  9999   99999999999999999999999875
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

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 233
d2a1ia1129 c.52.1.20 (A:99-227) DNA excision repair protein E 5e-22
d2a1jb178 a.60.2.5 (B:219-296) DNA excision repair protein E 1e-06
>d2a1ia1 c.52.1.20 (A:99-227) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 129 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.5 bits (212), Expect = 5e-22
 Identities = 43/123 (34%), Positives = 59/123 (47%), Gaps = 31/123 (25%)

Query: 1   KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFLN------------------ 42
           +GNP+LK +  V W F DV+ DY+LGQ++CAL+L L  + L+                  
Sbjct: 10  RGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALR 69

Query: 43  -LLF-------DNVLLWVFSTFGTSSC--LESWSNFSQEECGRYLETIKVYENKPADLTQ 92
            LL           L  +      + C  + +WS    EE GRYLET K YE KPADL  
Sbjct: 70  VLLVQVDVKDPQQALKELAKMCILADCTLILAWSP---EEAGRYLETYKAYEQKPADLLM 126

Query: 93  GQM 95
            ++
Sbjct: 127 EKL 129
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78 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 ?
Query233
d2a1ia1129 DNA excision repair protein ERCC-1 {Human (Homo sa 100.0
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 99.4
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 98.1
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 98.01
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 97.52
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 97.02
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 95.12
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 92.77
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 90.72
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 90.22
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 89.42
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 87.84
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 85.64
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 85.58
>d2a1ia1 c.52.1.20 (A:99-227) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: XPF/Rad1/Mus81 nuclease
domain: DNA excision repair protein ERCC-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=6e-41  Score=271.78  Aligned_cols=91  Identities=47%  Similarity=0.784  Sum_probs=86.4

Q ss_pred             CCCccccccccCceeecccccceeecCceeEEEEeehhHHH---------hhhhHHH-----------------HHHHHH
Q 045823            1 KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFL---------NLLFDNV-----------------LLWVFS   54 (233)
Q Consensus         1 kGNPLLk~IrnVpwEy~dIvpDYviG~t~cvLFLSLKYH~L---------q~L~k~y-----------------L~ELt~   54 (233)
                      ||||||+|||||||||+||+|||++|+++||||||||||+|         +.|+++|                 |+|||+
T Consensus        10 kgNplL~~i~~v~we~~di~~Dyvvg~~~~vLFLSLkYH~L~peYI~~Ri~~L~~~y~lrVLL~~VDv~d~~~~L~eL~~   89 (129)
T d2a1ia1          10 RGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAK   89 (129)
T ss_dssp             TTCGGGGGCCSSCEEECCCSSSEEEETTEEEEEEEHHHHHHSTTHHHHHHHHHTTSSSEEEEEEECCSSSCHHHHHHHHH
T ss_pred             cCCcHHHHHhcCCeeecCcCCCeEecCccEEEEEehhhhccChHHHHHHHHHhccCcceEEEEEEEeCCChHHHHHHHHH
Confidence            79999999999999999999999999999999999999999         3455666                 999999


Q ss_pred             HHhhccc--ccccCCCCHHHHHHHHHHHHhhcCCCcccccCC
Q 045823           55 TFGTSSC--LESWSNFSQEECGRYLETIKVYENKPADLTQGQ   94 (233)
Q Consensus        55 ~c~~~~~--IlAW~~~S~EEAArYLEt~K~yEnk~~d~Ik~k   94 (233)
                      +|+.+||  ||||   |+||||+|||+||.||++|+|.|+++
T Consensus        90 ~c~~~~~TLilaw---s~eEaa~YlE~~k~~e~~~~d~i~~~  128 (129)
T d2a1ia1          90 MCILADCTLILAW---SPEEAGRYLETYKAYEQKPADLLMEK  128 (129)
T ss_dssp             HHHHHTCEEEEES---SHHHHHHHHHHHHTCCSSCCCHHHHH
T ss_pred             HHHHcCCEEEEEc---CHHHHHHHHHHHHHhcCCCHHHHHhc
Confidence            9999999  9999   99999999999999999999999876
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>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
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} 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
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {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
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} 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
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} Back     information, alignment and structure