Citrus Sinensis ID: 023471

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-------240-------250-------260-------270-------280-
MQKSRKRKQVEVTETRQDPYPTHSRPTAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSNKT
cccHHHHccccccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccHHHHHHccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccHHHHHcccccHHHHHHHHHccccccHHHHHHHHHHcccccccccHHHHHHHHHcccccccccHHHHHHHHHHcccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccc
ccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccccccccccEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHccccccccHHHHHHcccccHHHHHHHHHHHccccEEEEccHHHHHHHHcccccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHcccccEccccccccccHHHHHcccccc
MQKSRKRKQVEVtetrqdpypthsrptaeeCRGIRDELLalhgfppefVKYRNQRLKHnmtrdknsvpldmneydegeeesVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAircgglaptKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHlqqddfpvdthVFEISKAigwvptaadrnkTYLHLNQRIPKELKFDLNCLLYTHGKLcrncikkggnrqrkesagnlcpllnyceksnkt
mqksrkrkqvevtetrqdpypthsrptaeeCRGIRDELLALHGFPPEFVKYRNQRLkhnmtrdknsvplDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGgnrqrkesagnlcpllnyceksnkt
MQKSRKRKQVEVTETRQDPYPTHSRPTAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSNKT
********************************GIRDELLALHGFPPEFVKYR*******************************DGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKG**********NLCPLLNYC******
********************PTHSRPTAEECRGIRDELLALHG****************MTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSN**
****************************EECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEY********LDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSNKT
*****************DPYPTHSRPTAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKS***
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MQKSRKRKQVEVTETRQDPYPTHSRPTAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSNKT
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 ?
Query281 2.2.26 [Sep-21-2011]
Q9SJQ6 1393 Protein ROS1 OS=Arabidops no no 0.441 0.089 0.349 2e-12
Q9SR66 1332 DEMETER-like protein 2 OS no no 0.419 0.088 0.338 7e-11
Q8LK56 1987 Transcriptional activator no no 0.419 0.059 0.347 2e-10
Q9WYK0213 Endonuclease III OS=Therm yes no 0.569 0.751 0.297 7e-10
O49498 1044 DEMETER-like protein 3 OS no no 0.548 0.147 0.261 5e-07
Q58829220 Putative endonuclease MJ1 yes no 0.651 0.831 0.242 6e-07
O05956212 Endonuclease III OS=Ricke yes no 0.601 0.797 0.293 4e-05
P46303279 Ultraviolet N-glycosylase yes no 0.619 0.623 0.255 0.0002
Q4UK93213 Endonuclease III OS=Ricke yes no 0.604 0.798 0.271 0.0002
P0AB83211 Endonuclease III OS=Esche N/A no 0.647 0.862 0.258 0.0002
>sp|Q9SJQ6|ROS1_ARATH Protein ROS1 OS=Arabidopsis thaliana GN=ROS1 PE=1 SV=2 Back     alignment and function desciption
 Score = 72.8 bits (177), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/126 (34%), Positives = 64/126 (50%), Gaps = 2/126 (1%)

Query: 108  KSTFPT--WEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLS 165
            +ST  T  W+ + AA+ K +   I+  G+    A  I+  L  L+   G + LE+LR + 
Sbjct: 877  RSTMDTVDWKAIRAADVKEVAETIKSRGMNHKLAERIQGFLDRLVNDHGSIDLEWLRDVP 936

Query: 166  IDEIKAELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLH 225
             D+ K  L  F G+G K+V CV +  L    FPVDT+V  I+  +GWVP         LH
Sbjct: 937  PDKAKEYLLSFNGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLH 996

Query: 226  LNQRIP 231
            L +  P
Sbjct: 997  LLEMYP 1002
Prevents DNA hypermethylation, specifically in the promoter of otherwise silenced loci. May be involved in DNA repair through its nicking activity on methylated DNA. Catalyzes the release of 5-methylcytosine (5-meC) from DNA by a glycosylase/lyase mechanism.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 2EC: .EC: 2EC: .EC: -
>sp|Q9SR66|DML2_ARATH DEMETER-like protein 2 OS=Arabidopsis thaliana GN=DML2 PE=3 SV=2 Back     alignment and function description
>sp|Q8LK56|DME_ARATH Transcriptional activator DEMETER OS=Arabidopsis thaliana GN=DME PE=1 SV=2 Back     alignment and function description
>sp|Q9WYK0|END3_THEMA Endonuclease III OS=Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) GN=nth PE=3 SV=1 Back     alignment and function description
>sp|O49498|DML3_ARATH DEMETER-like protein 3 OS=Arabidopsis thaliana GN=DML3 PE=2 SV=2 Back     alignment and function description
>sp|Q58829|Y1434_METJA Putative endonuclease MJ1434 OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ1434 PE=3 SV=1 Back     alignment and function description
>sp|O05956|END3_RICPR Endonuclease III OS=Rickettsia prowazekii (strain Madrid E) GN=nth PE=3 SV=1 Back     alignment and function description
>sp|P46303|UVEN_MICLC Ultraviolet N-glycosylase/AP lyase OS=Micrococcus luteus (strain ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230) GN=pdg PE=1 SV=2 Back     alignment and function description
>sp|Q4UK93|END3_RICFE Endonuclease III OS=Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) GN=nth PE=3 SV=1 Back     alignment and function description
>sp|P0AB83|END3_ECOLI Endonuclease III OS=Escherichia coli (strain K12) GN=nth 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 ?
Query281
255540783291 Endonuclease III, putative [Ricinus comm 0.971 0.938 0.702 1e-111
224133424309 predicted protein [Populus trichocarpa] 0.985 0.896 0.641 1e-106
357477261280 Ultraviolet N-glycosylase/AP lyase [Medi 0.921 0.925 0.655 1e-102
225457138310 PREDICTED: endonuclease III-like [Vitis 0.978 0.887 0.63 1e-101
297733838310 unnamed protein product [Vitis vinifera] 0.978 0.887 0.63 1e-101
297815970294 predicted protein [Arabidopsis lyrata su 0.982 0.938 0.616 1e-97
18408516293 HhH-GPD base excision DNA repair protein 0.975 0.935 0.607 5e-97
356513571284 PREDICTED: endonuclease III-like [Glycin 0.886 0.876 0.667 2e-96
413944180340 ROS1 protein [Zea mays] 0.935 0.773 0.555 1e-82
195645374276 ROS1 protein [Zea mays] gi|219887377|gb| 0.935 0.952 0.555 2e-82
>gi|255540783|ref|XP_002511456.1| Endonuclease III, putative [Ricinus communis] gi|223550571|gb|EEF52058.1| Endonuclease III, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  407 bits (1045), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 203/289 (70%), Positives = 230/289 (79%), Gaps = 16/289 (5%)

Query: 1   MQKSRKRK-QVEVTETR---------QDPYPTHSRPTAEECRGIRDELLALHGFPPEFVK 50
           MQK+RKRK +   TET+         ++PYPTH RPT EEC  IRD LLA HGFP EF K
Sbjct: 1   MQKNRKRKLKSAETETKSAKINNGNKEEPYPTHPRPTPEECLCIRDSLLAFHGFPQEFAK 60

Query: 51  YRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLKST 110
           YR QRL      D ++   D+N   +  EE+VLDGLVKTVLSQNTTE NS +AF +LKS 
Sbjct: 61  YRKQRLGG----DDDNKSSDVNS--DTAEETVLDGLVKTVLSQNTTEVNSQRAFDNLKSD 114

Query: 111 FPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIK 170
           FPTW+ VLAAE K IENAIRCGGLAP KA+CIKNIL CLLE KGK+CLEYLR +S+DEIK
Sbjct: 115 FPTWQDVLAAEPKWIENAIRCGGLAPAKASCIKNILNCLLEKKGKICLEYLRDMSVDEIK 174

Query: 171 AELSRFRGIGPKTVACVLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRI 230
           AELS+F+G+GPKTVACVLMFHLQQ+DFPVDTHVFEI+KA+GWVP  ADRNKTYLHLNQRI
Sbjct: 175 AELSQFKGVGPKTVACVLMFHLQQEDFPVDTHVFEIAKALGWVPEVADRNKTYLHLNQRI 234

Query: 231 PKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNLCPLLNYCEKSN 279
           P ELKFDLNCLLYTHGKLCR CIKK GN+ RKES  + CPLL+YC  S+
Sbjct: 235 PNELKFDLNCLLYTHGKLCRKCIKKRGNQSRKESHDDSCPLLSYCNSSS 283

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224133424|ref|XP_002321564.1| predicted protein [Populus trichocarpa] gi|222868560|gb|EEF05691.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357477261|ref|XP_003608916.1| Ultraviolet N-glycosylase/AP lyase [Medicago truncatula] gi|355509971|gb|AES91113.1| Ultraviolet N-glycosylase/AP lyase [Medicago truncatula] Back     alignment and taxonomy information
>gi|225457138|ref|XP_002283633.1| PREDICTED: endonuclease III-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|297733838|emb|CBI15085.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|297815970|ref|XP_002875868.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297321706|gb|EFH52127.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|18408516|ref|NP_566893.1| HhH-GPD base excision DNA repair protein-related protein [Arabidopsis thaliana] gi|332644814|gb|AEE78335.1| HhH-GPD base excision DNA repair protein-related protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356513571|ref|XP_003525486.1| PREDICTED: endonuclease III-like [Glycine max] Back     alignment and taxonomy information
>gi|413944180|gb|AFW76829.1| ROS1 protein [Zea mays] Back     alignment and taxonomy information
>gi|195645374|gb|ACG42155.1| ROS1 protein [Zea mays] gi|219887377|gb|ACL54063.1| unknown [Zea mays] 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 ?
Query281
TAIR|locus:2100382293 AT3G47830 [Arabidopsis thalian 0.914 0.877 0.652 3.5e-91
ASPGD|ASPL0000003678502 AN10840 [Emericella nidulans ( 0.345 0.193 0.5 2.3e-30
TAIR|locus:2044923 1393 DML1 "demeter-like 1" [Arabido 0.441 0.089 0.349 1.4e-12
TAIR|locus:2100138 1332 DML2 "demeter-like 2" [Arabido 0.419 0.088 0.338 1.6e-11
TAIR|locus:2184432 1987 DME "DEMETER" [Arabidopsis tha 0.419 0.059 0.347 4.5e-09
TIGR_CMR|CHY_1121210 CHY_1121 "endonuclease III" [C 0.637 0.852 0.272 1.1e-07
TAIR|locus:2124301 1044 DML3 "demeter-like protein 3" 0.398 0.107 0.303 1.6e-07
DICTYBASE|DDB_G0277247349 apnB "putative endonuclease II 0.900 0.724 0.246 3.9e-06
TIGR_CMR|CBU_1697218 CBU_1697 "endonuclease III" [C 0.615 0.793 0.28 1.2e-05
UNIPROTKB|P0AB83211 nth "endonuclease III; specifi 0.626 0.834 0.271 1.8e-05
TAIR|locus:2100382 AT3G47830 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 909 (325.0 bits), Expect = 3.5e-91, P = 3.5e-91
 Identities = 169/259 (65%), Positives = 204/259 (78%)

Query:    18 DPYPTHSRPTAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNE--YD 75
             +PYPT  RPTAEECR +RD LL+LHGFPPEF  YR QRL+     D +    ++     +
Sbjct:    30 NPYPTLLRPTAEECRDVRDALLSLHGFPPEFANYRRQRLRSFSAVDDHDTQCNLKSETLN 89

Query:    76 EGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLA 135
             E EEESVLDGLVK +LSQNTTE+NS +AFASLK+TFP W+ VL AE K IENAIRCGGLA
Sbjct:    90 ETEEESVLDGLVKILLSQNTTESNSQRAFASLKATFPKWDDVLNAESKSIENAIRCGGLA 149

Query:   136 PTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQD 195
             P KA CIKNIL  L   +G+LCLEYLRGLS++E+K ELS F+G+GPKTV+CVLMF+LQ +
Sbjct:   150 PKKAVCIKNILNRLQNERGRLCLEYLRGLSVEEVKTELSHFKGVGPKTVSCVLMFNLQHN 209

Query:   196 DFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKK 255
             DFPVDTHVFEI+KA+GWVP  ADRNKTY+HLN++IP ELKFDLNCLLYTHGK+C NC K 
Sbjct:   210 DFPVDTHVFEIAKALGWVPKTADRNKTYVHLNRKIPDELKFDLNCLLYTHGKICSNCKKN 269

Query:   256 GGNRQRKESAGNLCPLLNY 274
                 + K ++ + CPL+ +
Sbjct:   270 VAKPKAKVASPDDCPLVGF 288
GO:0003824 "catalytic activity" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0006281 "DNA repair" evidence=IEA
GO:0006284 "base-excision repair" evidence=IEA
ASPGD|ASPL0000003678 AN10840 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
TAIR|locus:2044923 DML1 "demeter-like 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2100138 DML2 "demeter-like 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2184432 DME "DEMETER" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1121 CHY_1121 "endonuclease III" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TAIR|locus:2124301 DML3 "demeter-like protein 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0277247 apnB "putative endonuclease III" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
TIGR_CMR|CBU_1697 CBU_1697 "endonuclease III" [Coxiella burnetii RSA 493 (taxid:227377)] Back     alignment and assigned GO terms
UNIPROTKB|P0AB83 nth "endonuclease III; specific for apurinic and/or apyrimidinic sites" [Escherichia coli K-12 (taxid:83333)] 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 ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer3.2.2.21LOW CONFIDENCE prediction!
3rd Layer4.2.99LOW CONFIDENCE prediction!
4th Layer4.2.99.18LOW CONFIDENCE prediction!
3rd Layer3.2.20.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
gw1.XV.1362.1
hypothetical protein (272 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query281
COG0177211 COG0177, Nth, Predicted EndoIII-related endonuclea 5e-31
cd00056158 cd00056, ENDO3c, endonuclease III; includes endonu 6e-29
smart00478149 smart00478, ENDO3c, endonuclease III 1e-25
pfam00730144 pfam00730, HhH-GPD, HhH-GPD superfamily base excis 1e-18
COG0122285 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-o 2e-16
TIGR01083191 TIGR01083, nth, endonuclease III 3e-12
COG2231215 COG2231, COG2231, Uncharacterized protein related 1e-09
TIGR00588310 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg) 1e-07
PRK10702211 PRK10702, PRK10702, endonuclease III; Provisional 1e-06
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information 
 Score =  114 bits (288), Expect = 5e-31
 Identities = 64/211 (30%), Positives = 95/211 (45%), Gaps = 29/211 (13%)

Query: 76  EGEEESVLDGLVKTVLSQNTTEANSLKAFASLKSTFPTWEHVLAAEQKCIENAIRCGGLA 135
           E + +   + LV  +LS  TT+    KA  +L   +PT E +L A+++ +E  I+  GL 
Sbjct: 23  ELDFKDPFELLVAVILSAQTTDEVVNKATPALFKRYPTPEDLLNADEEELEELIKSIGLY 82

Query: 136 PTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQD 195
             KA  IK + + LLE       ++  G  + + + EL    G+G KT   VL F     
Sbjct: 83  RNKAKNIKELARILLE-------KF--GGEVPDTREELLSLPGVGRKTANVVLSFAFGIP 133

Query: 196 DFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGK-LCR---- 250
              VDTHV  +S  +G VP      +    L + IPKEL  DL+  L  HG+ +C+    
Sbjct: 134 AIAVDTHVHRVSNRLGLVPGKTPE-EVEEALMKLIPKELWTDLHHWLILHGRYICKARKP 192

Query: 251 NCIKKGGNRQRKESAGNLCPLLNYCEKSNKT 281
            C                CPL + C  + KT
Sbjct: 193 RC--------------EECPLADLCPSAGKT 209

Length = 211
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases Back     alignment and domain information
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III Back     alignment and domain information
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair protein Back     alignment and domain information
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|130155 TIGR01083, nth, endonuclease III Back     alignment and domain information
>gnl|CDD|225140 COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|211589 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg) Back     alignment and domain information
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 281
COG0177211 Nth Predicted EndoIII-related endonuclease [DNA re 100.0
PRK10702211 endonuclease III; Provisional 100.0
TIGR01084275 mutY A/G-specific adenine glycosylase. This equiva 100.0
PRK10880 350 adenine DNA glycosylase; Provisional 100.0
TIGR01083191 nth endonuclease III. This equivalog model identif 100.0
COG2231215 Uncharacterized protein related to Endonuclease II 100.0
KOG1921286 consensus Endonuclease III [Replication, recombina 100.0
PRK13913218 3-methyladenine DNA glycosylase; Provisional 100.0
PRK13910 289 DNA glycosylase MutY; Provisional 100.0
COG1194 342 MutY A/G-specific DNA glycosylase [DNA replication 100.0
cd00056158 ENDO3c endonuclease III; includes endonuclease III 100.0
smart00478149 ENDO3c endonuclease III. includes endonuclease III 100.0
PRK01229208 N-glycosylase/DNA lyase; Provisional 99.97
KOG2457 555 consensus A/G-specific adenine DNA glycosylase [Re 99.96
TIGR00588310 ogg 8-oxoguanine DNA-glycosylase (ogg). All protei 99.95
COG0122285 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine 99.94
TIGR03252177 uncharacterized HhH-GPD family protein. This model 99.93
PRK10308283 3-methyl-adenine DNA glycosylase II; Provisional 99.92
KOG1918254 consensus 3-methyladenine DNA glycosidase [Replica 99.87
KOG2875323 consensus 8-oxoguanine DNA glycosylase [Replicatio 99.87
PF00730108 HhH-GPD: HhH-GPD superfamily base excision DNA rep 99.81
COG1059210 Thermostable 8-oxoguanine DNA glycosylase [DNA rep 99.36
PF0063330 HHH: Helix-hairpin-helix motif; InterPro: IPR00044 98.09
TIGR00624179 tag DNA-3-methyladenine glycosylase I. This family 97.17
PRK10353187 3-methyl-adenine DNA glycosylase I; Provisional 97.09
PF03352179 Adenine_glyco: Methyladenine glycosylase; InterPro 96.95
PF1057617 EndIII_4Fe-2S: Iron-sulfur binding domain of endon 96.45
COG2818188 Tag 3-methyladenine DNA glycosylase [DNA replicati 96.43
smart0052526 FES FES domain. iron-sulpphur binding domain in DN 95.49
smart0027826 HhH1 Helix-hairpin-helix DNA-binding motif class 1 95.33
PF1471668 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HU 95.13
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 95.08
PF09674232 DUF2400: Protein of unknown function (DUF2400); In 93.89
smart00483 334 POLXc DNA polymerase X family. includes vertebrate 93.53
TIGR02757229 conserved hypothetical protein TIGR02757. Members 93.51
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 93.17
PRK13901196 ruvA Holliday junction DNA helicase RuvA; Provisio 92.75
cd00141 307 NT_POLXc Nucleotidyltransferase (NT) domain of fam 92.7
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 91.67
PRK02515132 psbU photosystem II complex extrinsic protein prec 91.61
TIGR0042669 competence protein ComEA helix-hairpin-helix repea 90.92
PRK00076196 recR recombination protein RecR; Reviewed 90.89
PRK13844200 recombination protein RecR; Provisional 90.72
TIGR00615195 recR recombination protein RecR. This family is ba 90.7
COG0353198 RecR Recombinational DNA repair protein (RecF path 90.44
COG0632201 RuvA Holliday junction resolvasome, DNA-binding su 89.76
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 89.75
PRK14601183 ruvA Holliday junction DNA helicase RuvA; Provisio 89.65
COG1555149 ComEA DNA uptake protein and related DNA-binding p 89.16
TIGR00575652 dnlj DNA ligase, NAD-dependent. The member of this 89.11
PRK08609 570 hypothetical protein; Provisional 88.58
PRK00024224 hypothetical protein; Reviewed 88.13
PRK14606188 ruvA Holliday junction DNA helicase RuvA; Provisio 88.08
PF1452060 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU 87.97
PRK14603197 ruvA Holliday junction DNA helicase RuvA; Provisio 87.95
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 87.42
PRK14605194 ruvA Holliday junction DNA helicase RuvA; Provisio 87.3
PRK14604195 ruvA Holliday junction DNA helicase RuvA; Provisio 87.22
PRK14602203 ruvA Holliday junction DNA helicase RuvA; Provisio 86.96
PF0237187 Transposase_20: Transposase IS116/IS110/IS902 fami 86.31
PRK07945 335 hypothetical protein; Provisional 86.21
PF09171246 DUF1886: Domain of unknown function (DUF1886); Int 85.63
TIGR00608218 radc DNA repair protein radc. This family is based 85.43
PRK07956665 ligA NAD-dependent DNA ligase LigA; Validated 85.33
PRK00024224 hypothetical protein; Reviewed 85.26
PRK00116192 ruvA Holliday junction DNA helicase RuvA; Reviewed 85.19
PF1283665 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE 84.69
PRK14600186 ruvA Holliday junction DNA helicase RuvA; Provisio 84.62
COG2003224 RadC DNA repair proteins [DNA replication, recombi 84.26
COG1796 326 POL4 DNA polymerase IV (family X) [DNA replication 84.24
KOG2841254 consensus Structure-specific endonuclease ERCC1-XP 83.36
PRK13482352 DNA integrity scanning protein DisA; Provisional 82.57
PF1173193 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd 82.53
TIGR00608218 radc DNA repair protein radc. This family is based 82.32
PRK14350669 ligA NAD-dependent DNA ligase LigA; Provisional 81.88
smart00483 334 POLXc DNA polymerase X family. includes vertebrate 81.54
PF1282664 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS 81.42
PRK14351689 ligA NAD-dependent DNA ligase LigA; Provisional 80.76
TIGR00084191 ruvA Holliday junction DNA helicase, RuvA subunit. 80.57
PF1283665 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE 80.53
TIGR01448 720 recD_rel helicase, putative, RecD/TraA family. Thi 80.41
PF1039152 DNA_pol_lambd_f: Fingers domain of DNA polymerase 80.36
TIGR01259120 comE comEA protein. This model describes the ComEA 80.09
COG2003224 RadC DNA repair proteins [DNA replication, recombi 80.03
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information 
Probab=100.00  E-value=1e-52  Score=357.91  Aligned_cols=206  Identities=32%  Similarity=0.449  Sum_probs=193.4

Q ss_pred             HHHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHH
Q 023471           28 AEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASL  107 (281)
Q Consensus        28 ~~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L  107 (281)
                      .....++.+.|.+.|+......                            ...|||++||++||||||+++.+.+++.+|
T Consensus         3 ~~~~~~i~~~l~~~~p~~~~~l----------------------------~~~~pf~lLva~iLSaqttD~~vn~at~~L   54 (211)
T COG0177           3 KKKALEILDRLRELYPEPKTEL----------------------------DFKDPFELLVAVILSAQTTDEVVNKATPAL   54 (211)
T ss_pred             HhhHHHHHHHHHHHCCCCCCcc----------------------------CcCCcHHHHHHHHHhccCchHHHHHHHHHH
Confidence            3567888889988888766411                            258999999999999999999999999999


Q ss_pred             HhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHH
Q 023471          108 KSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACV  187 (281)
Q Consensus       108 ~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~i  187 (281)
                      ++.|+||++|+++++++|++.|+.+||+++||++|+++++.|.++|||         .+|+.+++|++|||||+|||++|
T Consensus        55 f~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g---------~vP~~~~eL~~LPGVGrKTAnvV  125 (211)
T COG0177          55 FKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG---------EVPDTREELLSLPGVGRKTANVV  125 (211)
T ss_pred             HHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCC---------CCCchHHHHHhCCCcchHHHHHH
Confidence            999999999999999999999999999999999999999999999999         78999999999999999999999


Q ss_pred             HHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCCC
Q 023471          188 LMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGN  267 (281)
Q Consensus       188 l~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C~  267 (281)
                      |.++||.++|+|||||+|+++|+||++ ..+++++++.|.+++|++.|..+|.+||.|||.  +|++++ |   +   |+
T Consensus       126 L~~a~g~p~i~VDTHV~Rvs~R~gl~~-~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR~--iC~ar~-P---~---C~  195 (211)
T COG0177         126 LSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIPKELWTDLHHWLILHGRY--ICKARK-P---R---CE  195 (211)
T ss_pred             HHhhcCCCcccccchHHHHHHHhCCCC-CCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhhh--hccCCC-C---C---cC
Confidence            999999999999999999999999987 789999999999999999999999999999999  999984 4   3   99


Q ss_pred             CCCChhhcccccC
Q 023471          268 LCPLLNYCEKSNK  280 (281)
Q Consensus       268 ~Cpl~~~C~~~~~  280 (281)
                      .|||+++|+++++
T Consensus       196 ~C~l~~~C~~~~~  208 (211)
T COG0177         196 ECPLADLCPSAGK  208 (211)
T ss_pred             cccchhhCchhcc
Confidence            9999999999976

>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>TIGR01084 mutY A/G-specific adenine glycosylase Back     alignment and domain information
>PRK10880 adenine DNA glycosylase; Provisional Back     alignment and domain information
>TIGR01083 nth endonuclease III Back     alignment and domain information
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG1921 consensus Endonuclease III [Replication, recombination and repair] Back     alignment and domain information
>PRK13913 3-methyladenine DNA glycosylase; Provisional Back     alignment and domain information
>PRK13910 DNA glycosylase MutY; Provisional Back     alignment and domain information
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases Back     alignment and domain information
>smart00478 ENDO3c endonuclease III Back     alignment and domain information
>PRK01229 N-glycosylase/DNA lyase; Provisional Back     alignment and domain information
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair] Back     alignment and domain information
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg) Back     alignment and domain information
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR03252 uncharacterized HhH-GPD family protein Back     alignment and domain information
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional Back     alignment and domain information
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair] Back     alignment and domain information
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair] Back     alignment and domain information
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4 Back     alignment and domain information
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] 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
>TIGR00624 tag DNA-3-methyladenine glycosylase I Back     alignment and domain information
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional Back     alignment and domain information
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3 Back     alignment and domain information
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4 Back     alignment and domain information
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00525 FES FES domain Back     alignment and domain information
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1 Back     alignment and domain information
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>TIGR02757 conserved hypothetical protein TIGR02757 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
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional Back     alignment and domain information
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region Back     alignment and domain information
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>PRK13844 recombination protein RecR; Provisional Back     alignment and domain information
>TIGR00615 recR recombination protein RecR Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit Back     alignment and domain information
>PRK14601 ruvA Holliday junction DNA helicase RuvA; 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
>TIGR00575 dnlj DNA ligase, NAD-dependent Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>PRK00024 hypothetical protein; Reviewed Back     alignment and domain information
>PRK14606 ruvA Holliday junction DNA helicase RuvA; 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
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>PRK14604 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
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA Back     alignment and domain information
>PRK07945 hypothetical protein; Provisional Back     alignment and domain information
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases Back     alignment and domain information
>TIGR00608 radc DNA repair protein radc Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>PRK00024 hypothetical protein; Reviewed Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed 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
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional Back     alignment and domain information
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair] Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria [] Back     alignment and domain information
>TIGR00608 radc DNA repair protein radc Back     alignment and domain information
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B Back     alignment and domain information
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit 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
>TIGR01448 recD_rel helicase, putative, RecD/TraA family Back     alignment and domain information
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains Back     alignment and domain information
>TIGR01259 comE comEA protein Back     alignment and domain information
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair] 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 ?
Query281
3i0x_A291 Crystal Structure Of Clostridium Acetobutylicum 8-O 1e-06
3i0w_A290 Crystal Structure Of Clostridium Acetobutylicum 8-O 1e-06
3f10_A292 Crystal Structure Of Clostridium Acetobutylicum 8-O 1e-06
3f0z_A292 Crystal Structure Of Clostridium Acetobutylicum 8-O 3e-06
2abk_A211 Refinement Of The Native Structure Of Endonuclease 2e-05
1orn_A226 Structure Of A Trapped Endonuclease Iii-Dna Covalen 2e-04
1p59_A226 Structure Of A Non-Covalent Endonuclease Iii-Dna Co 4e-04
>pdb|3I0X|A Chain A, Crystal Structure Of Clostridium Acetobutylicum 8-Oxoguanine GlycosylaseLYASE IN COMPLEX WITH DSDNA CONTAINING ADENINE Opposite To 8-Oxog Length = 291 Back     alignment and structure 
Iteration: 1

 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 35/51 (68%), Gaps = 1/51 (1%)
Query: 154 GKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQ-DDFPVDTHV 203
           G+L LEY++ L+ +E   EL +F G+GP+   C+++F +Q+   FPVDT V
Sbjct: 194 GELNLEYIKSLNDNECHEELKKFMGVGPQVADCIMLFSMQKYSAFPVDTWV 244
>pdb|3I0W|A Chain A, Crystal Structure Of Clostridium Acetobutylicum 8-Oxoguanine GlycosylaseLYASE IN COMPLEX WITH DSDNA CONTAINING CYTOSINE Opposite To 8-Oxog Length = 290 Back     alignment and structure
>pdb|3F10|A Chain A, Crystal Structure Of Clostridium Acetobutylicum 8-Oxoguanine Dna Glycosylase In Complex With 8-Oxoguanosine Length = 292 Back     alignment and structure
>pdb|3F0Z|A Chain A, Crystal Structure Of Clostridium Acetobutylicum 8-Oxoguanine GlycosylaseLYASE IN ITS APO-Form Length = 292 Back     alignment and structure
>pdb|2ABK|A Chain A, Refinement Of The Native Structure Of Endonuclease Iii To A Resolution Of 1.85 Angstrom Length = 211 Back     alignment and structure
>pdb|1ORN|A Chain A, Structure Of A Trapped Endonuclease Iii-Dna Covalent Intermediate: Estranged-Guanine Complex Length = 226 Back     alignment and structure
>pdb|1P59|A Chain A, Structure Of A Non-Covalent Endonuclease Iii-Dna Complex Length = 226 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 ?
Query281
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-hel 7e-36
3fhg_A207 Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel 1e-19
2xhi_A360 N-glycosylase/DNA lyase; lyase-DNA complex, lyase/ 2e-19
3i0w_A290 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 1e-17
2jhn_A295 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, 3e-16
2h56_A233 DNA-3-methyladenine glycosidase; 10174367, EC 3.2. 1e-15
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4F 2e-15
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.8 1e-14
3n0u_A219 Probable N-glycosylase/DNA lyase; structural genom 4e-14
2yg9_A225 DNA-3-methyladenine glycosidase II, putative; hydr 4e-13
3s6i_A228 DNA-3-methyladenine glycosylase 1; DNA glycosylase 1e-12
1mpg_A282 ALKA, 3-methyladenine DNA glycosylase II; DNA repa 8e-10
3fhf_A214 Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel 3e-08
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 7e-05
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A* Length = 218 Back     alignment and structure
 Score =  127 bits (320), Expect = 7e-36
 Identities = 31/193 (16%), Positives = 66/193 (34%), Gaps = 32/193 (16%)

Query: 86  LVKTVLSQNTTEANSLKAFASLKSTFP-------TWEHVLAAEQKCIENAIRCGGLAPTK 138
           L+  VL+QNT     LK+  +LK+ F          + +   E   +   +R  G    K
Sbjct: 34  LLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQK 93

Query: 139 AACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFP 198
           A  + ++   +L+       +       +  +  L   +GIG ++   +L +   ++   
Sbjct: 94  AKRLIDLSGNILKD-----FQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMV 148

Query: 199 VDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDL----------------NCLL 242
           VD + +   K +G      D  + +    + + + L   L                +  +
Sbjct: 149 VDKYSYLFLKKLGIEIEDYDELQHFFE--KGVQENLNSALALYENTISLAQLYARFHGKI 206

Query: 243 YTHGKLCRNCIKK 255
               K  +    K
Sbjct: 207 VEFSK--QKLELK 217
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Length = 207 Back     alignment and structure
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex, separation-OF-function helix-hairpin-helix, DNA repair; HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A* 1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A 1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ... Length = 360 Back     alignment and structure
>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Length = 290 Back     alignment and structure
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Length = 295 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} Length = 233 Back     alignment and structure
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Length = 226 Back     alignment and structure
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Length = 211 Back     alignment and structure
>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA repair, 8-oxoguanine, base EX repair, PSI-2, protein structure initiative; 1.50A {Thermotoga maritima} Length = 219 Back     alignment and structure
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A Length = 225 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} Length = 228 Back     alignment and structure
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, ALK hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A* 3ogd_A* 3oh9_A* 3oh6_A* Length = 282 Back     alignment and structure
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A* Length = 214 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query281
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4F 100.0
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.8 100.0
3n5n_X287 A/G-specific adenine DNA glycosylase; alpha-helice 100.0
1kea_A221 Possible G-T mismatches repair enzyme; DNA repair, 100.0
1kg2_A225 A/G-specific adenine glycosylase; DNA repair, hydr 100.0
3fsp_A 369 A/G-specific adenine glycosylase; protein-DNA comp 100.0
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-hel 100.0
2h56_A233 DNA-3-methyladenine glycosidase; 10174367, EC 3.2. 100.0
4b21_A232 Probable DNA-3-methyladenine glycosylase 2; hydrol 100.0
2yg9_A225 DNA-3-methyladenine glycosidase II, putative; hydr 100.0
3fhg_A207 Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel 100.0
3fhf_A214 Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; hel 99.98
3s6i_A228 DNA-3-methyladenine glycosylase 1; DNA glycosylase 99.98
3i0w_A290 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 99.97
4e9f_A161 Methyl-CPG-binding domain protein 4; HHH DNA glyco 99.97
3n0u_A219 Probable N-glycosylase/DNA lyase; structural genom 99.97
2xhi_A360 N-glycosylase/DNA lyase; lyase-DNA complex, lyase/ 99.96
1mpg_A282 ALKA, 3-methyladenine DNA glycosylase II; DNA repa 99.96
2jhn_A295 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, 99.96
2ofk_A183 3-methyladenine DNA glycosylase I, constitutive; D 97.22
2jg6_A186 DNA-3-methyladenine glycosidase; 3-methyladenine-D 97.14
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, tran 94.31
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, trans 94.08
1jms_A 381 Terminal deoxynucleotidyltransferase; polymerase; 92.3
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 92.21
4gfj_A685 Topoisomerase V; helix-hairpin-helix, DNA repair e 91.97
4glx_A586 DNA ligase; inhibitor, ligase-ligase inhibitor-DNA 91.92
3vdp_A212 Recombination protein RECR; zinc finger, DNA repai 91.82
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 91.75
2bcq_A 335 DNA polymerase lambda; misalignment, extrahelical, 91.45
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin- 91.03
1vdd_A 228 Recombination protein RECR; helix-hairpin-helix, z 90.52
4gfj_A685 Topoisomerase V; helix-hairpin-helix, DNA repair e 89.39
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma 88.64
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin- 88.55
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 88.17
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 88.13
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 87.96
2owo_A671 DNA ligase; protein-DNA complex, ligase-DNA comple 87.76
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, tran 87.29
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, D 86.42
2duy_A75 Competence protein comea-related protein; helix-ha 86.13
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, trans 86.07
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; 85.38
1jms_A 381 Terminal deoxynucleotidyltransferase; polymerase; 84.58
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, 83.98
2bcq_A 335 DNA polymerase lambda; misalignment, extrahelical, 83.65
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligome 83.07
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA 82.96
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 82.86
1wcn_A70 Transcription elongation protein NUSA; RNA-binding 82.78
2csb_A519 Topoisomerase V, TOP61; topoisomerase IB, helix-tu 81.65
2duy_A75 Competence protein comea-related protein; helix-ha 81.34
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynt 81.08
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Back     alignment and structure
Probab=100.00  E-value=1.5e-49  Score=346.37  Aligned_cols=206  Identities=24%  Similarity=0.292  Sum_probs=191.0

Q ss_pred             HHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHHHH
Q 023471           29 EECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFASLK  108 (281)
Q Consensus        29 ~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~L~  108 (281)
                      +.+.++++.|.++||...++-                            ...|+||+||++||+|||++++|..++.+|+
T Consensus         8 ~~~~~i~~~L~~~y~~~~~~l----------------------------~~~~pfe~Lv~~IlsQqts~~~v~~~~~~l~   59 (226)
T 1orn_A            8 QQIRYCLDEMAKMFPDAHCEL----------------------------VHRNPFELLIAVVLSAQCTDALVNKVTKRLF   59 (226)
T ss_dssp             HHHHHHHHHHHHHCTTCCCCS----------------------------CCSSHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCccCCCC----------------------------CCCCHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            678899999999999865311                            2579999999999999999999999999999


Q ss_pred             hhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHHHH
Q 023471          109 STFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVL  188 (281)
Q Consensus       109 ~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~il  188 (281)
                      +.||||++|+++++++|+++|+++||+++||++|+++|+.+.++||+         +.++++++|++|||||+|||++|+
T Consensus        60 ~~fpt~~~la~a~~~~l~~~i~~~G~~~~KA~~l~~~a~~i~~~~~g---------~~p~~~~~L~~lpGIG~~TA~~il  130 (226)
T 1orn_A           60 EKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNG---------EVPRDRDELMKLPGVGRKTANVVV  130 (226)
T ss_dssp             HHCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTT---------SCCSCHHHHTTSTTCCHHHHHHHH
T ss_pred             HHCCCHHHHHcCCHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHhCC---------CcHHHHHHHHHCCCccHHHHHHHH
Confidence            99999999999999999999999999999999999999999998876         456789999999999999999999


Q ss_pred             HHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCCCC
Q 023471          189 MFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAGNL  268 (281)
Q Consensus       189 ~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C~~  268 (281)
                      +|++|+++||||+|+.|++.|+|+++...++++++..+++++|++.|.++|++||+||+.  +|++++ |   +   |+.
T Consensus       131 ~~a~g~~~~~vD~~v~Rv~~rlg~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~lv~~G~~--~C~~~~-P---~---C~~  201 (226)
T 1orn_A          131 SVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRY--HCKAQS-P---Q---CPS  201 (226)
T ss_dssp             HHHHCCCCCCCCHHHHHHHHHHTSSCTTCCHHHHHHHHHHHSCGGGHHHHHHHHHHHHHH--TSCSSC-C---C---GGG
T ss_pred             HHHCCCceeeeCHHHHHHHHHhCCCCCCCCHHHHHHHHHHhcChhhHHHHHHHHHHHHHH--HcCCCC-C---C---CCC
Confidence            999999999999999999999999876789999999999999999999999999999999  999884 4   3   999


Q ss_pred             CCChhhcccccC
Q 023471          269 CPLLNYCEKSNK  280 (281)
Q Consensus       269 Cpl~~~C~~~~~  280 (281)
                      |||++.|++|.+
T Consensus       202 Cpl~~~C~~~~~  213 (226)
T 1orn_A          202 CPLLHLCREGKK  213 (226)
T ss_dssp             CTTGGGCHHHHH
T ss_pred             CCChhhhhhHhh
Confidence            999999998753
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Back     alignment and structure
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Back     alignment and structure
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation; 2.00A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.96.1.2 Back     alignment and structure
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Back     alignment and structure
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Back     alignment and structure
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_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
>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
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A Back     alignment and structure
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Back     alignment and structure
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_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
>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Back     alignment and structure
>4e9f_A Methyl-CPG-binding domain protein 4; HHH DNA glycosylase family, hydrolase-DNA complex; HET: DNA 3DR; 1.79A {Homo sapiens} PDB: 4e9e_A* 4e9g_A* 4e9h_A* 4ea5_A* 4dk9_A* 1ngn_A 4ea4_A* 4ew4_A* 4evv_A* 4ew0_A* 3iho_A Back     alignment and structure
>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA repair, 8-oxoguanine, base EX repair, PSI-2, protein structure initiative; 1.50A {Thermotoga maritima} Back     alignment and structure
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex, separation-OF-function helix-hairpin-helix, DNA repair; HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A* 1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A 1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ... Back     alignment and structure
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, ALK hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A* 3ogd_A* 3oh9_A* 3oh6_A* Back     alignment and structure
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Back     alignment and structure
>2ofk_A 3-methyladenine DNA glycosylase I, constitutive; DNA repair, base excision, helix-hairpin-helix, hydrolase; HET: PGE; 1.50A {Salmonella typhi} PDB: 2ofi_A* 1lmz_A 1nku_A 1p7m_A* Back     alignment and structure
>2jg6_A DNA-3-methyladenine glycosidase; 3-methyladenine-DNA-glycosylase-I, hydrolase; 1.70A {Staphylococcus aureus} PDB: 4aia_A* 4ai5_A* 4ai4_A 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
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Back     alignment and structure
>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
>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19} 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
>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D 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
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Back     alignment and structure
>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
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Back     alignment and structure
>4gfj_A Topoisomerase V; helix-hairpin-helix, DNA repair enzyme, DNA B isomerase; 2.91A {Methanopyrus kandleri AV19} 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
>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
>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
>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
>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
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli} 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
>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
>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
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} 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
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1kdh_A* 1kej_A* Back     alignment and structure
>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
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_A* ... Back     alignment and structure
>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
>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
>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
>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
>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix-H helix, HHH motif, three helix bundle, methanopyrus kandleri isomerase; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_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
>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

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 281
d1pu6a_217 a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III 3e-19
d2noha1190 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Hum 2e-13
d2abka_211 a.96.1.1 (A:) Endonuclease III {Escherichia coli [ 1e-09
d1orna_214 a.96.1.1 (A:) Endonuclease III {Escherichia coli [ 1e-07
d1kg2a_224 a.96.1.2 (A:) Catalytic domain of MutY {Escherichi 6e-07
d1ngna_144 a.96.1.2 (A:) Mismatch-specific thymine glycosylas 7e-07
d1keaa_217 a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Me 3e-05
d1rrqa1221 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacil 1e-04
>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} Length = 217 Back     information, alignment and structure

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: 3-Methyladenine DNA glycosylase III (MagIII)
domain: 3-Methyladenine DNA glycosylase III (MagIII)
species: Helicobacter pylori [TaxId: 210]

 Score = 81.7 bits (201), Expect = 3e-19
 Identities = 28/193 (14%), Positives = 62/193 (32%), Gaps = 32/193 (16%)

Query: 86  LVKTVLSQNTTEANSLKAFASLKS-------TFPTWEHVLAAEQKCIENAIRCGGLAPTK 138
           L+  VL+QNT     LK+  +LK+            + +   E   +   +R  G    K
Sbjct: 33  LLGAVLTQNTKFEAVLKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQK 92

Query: 139 AACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVACVLMFHLQQDDFP 198
           A  + ++   +         +       +  +  L   +GIG ++   +L +   ++   
Sbjct: 93  AKRLIDLSGNI-----LKDFQSFENFKQEVTREWLLDQKGIGKESADAILCYACAKEVMV 147

Query: 199 VDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKF----------------DLNCLL 242
           VD + +   K +G      D ++      + + + L                    +  +
Sbjct: 148 VDKYSYLFLKKLGIEI--EDYDELQHFFEKGVQENLNSALALYENTISLAQLYARFHGKI 205

Query: 243 YTHGKLCRNCIKK 255
               K  +    K
Sbjct: 206 VEFSK--QKLELK 216
>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Length = 190 Back     information, alignment and structure
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Length = 211 Back     information, alignment and structure
>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Length = 214 Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Length = 224 Back     information, alignment and structure
>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 144 Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Length = 217 Back     information, alignment and structure
>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Length = 221 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 ?
Query281
d1orna_214 Endonuclease III {Escherichia coli [TaxId: 562]} 100.0
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium 100.0
d2abka_211 Endonuclease III {Escherichia coli [TaxId: 562]} 100.0
d1rrqa1221 Catalytic domain of MutY {Bacillus stearothermophi 100.0
d1kg2a_224 Catalytic domain of MutY {Escherichia coli [TaxId: 100.0
d1pu6a_217 3-Methyladenine DNA glycosylase III (MagIII) {Heli 100.0
d2noha1190 8-oxoguanine glycosylase {Human (Homo sapiens) [Ta 99.96
d1mpga1183 3-Methyladenine DNA glycosylase II (gene alkA or a 99.95
d1ngna_144 Mismatch-specific thymine glycosylase domain of th 99.95
d1nkua_187 3-Methyladenine DNA glycosylase I (Tag) {Escherich 97.24
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 95.12
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 94.96
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 94.7
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 94.54
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 94.49
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 94.45
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 93.85
d2fmpa182 DNA polymerase beta, N-terminal (8 kD)-domain {Hum 93.66
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 93.21
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 92.97
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filif 92.67
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [Tax 92.05
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia c 91.82
d2bcqa176 DNA polymerase lambda {Human (Homo sapiens) [TaxId 91.7
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 91.01
d1vdda_199 Recombination protein RecR {Deinococcus radioduran 90.98
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobact 90.62
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sa 90.29
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 90.06
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archa 89.84
d1cuka278 DNA helicase RuvA subunit, middle domain {Escheric 89.65
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus 89.52
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furi 88.85
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) 88.71
d2edua191 KIF22, C-terminal domain {Human (Homo sapiens) [Ta 88.59
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archa 88.59
d1jmsa195 Terminal deoxynucleotidyl transferase {Mouse (Mus 86.7
d1jmsa360 Terminal deoxynucleotidyl transferase {Mouse (Mus 86.46
d2fmpa257 DNA polymerase beta {Human (Homo sapiens) [TaxId: 86.06
d2duya165 Uncharacterized protein TTHA1967 {Thermus thermoph 84.8
d2bcqa257 DNA polymerase lambda {Human (Homo sapiens) [TaxId 84.38
d2axtu198 Photosystem II 12 kDa extrinsic protein PsbU {Ther 81.76
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker 80.49
>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.8e-50  Score=346.28  Aligned_cols=208  Identities=25%  Similarity=0.293  Sum_probs=193.1

Q ss_pred             CHHHHHHHHHHHHHhhCCChhhhHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHhhhccHHHHHHHHHH
Q 023471           27 TAEECRGIRDELLALHGFPPEFVKYRNQRLKHNMTRDKNSVPLDMNEYDEGEEESVLDGLVKTVLSQNTTEANSLKAFAS  106 (281)
Q Consensus        27 ~~~~~~~v~~~L~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fe~Lv~~ILsqqts~~~a~~~~~~  106 (281)
                      +.++++.+++.|.++||....+.                            +..|||++||++||||||+++++..++.+
T Consensus         3 ~~~~~~~~~~~l~~~y~~~~~~l----------------------------~~~dp~~vLVs~iLsqqT~~~~v~~~~~~   54 (214)
T d1orna_           3 TKQQIRYCLDEMAKMFPDAHCEL----------------------------VHRNPFELLIAVVLSAQCTDALVNKVTKR   54 (214)
T ss_dssp             CHHHHHHHHHHHHHHCTTCCCCS----------------------------CCSSHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCC----------------------------CCCCHHHHHHHHHHHhcChHHHHHHHHhh
Confidence            45789999999999998755422                            23699999999999999999999999999


Q ss_pred             HHhhCCCHHHHHhCCHHHHHHHhhhCCCchHHHHHHHHHHHHHHHHcCCCchHHHhcCChHHHHHHHhcCcCccHHHHHH
Q 023471          107 LKSTFPTWEHVLAAEQKCIENAIRCGGLAPTKAACIKNILKCLLESKGKLCLEYLRGLSIDEIKAELSRFRGIGPKTVAC  186 (281)
Q Consensus       107 L~~~~pt~~~la~~~~eel~~~i~~~G~~~~KA~~I~~~a~~i~~~~g~~~l~~l~~~~~~~~~~~L~~l~GIG~~tA~~  186 (281)
                      |+++|||+++++.++.+++.+.|+++||+++||++|+++++.|.++|||         ..+..+++|++|||||+|||++
T Consensus        55 l~~~~pt~~~la~~~~~e~~~~i~~~g~y~~ka~~l~~~a~~i~~~~~g---------~vp~~~~~L~~LpGVG~kTA~~  125 (214)
T d1orna_          55 LFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNG---------EVPRDRDELMKLPGVGRKTANV  125 (214)
T ss_dssp             HHHHCCSHHHHHSSCHHHHHHHTGGGSSHHHHHHHHHHHHHHHHHHSTT---------SCCSCHHHHTTSTTCCHHHHHH
T ss_pred             hhcccCchhhhhhccHHHhhhhhhhhhhhhHHHHHHHHHhhhHHHHhCC---------CCCCCHHHHHhCcCcccchHHH
Confidence            9999999999999999999999999999999999999999999999988         4667789999999999999999


Q ss_pred             HHHHhcCCCccccchHHHHHHHHhCCCCCCCCHHHHHHHHHhhCCcccHHHHHHHHHHhcccCCCCcCCCCCCCcCCCCC
Q 023471          187 VLMFHLQQDDFPVDTHVFEISKAIGWVPTAADRNKTYLHLNQRIPKELKFDLNCLLYTHGKLCRNCIKKGGNRQRKESAG  266 (281)
Q Consensus       187 il~~~~~~~~~~vD~~v~Ri~~rlG~~~~~~~~~~~~~~l~~~~p~~~~~~~h~~lv~~G~~c~~C~~~~~p~~p~~~~C  266 (281)
                      ||+|+||+++|+||+||.||+.|+|+++...++..++..+++++|.+.+.+||++||+||+.  +|++++ |   +   |
T Consensus       126 il~~a~~~~~~~VDtnv~RV~~Rlg~~~~~~~~~~~~~~l~~~~p~~~~~~~~~~l~~~G~~--iC~~~~-P---~---C  196 (214)
T d1orna_         126 VVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRY--HCKAQS-P---Q---C  196 (214)
T ss_dssp             HHHHHHCCCCCCCCHHHHHHHHHHTSSCTTCCHHHHHHHHHHHSCGGGHHHHHHHHHHHHHH--TSCSSC-C---C---G
T ss_pred             HHHHHhcCCcccccchHHHHHHHHHHhhcccchhhhhhhhhhcCccccHHHHHHHHHHHHHH--HCcCCC-C---C---C
Confidence            99999999999999999999999999987778889999999999999999999999999999  999984 4   3   9


Q ss_pred             CCCCChhhcccccC
Q 023471          267 NLCPLLNYCEKSNK  280 (281)
Q Consensus       267 ~~Cpl~~~C~~~~~  280 (281)
                      +.|||++.|++|++
T Consensus       197 ~~Cpl~~~C~~~~k  210 (214)
T d1orna_         197 PSCPLLHLCREGKK  210 (214)
T ss_dssp             GGCTTGGGCHHHHH
T ss_pred             CCCCCcccChhhcc
Confidence            99999999999865
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Back     information, alignment and structure
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} 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
>d1mpga1 a.96.1.3 (A:100-282) 3-Methyladenine DNA glycosylase II (gene alkA or aidA) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1nkua_ a.96.1.4 (A:) 3-Methyladenine DNA glycosylase I (Tag) {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
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} 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
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {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
>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
>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {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
>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
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} 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
>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} 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
>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
>d2edua1 a.60.2.7 (A:8-98) KIF22, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1jmsa1 a.60.6.1 (A:148-242) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1jmsa3 a.60.12.1 (A:243-302) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2fmpa2 a.60.12.1 (A:92-148) DNA polymerase beta {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2duya1 a.60.2.7 (A:11-75) Uncharacterized protein TTHA1967 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2bcqa2 a.60.12.1 (A:329-385) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2axtu1 a.60.12.2 (U:37-134) Photosystem II 12 kDa extrinsic protein PsbU {Thermosynechococcus elongatus [TaxId: 146786]} 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