Citrus Sinensis ID: 023088

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-------
MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAVMKP
ccccccccccccccccccccccccccccccccccccccccccEEEEEEHHHHHHHHHcccHHHHHHHHHccccEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccEEEEEccccccEEEEEEEEccccccEEEEccccccccccccccEEEEEEccEEEEEEEEccccccccccHHHHHHHHHHHHHHHHHHcccccEEEEcccccccccccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHcccEEEEEEcccccc
cccEEEEcccccccccccccccccccccccccccccccccccEEEEEEcccHHHHHccccHHHHHHHHHccccEEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHccccccccEHHHcccccccEEEEEEEcccccEEEEEcccccHHHcccccEEEEEEcccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHEccHHHHHHccccccccccccccccccccHHHHHHHHHHHHcccEEccHHHcccccc
mkrffkpiekecsakkpalspskkdgettetsseenskkdplkFVTWNANSLLLRVknnwpefsnfittfdpdvialqevrmpaagskdapknhqelkddtKASREEKLILMRAlssppfknyqIWWSLADSKYAGTALLVKKcfqpkkvsFSLEKTalkyepdgrVILAEFETFYLLntyapnngwkeeENSFQRRRKWDKRIQEFVLQcsgkpliwcgdlnvsheeidvshpeFFAAAklngyvppnkedwgqpgftiAERKRFGAILKEYLIFLCFYELAVMKP
mkrffkpiekecsakkpalspskkdgettetsseenskkdplkfVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMpaagskdapknhqelkddtkasREEKLILMRalssppfkNYQIWWSLADSKYAGTALLVKKcfqpkkvsfslektalkyepdGRVILAEFETFYLLNTyapnngwkeeeNSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAVMKP
MKRFFKPIEKECsakkpalspskkdgettetsseenskkDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAVMKP
*****************************************LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEV****************************LILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAV***
******************************************KFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAVM**
MKRFFKPIEKEC***************************DPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMP******************KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAVMKP
*********K****************************KDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAVMK*
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MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYELAVMKP
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 ?
Query287 2.2.26 [Sep-21-2011]
P43138317 DNA-(apurinic or apyrimid yes no 0.780 0.706 0.297 2e-21
P28352317 DNA-(apurinic or apyrimid yes no 0.780 0.706 0.297 3e-21
A2T6Y4318 DNA-(apurinic or apyrimid yes no 0.770 0.694 0.293 1e-20
A1YFZ3318 DNA-(apurinic or apyrimid N/A no 0.770 0.694 0.293 1e-20
A2T7I6318 DNA-(apurinic or apyrimid N/A no 0.770 0.694 0.293 2e-20
P27695318 DNA-(apurinic or apyrimid yes no 0.770 0.694 0.293 2e-20
A1YES6318 DNA-(apurinic or apyrimid N/A no 0.731 0.660 0.298 4e-20
P51173361 DNA-(apurinic or apyrimid yes no 0.641 0.509 0.289 1e-18
P23196318 DNA-(apurinic or apyrimid yes no 0.731 0.660 0.290 1e-18
P45951536 Apurinic endonuclease-red no no 0.620 0.332 0.305 1e-16
>sp|P43138|APEX1_RAT DNA-(apurinic or apyrimidinic site) lyase OS=Rattus norvegicus GN=Apex1 PE=1 SV=2 Back     alignment and function desciption
 Score =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 83/279 (29%), Positives = 133/279 (47%), Gaps = 55/279 (19%)

Query: 6   KPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNWPEFSN 65
           K  EKE + + P L     D +T+ +      K   LK  +WN + L   +K    +  +
Sbjct: 30  KKTEKEAAGEGPVLYEDPPDQKTSASG-----KSATLKICSWNVDGLRAWIKK---KGLD 81

Query: 66  FITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQI 125
           ++    PD++ LQE +         P   QEL                     P   +Q 
Sbjct: 82  WVKEEAPDILCLQETK---CSENKLPAELQEL---------------------PGLTHQY 117

Query: 126 WWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPN 184
           W + +D + Y+G  LL ++C  P KVS+ + +   +++ +GRVI+AEFE+F L+  Y PN
Sbjct: 118 WSAPSDKEGYSGVGLLSRQC--PLKVSYGIGEE--EHDQEGRVIVAEFESFILVTAYVPN 173

Query: 185 NGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN 243
            G        + R++WD+  ++F+    S KPL+ CGDLNV+HEEID+ +P+        
Sbjct: 174 AG--RGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLRNPK-------- 223

Query: 244 GYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCFYEL 282
                NK++    GFT  ER+ FG +L+   +   F  L
Sbjct: 224 ----GNKKN---AGFTPQERQGFGEMLQAVPLADSFRHL 255
Multifunctional protein that plays a central role in the cellular response to oxidative stress. The two major activities of APEX1 in DNA repair and redox regulation of transcriptional factors. Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Does also incise at AP sites in the DNA strand of DNA/RNA hybrids, single-stranded DNA regions of R-loop structures, and single-stranded RNA molecules. Has a 3'-5' exoribonuclease activity on mismatched deoxyribonucleotides at the 3' termini of nicked or gapped DNA molecules during short-patch BER. Possesses a DNA 3' phosphodiesterase activity capable of removing lesions (such as phosphoglycolate) blocking the 3' side of DNA strand breaks. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. Acts as a loading factor for POLB onto non-incised AP sites in DNA and stimulates the 5'-terminal deoxyribose 5'-phosphate (dRp) excision activity of POLB. Plays a role in the protection from granzymes-mediated cellular repair leading to cell death. Also involved in the DNA cleavage step of class switch recombination (CSR). On the other hand, APEX1 also exerts reversible nuclear redox activity to regulate DNA binding affinity and transcriptional activity of transcriptional factors by controlling the redox status of their DNA-binding domain, such as the FOS/JUN AP-1 complex after exposure to IR. Involved in calcium-dependent down-regulation of parathyroid hormone (PTH) expression by binding to negative calcium response elements (nCaREs). Together with HNRNPL or the dimer XRCC5/XRCC6, associates with nCaRE, acting as an activator of transcriptional repression. Stimulates the YBX1-mediated MDR1 promoter activity, when acetylated at Lys-6, leading to drug resistance. Acts also as an endoribonuclease involved in the control of single-stranded RNA metabolism. Plays a role in regulating MYC mRNA turnover by preferentially cleaving in between UA and CA dinucleotides of the MYC coding region determinant (CRD). In association with NMD1, plays a role in the rRNA quality control process during cell cycle progression. Associates, together with YBX1, on the MDR1 promoter. Together with NPM1, associates with rRNA. Binds DNA and RNA.
Rattus norvegicus (taxid: 10116)
EC: 4EC: .EC: 2EC: .EC: 9EC: 9EC: .EC: 1EC: 8
>sp|P28352|APEX1_MOUSE DNA-(apurinic or apyrimidinic site) lyase OS=Mus musculus GN=Apex1 PE=1 SV=2 Back     alignment and function description
>sp|A2T6Y4|APEX1_PANTR DNA-(apurinic or apyrimidinic site) lyase OS=Pan troglodytes GN=APEX1 PE=3 SV=1 Back     alignment and function description
>sp|A1YFZ3|APEX1_PANPA DNA-(apurinic or apyrimidinic site) lyase OS=Pan paniscus GN=APEX1 PE=3 SV=1 Back     alignment and function description
>sp|A2T7I6|APEX1_PONPY DNA-(apurinic or apyrimidinic site) lyase OS=Pongo pygmaeus GN=APEX1 PE=3 SV=1 Back     alignment and function description
>sp|P27695|APEX1_HUMAN DNA-(apurinic or apyrimidinic site) lyase OS=Homo sapiens GN=APEX1 PE=1 SV=2 Back     alignment and function description
>sp|A1YES6|APEX1_GORGO DNA-(apurinic or apyrimidinic site) lyase OS=Gorilla gorilla gorilla GN=APEX1 PE=3 SV=1 Back     alignment and function description
>sp|P51173|APEA_DICDI DNA-(apurinic or apyrimidinic site) lyase OS=Dictyostelium discoideum GN=apeA PE=2 SV=2 Back     alignment and function description
>sp|P23196|APEX1_BOVIN DNA-(apurinic or apyrimidinic site) lyase OS=Bos taurus GN=APEX1 PE=1 SV=2 Back     alignment and function description
>sp|P45951|ARP_ARATH Apurinic endonuclease-redox protein OS=Arabidopsis thaliana GN=ARP PE=2 SV=2 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 ?
Query287
225456791357 PREDICTED: DNA-(apurinic or apyrimidinic 0.940 0.756 0.764 1e-120
449487730361 PREDICTED: LOW QUALITY PROTEIN: DNA-(apu 0.947 0.753 0.764 1e-120
224133800366 predicted protein [Populus trichocarpa] 0.947 0.743 0.774 1e-120
449469598361 PREDICTED: DNA-(apurinic or apyrimidinic 0.947 0.753 0.764 1e-120
297816036 684 hypothetical protein ARALYDRAFT_347932 [ 0.979 0.410 0.742 1e-118
4678346 686 putative protein [Arabidopsis thaliana] 0.944 0.395 0.759 1e-118
42565714364 endonuclease/exonuclease/phosphatase dom 0.944 0.744 0.759 1e-117
356508768355 PREDICTED: exodeoxyribonuclease-like [Gl 0.919 0.743 0.733 1e-113
358348989367 DNA-(apurinic or apyrimidinic site) lyas 0.940 0.735 0.728 1e-109
358348991278 DNA-(apurinic or apyrimidinic site) lyas 0.940 0.971 0.728 1e-109
>gi|225456791|ref|XP_002277389.1| PREDICTED: DNA-(apurinic or apyrimidinic site) lyase [Vitis vinifera] gi|297733638|emb|CBI14885.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  438 bits (1126), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 208/272 (76%), Positives = 236/272 (86%), Gaps = 2/272 (0%)

Query: 1   MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNW 60
           MKR+F+PI K+ S+KKP+LS    D  T + S EE  KK+PLKF+TWNANS L+RVKNNW
Sbjct: 1   MKRYFQPIGKDGSSKKPSLSKEDGDENTDQVSEEE--KKEPLKFLTWNANSFLIRVKNNW 58

Query: 61  PEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPF 120
           PEF+ F++  DPDVIA+QEVRMPAAGSK APKNH ELKDDT +SREEK ILM ALS PPF
Sbjct: 59  PEFTKFVSDLDPDVIAVQEVRMPAAGSKGAPKNHGELKDDTSSSREEKKILMHALSRPPF 118

Query: 121 KNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNT 180
            NY++WWSLADSKYAGTAL VKKCFQPKKVSFS+++ A K+EP+GRVILAEFE+F LLNT
Sbjct: 119 GNYRVWWSLADSKYAGTALFVKKCFQPKKVSFSIDQKASKHEPEGRVILAEFESFRLLNT 178

Query: 181 YAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAA 240
           Y PNNGWK+EE SFQRRRKWDKR+ EFV+Q S KPLIWCGDLNVSHEEIDVSHPEFF+AA
Sbjct: 179 YVPNNGWKDEETSFQRRRKWDKRMLEFVVQSSDKPLIWCGDLNVSHEEIDVSHPEFFSAA 238

Query: 241 KLNGYVPPNKEDWGQPGFTIAERKRFGAILKE 272
           K NGYVPPNKED GQPGFT+AER+RFG ILKE
Sbjct: 239 KHNGYVPPNKEDCGQPGFTLAERRRFGGILKE 270

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449487730|ref|XP_004157772.1| PREDICTED: LOW QUALITY PROTEIN: DNA-(apurinic or apyrimidinic site) lyase-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224133800|ref|XP_002321664.1| predicted protein [Populus trichocarpa] gi|222868660|gb|EEF05791.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449469598|ref|XP_004152506.1| PREDICTED: DNA-(apurinic or apyrimidinic site) lyase-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297816036|ref|XP_002875901.1| hypothetical protein ARALYDRAFT_347932 [Arabidopsis lyrata subsp. lyrata] gi|297321739|gb|EFH52160.1| hypothetical protein ARALYDRAFT_347932 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|4678346|emb|CAB41156.1| putative protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|42565714|ref|NP_566904.2| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana] gi|53828525|gb|AAU94372.1| At3g48425 [Arabidopsis thaliana] gi|55733769|gb|AAV59281.1| At3g48425 [Arabidopsis thaliana] gi|332644894|gb|AEE78415.1| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356508768|ref|XP_003523126.1| PREDICTED: exodeoxyribonuclease-like [Glycine max] Back     alignment and taxonomy information
>gi|358348989|ref|XP_003638523.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] gi|355504458|gb|AES85661.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] Back     alignment and taxonomy information
>gi|358348991|ref|XP_003638524.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] gi|355504459|gb|AES85662.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] 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 ?
Query287
TAIR|locus:505006392364 AT3G48425 [Arabidopsis thalian 0.947 0.747 0.714 1.4e-103
GENEDB_PFALCIPARUM|PFC0250c617 PFC0250c "AP endonuclease (DNA 0.770 0.358 0.412 3.2e-39
UNIPROTKB|O97240617 PFC0250c "AP endonuclease (DNA 0.770 0.358 0.412 3.2e-39
MGI|MGI:88042317 Apex1 "apurinic/apyrimidinic e 0.505 0.457 0.367 4.9e-24
RGD|2126317 Apex1 "APEX nuclease (multifun 0.505 0.457 0.367 4.9e-24
UNIPROTKB|J9PA46318 APEX1 "Uncharacterized protein 0.505 0.455 0.367 1e-23
UNIPROTKB|A1YFZ3318 APEX1 "DNA-(apurinic or apyrim 0.505 0.455 0.360 1.3e-23
UNIPROTKB|A2T6Y4318 APEX1 "DNA-(apurinic or apyrim 0.505 0.455 0.360 1.3e-23
UNIPROTKB|Q9Z2J2317 APE "Apurinic/apyrimidinic end 0.505 0.457 0.367 1.6e-23
UNIPROTKB|A1YES6318 APEX1 "DNA-(apurinic or apyrim 0.501 0.452 0.371 1.6e-23
TAIR|locus:505006392 AT3G48425 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1026 (366.2 bits), Expect = 1.4e-103, P = 1.4e-103
 Identities = 195/273 (71%), Positives = 216/273 (79%)

Query:     1 MKRFFKPIEKECXXXXXXXXXX-XXXXXXXXXXXXXXXXXDPLKFVTWNANSLLLRVKNN 59
             MKRFFKPIEKE                             +P KF+TWNANS LLRVKN+
Sbjct:     1 MKRFFKPIEKENSPAAKKPCLSPEKRDGDGDGVEEEKNQNEPSKFMTWNANSFLLRVKND 60

Query:    60 WPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPP 119
             W +FS F++ FDPDVIA+QEVRMPAAG K  PKNH+EL DDTK  REEK IL RALSSPP
Sbjct:    61 WSQFSKFVSDFDPDVIAIQEVRMPAAGGKGKPKNHEELSDDTKVLREEKQILTRALSSPP 120

Query:   120 FKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLN 179
             F NY +WWSLADSKYAGTALLVKKCF+P+KV F+L+K A K+EPDGRVILAEFETF LLN
Sbjct:   121 FGNYGVWWSLADSKYAGTALLVKKCFKPRKVYFNLDKLASKHEPDGRVILAEFETFRLLN 180

Query:   180 TYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAA 239
             TY+PNNGWK+EEN+FQRRRKWDKRI EF+ + S KPLIWCGDLNVSHEEIDVSHPEFFA 
Sbjct:   181 TYSPNNGWKDEENAFQRRRKWDKRIVEFLNKTSDKPLIWCGDLNVSHEEIDVSHPEFFAT 240

Query:   240 AKLNGYVPPNKEDWGQPGFTIAERKRFGAILKE 272
             AKLNGYVPPNKED GQPGFT +ER RFGA +KE
Sbjct:   241 AKLNGYVPPNKEDCGQPGFTPSERGRFGATIKE 273
GO:0004518 "nuclease activity" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0006281 "DNA repair" evidence=IEA
GO:0016787 "hydrolase activity" evidence=ISS
GO:0009507 "chloroplast" evidence=IDA
GENEDB_PFALCIPARUM|PFC0250c PFC0250c "AP endonuclease (DNA-(apurinic or apyrimidinic site) lyase), putative" [Plasmodium falciparum (taxid:5833)] Back     alignment and assigned GO terms
UNIPROTKB|O97240 PFC0250c "AP endonuclease (DNA-[apurinic or apyrimidinic site] lyase), putative" [Plasmodium falciparum 3D7 (taxid:36329)] Back     alignment and assigned GO terms
MGI|MGI:88042 Apex1 "apurinic/apyrimidinic endonuclease 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|2126 Apex1 "APEX nuclease (multifunctional DNA repair enzyme) 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|J9PA46 APEX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|A1YFZ3 APEX1 "DNA-(apurinic or apyrimidinic site) lyase" [Pan paniscus (taxid:9597)] Back     alignment and assigned GO terms
UNIPROTKB|A2T6Y4 APEX1 "DNA-(apurinic or apyrimidinic site) lyase" [Pan troglodytes (taxid:9598)] Back     alignment and assigned GO terms
UNIPROTKB|Q9Z2J2 APE "Apurinic/apyrimidinic endonuclease" [Cricetulus griseus (taxid:10029)] Back     alignment and assigned GO terms
UNIPROTKB|A1YES6 APEX1 "DNA-(apurinic or apyrimidinic site) lyase" [Gorilla gorilla gorilla (taxid:9595)] 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 Layer4.2.99LOW CONFIDENCE prediction!
4th Layer4.2.99.18LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00015903001
SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (357 aa)
(Vitis vinifera)
Predicted Functional Partners:
GSVIVG00021219001
RecName- Full=Uracil-DNA glycosylase; EC=3.2.2.-;; Excises uracil residues from the DNA which c [...] (328 aa)
   •  • 0.581
GSVIVG00022496001
SubName- Full=Chromosome chr14 scaffold_27, whole genome shotgun sequence; (330 aa)
   • •• 0.565

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 ?
Query287
cd09087253 cd09087, Ape1-like_AP-endo, Human Ape1-like subfam 2e-65
cd09073251 cd09073, ExoIII_AP-endo, Escherichia coli exonucle 4e-36
COG0708261 COG0708, XthA, Exonuclease III [DNA replication, r 1e-33
TIGR00633255 TIGR00633, xth, exodeoxyribonuclease III (xth) 1e-32
TIGR00195254 TIGR00195, exoDNase_III, exodeoxyribonuclease III 5e-27
cd09085252 cd09085, Mth212-like_AP-endo, Methanothermobacter 1e-20
PRK13911250 PRK13911, PRK13911, exodeoxyribonuclease III; Prov 1e-18
cd09086254 cd09086, ExoIII-like_AP-endo, Escherichia coli exo 1e-16
cd09088309 cd09088, Ape2-like_AP-endo, Human Ape2-like subfam 4e-14
cd09076236 cd09076, L1-EN, Endonuclease domain (L1-EN) of the 2e-13
cd08372241 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase 3e-13
cd10281253 cd10281, Nape_like_AP-endo, Neisseria meningitides 2e-12
PRK11756268 PRK11756, PRK11756, exonuclease III; Provisional 0.001
pfam03372143 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease 0.002
pfam03372143 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease 0.004
>gnl|CDD|197321 cd09087, Ape1-like_AP-endo, Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information 
 Score =  205 bits (523), Expect = 2e-65
 Identities = 74/236 (31%), Positives = 114/236 (48%), Gaps = 51/236 (21%)

Query: 42  LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
           LK ++WN N L   +K       +++   DPD++ LQE ++         K         
Sbjct: 1   LKIISWNVNGLRALLKKG---LLDYVKKEDPDILCLQETKLQEGDVPKELKEL------- 50

Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
                              K Y  +W+ A+ K Y+GTA+L KK   P  V++ +     +
Sbjct: 51  ------------------LKGYHQYWNAAEKKGYSGTAILSKKK--PLSVTYGIGIE--E 88

Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-SGKPLIWC 219
           ++ +GRVI AEFE FYL+NTY PN+G   E     RR++WD   + ++ +  S KP+IWC
Sbjct: 89  HDQEGRVITAEFENFYLVNTYVPNSGRGLE--RLDRRKEWDVDFRAYLKKLDSKKPVIWC 146

Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLI 275
           GDLNV+HEEID+++P+                     GFT  ER+ F  +L+   +
Sbjct: 147 GDLNVAHEEIDLANPKTNK---------------KSAGFTPEERESFTELLEAGFV 187

This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily. Length = 253
>gnl|CDD|197307 cd09073, ExoIII_AP-endo, Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|223780 COG0708, XthA, Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|233064 TIGR00633, xth, exodeoxyribonuclease III (xth) Back     alignment and domain information
>gnl|CDD|188032 TIGR00195, exoDNase_III, exodeoxyribonuclease III Back     alignment and domain information
>gnl|CDD|197319 cd09085, Mth212-like_AP-endo, Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional Back     alignment and domain information
>gnl|CDD|197320 cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|197322 cd09088, Ape2-like_AP-endo, Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|197310 cd09076, L1-EN, Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains Back     alignment and domain information
>gnl|CDD|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily Back     alignment and domain information
>gnl|CDD|197336 cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|236970 PRK11756, PRK11756, exonuclease III; Provisional Back     alignment and domain information
>gnl|CDD|217520 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase family Back     alignment and domain information
>gnl|CDD|217520 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase family Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 287
COG0708261 XthA Exonuclease III [DNA replication, recombinati 100.0
PRK13911250 exodeoxyribonuclease III; Provisional 100.0
PRK11756268 exonuclease III; Provisional 100.0
TIGR00195254 exoDNase_III exodeoxyribonuclease III. The model b 100.0
TIGR00633255 xth exodeoxyribonuclease III (xth). This family is 99.97
PRK05421263 hypothetical protein; Provisional 99.71
KOG1294335 consensus Apurinic/apyrimidinic endonuclease and r 99.66
PF03372249 Exo_endo_phos: Endonuclease/Exonuclease/phosphatas 99.51
TIGR03395283 sphingomy sphingomyelin phosphodiesterase. Members 99.5
PRK15251271 cytolethal distending toxin subunit CdtB; Provisio 99.47
COG3568259 ElsH Metal-dependent hydrolase [General function p 99.41
PTZ00297 1452 pantothenate kinase; Provisional 99.33
PLN03144606 Carbon catabolite repressor protein 4 homolog; Pro 99.29
KOG3873 422 consensus Sphingomyelinase family protein [Signal 99.23
KOG2756349 consensus Predicted Mg2+-dependent phosphodiestera 99.18
KOG2338 495 consensus Transcriptional effector CCR4-related pr 99.11
smart00476276 DNaseIc deoxyribonuclease I. Deoxyribonuclease I c 99.06
smart00128310 IPPc Inositol polyphosphate phosphatase, catalytic 98.63
COG3021309 Uncharacterized protein conserved in bacteria [Fun 98.46
PF14529119 Exo_endo_phos_2: Endonuclease-reverse transcriptas 98.39
COG5239378 CCR4 mRNA deadenylase, exonuclease subunit and rel 97.82
KOG0566 1080 consensus Inositol-1,4,5-triphosphate 5-phosphatas 97.12
KOG0620 361 consensus Glucose-repressible alcohol dehydrogenas 93.38
PLN03191621 Type I inositol-1,4,5-trisphosphate 5-phosphatase 83.63
PTZ00312 356 inositol-1,4,5-triphosphate 5-phosphatase; Provisi 81.65
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information 
Probab=100.00  E-value=6.5e-44  Score=315.27  Aligned_cols=197  Identities=29%  Similarity=0.504  Sum_probs=168.2

Q ss_pred             cEEEEEecCccchhhhcCchhHHHHHhhcCCCEEEEeeecCCCCCCCCCCccccccchhhhhhHHHHHHHHHhhCCCCCC
Q 023088           42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFK  121 (287)
Q Consensus        42 lkIiTwNv~gl~~~~~~~~~~l~~~l~~~~pDIv~LQEt~~~~~~~~~~~~~~~~l~d~~~~~~~~~~~~~~~L~~~~~~  121 (287)
                      |||+||||||++.+.+    .+.+||.+++|||||||||+.....+|..                       .+   ...
T Consensus         1 mkI~SwNVNgiRar~~----~~~~~l~~~~pDVlclQEtK~~~~~fp~~-----------------------~~---~~~   50 (261)
T COG0708           1 MKIASWNVNGLRARLK----KLLDWLEEEQPDVLCLQETKAQDEQFPRE-----------------------EL---EAL   50 (261)
T ss_pred             CeeEEEehhhHHHHHH----HHHHHHHHhCCCEEEEEecccCcccCCHh-----------------------HH---hhC
Confidence            7999999999999984    59999999999999999999999887631                       12   137


Q ss_pred             CceEEEEccCCCceeEEEEEecCCCcceEeecCcccccccCCCCCEEEEEeCCEEEEEEeeCCCCCCCchhhHHHHHHHH
Q 023088          122 NYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWD  201 (287)
Q Consensus       122 gy~~~~~~~~~~~~GVAIlsr~~i~p~~~~~~l~~~~~~~d~egR~l~~~~~~~~linvY~P~~~~~~~~~~~~~r~~f~  201 (287)
                      ||+.++.++.++++||||+||.+  |..+..++++ ....|.+||+|.++++.++|+|+|+|+++.. ..+++.+|++|+
T Consensus        51 GY~~~~~~gqKgysGVailsr~~--~~~v~~g~~~-~~~~d~e~R~I~a~~~~~~v~~~Y~PnG~~~-~~~k~~yKl~f~  126 (261)
T COG0708          51 GYHHVFNHGQKGYSGVAILSKKP--PDDVRRGFPG-EEEDDEEGRVIEAEFDGFRVINLYFPNGSSI-GLEKFDYKLRFL  126 (261)
T ss_pred             CceEEEecCcCCcceEEEEEccC--chhhhcCCCC-CccccccCcEEEEEECCEEEEEEEcCCCCCC-CCcchHHHHHHH
Confidence            99666666778899999999986  5577778764 1236789999999999999999999999872 236799999999


Q ss_pred             HHHHHHHHhC--CCCCEEEEecCCCCCCCccccCc-hhhhhhhcCCCCCCCCCCCCCCCCCHHHHHHHHHHHHcCCeeee
Q 023088          202 KRIQEFVLQC--SGKPLIWCGDLNVSHEEIDVSHP-EFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLC  278 (287)
Q Consensus       202 ~~L~~~l~~~--~~~pvIl~GDFN~~~~~~D~~~~-~~~~~~k~~~~~~~~~~~~~~~~~~~~er~~l~~l~~~g~lvD~  278 (287)
                      +.|.+++.++  .+.|+|+|||||++|.++|+++| +.+.             +.+.++|+++||+||++|++.| ++|+
T Consensus       127 ~~l~~~l~~l~~~~~~~vl~GD~NIap~~iDv~~~~~~~~-------------n~~~~~f~~eeR~~~~~ll~~G-~~D~  192 (261)
T COG0708         127 DALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWL-------------NEGNSGFLPEERAWFRRLLNAG-FVDT  192 (261)
T ss_pred             HHHHHHHHHHhhcCCCEEEecccccCCchhcccCchhhhh-------------cCCCCCCCHHHHHHHHHHHHcc-hhhh
Confidence            9999999874  57999999999999999999998 4332             3578999999999999999999 8999


Q ss_pred             eeccccCC
Q 023088          279 FYELAVMK  286 (287)
Q Consensus       279 ~R~~~p~~  286 (287)
                      +|.+||..
T Consensus       193 ~R~~~p~~  200 (261)
T COG0708         193 FRLFHPEP  200 (261)
T ss_pred             hHhhCCCC
Confidence            99999974

>PRK13911 exodeoxyribonuclease III; Provisional Back     alignment and domain information
>PRK11756 exonuclease III; Provisional Back     alignment and domain information
>TIGR00195 exoDNase_III exodeoxyribonuclease III Back     alignment and domain information
>TIGR00633 xth exodeoxyribonuclease III (xth) Back     alignment and domain information
>PRK05421 hypothetical protein; Provisional Back     alignment and domain information
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] Back     alignment and domain information
>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling [] Back     alignment and domain information
>TIGR03395 sphingomy sphingomyelin phosphodiesterase Back     alignment and domain information
>PRK15251 cytolethal distending toxin subunit CdtB; Provisional Back     alignment and domain information
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only] Back     alignment and domain information
>PTZ00297 pantothenate kinase; Provisional Back     alignment and domain information
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional Back     alignment and domain information
>KOG3873 consensus Sphingomyelinase family protein [Signal transduction mechanisms] Back     alignment and domain information
>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms] Back     alignment and domain information
>KOG2338 consensus Transcriptional effector CCR4-related protein [Transcription] Back     alignment and domain information
>smart00476 DNaseIc deoxyribonuclease I Back     alignment and domain information
>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues Back     alignment and domain information
>COG3021 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B Back     alignment and domain information
>COG5239 CCR4 mRNA deadenylase, exonuclease subunit and related nucleases [RNA processing and modification] Back     alignment and domain information
>KOG0566 consensus Inositol-1,4,5-triphosphate 5-phosphatase (synaptojanin), INP51/INP52/INP53 family [Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG0620 consensus Glucose-repressible alcohol dehydrogenase transcriptional effector CCR4 and related proteins [Transcription] Back     alignment and domain information
>PLN03191 Type I inositol-1,4,5-trisphosphate 5-phosphatase 2; Provisional Back     alignment and domain information
>PTZ00312 inositol-1,4,5-triphosphate 5-phosphatase; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query287
1e9n_A318 A Second Divalent Metal Ion In The Active Site Of A 5e-20
2isi_A317 Crystal Structure Of Ape1 From Homo Sapiens In A Ne 6e-20
2o3h_A285 Crystal Structure Of The Human C65a Ape Length = 28 7e-20
1bix_A287 The Crystal Structure Of The Human Dna Repair Endon 8e-20
1de8_B276 Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bo 8e-20
1dew_A279 Crystal Structure Of Human Ape1 Bound To Abasic Dna 9e-20
2o3c_A282 Crystal Structure Of Zebrafish Ape Length = 282 2e-16
3g91_A265 1.2 Angstrom Structure Of The Exonuclease Iii Homol 2e-10
3fzi_A265 1.9 Angstrom Structure Of The Thermophilic Exonucle 3e-10
3g00_A265 Mth0212 In Complex With A 9bp Blunt End Dsdna At 1. 1e-09
2jc4_A256 3'-5' Exonuclease (Nexo) From Neisseria Meningitidi 9e-08
2voa_A257 Structure Of An Ap Endonuclease From Archaeoglobus 1e-06
2jc5_A259 Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From 3e-05
4b5h_A259 Substate Bound Inactive Mutant Of Neisseria Ap Endo 1e-04
>pdb|1E9N|A Chain A, A Second Divalent Metal Ion In The Active Site Of A New Crystal Form Of Human ApurinicAPYRIMIDINIC ENDONUCLEASE, Ape1, And Its Implications For The Catalytic Mechanism Length = 318 Back     alignment and structure 
Iteration: 1

 Score = 94.7 bits (234), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 119/243 (48%), Gaps = 50/243 (20%)
Query: 42  LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
           LK  +WN + L   +K    +  +++    PD++ LQE +         P   QEL    
Sbjct: 62  LKICSWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 111
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
                            P  ++Q W + +D + Y+G  LL ++C  P KVS+ +     +
Sbjct: 112 -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 150
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
           ++ +GRVI+AEF++F L+  Y PN G        + R++WD+  ++F+    S KPL+ C
Sbjct: 151 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 208
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFLCF 279
           GDLNV+HEEID+ +P+             NK++    GFT  ER+ FG +L+   +   F
Sbjct: 209 GDLNVAHEEIDLRNPKG------------NKKN---AGFTPQERQGFGELLQAVPLADSF 253
Query: 280 YEL 282
             L
Sbjct: 254 RHL 256
>pdb|2ISI|A Chain A, Crystal Structure Of Ape1 From Homo Sapiens In A New Crystal Form Complexed With A Ligand Length = 317 Back     alignment and structure
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape Length = 285 Back     alignment and structure
>pdb|1BIX|A Chain A, The Crystal Structure Of The Human Dna Repair Endonuclease Hap1 Suggests The Recognition Of Extra-Helical Deoxyribose At Dna Abasic Sites Length = 287 Back     alignment and structure
>pdb|1DE8|B Chain B, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To Abasic Dna Length = 276 Back     alignment and structure
>pdb|1DEW|A Chain A, Crystal Structure Of Human Ape1 Bound To Abasic Dna Length = 279 Back     alignment and structure
>pdb|2O3C|A Chain A, Crystal Structure Of Zebrafish Ape Length = 282 Back     alignment and structure
>pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue Mth0212 Length = 265 Back     alignment and structure
>pdb|3FZI|A Chain A, 1.9 Angstrom Structure Of The Thermophilic Exonuclease Iii Homologue Mth0212 Length = 265 Back     alignment and structure
>pdb|3G00|A Chain A, Mth0212 In Complex With A 9bp Blunt End Dsdna At 1.7 Angstrom Length = 265 Back     alignment and structure
>pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis Length = 256 Back     alignment and structure
>pdb|2VOA|A Chain A, Structure Of An Ap Endonuclease From Archaeoglobus Fulgidus Length = 257 Back     alignment and structure
>pdb|2JC5|A Chain A, Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis Length = 259 Back     alignment and structure
>pdb|4B5H|A Chain A, Substate Bound Inactive Mutant Of Neisseria Ap Endonuclease In Presence Of Metal Ions Length = 259 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 ?
Query287
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 7e-39
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 5e-38
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 2e-35
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 3e-33
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48 2e-30
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 8e-30
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 9e-19
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 6e-15
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 9e-15
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosph 9e-13
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 9e-09
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like fold 4e-08
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 7e-08
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 3e-07
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 7e-07
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM 4e-04
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 5e-04
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_A Length = 285 Back     alignment and structure
 Score =  136 bits (346), Expect = 7e-39
 Identities = 77/264 (29%), Positives = 121/264 (45%), Gaps = 56/264 (21%)

Query: 13  SAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLR--VKNNWPEFSNFITTF 70
           S          +D    +TS     K   LK  +WN + L  R  +K       +++   
Sbjct: 2   SHMASEGPALYEDPPDQKTSPS--GKPATLKIASWNVDGL--RAWIKKK---GLDWVKEE 54

Query: 71  DPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLA 130
            PD++ LQE                     TK S  +   L   L   P  ++Q W + +
Sbjct: 55  APDILCLQE---------------------TKCSENK---LPAELQELPGLSHQYWSAPS 90

Query: 131 DSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKE 189
           D + Y+G  LL ++   P KVS+ +     +++ +GRVI+AEF++F L+  Y PN G   
Sbjct: 91  DKEGYSGVGLLSRQ--CPLKVSYGIGDE--EHDQEGRVIVAEFDSFVLVTAYVPNAGRGL 146

Query: 190 EENSFQRRRKWDKRIQEFVLQC-SGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPP 248
               +  R++WD+  ++F+    S KPL+ CGDLNV+HEEID+ +P+             
Sbjct: 147 VRLEY--RQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPK------------G 192

Query: 249 NKEDWGQPGFTIAERKRFGAILKE 272
           NK      GFT  ER+ FG +L+ 
Sbjct: 193 NK---KNAGFTPQERQGFGELLQA 213
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A Length = 318 Back     alignment and structure
>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5' exonuclease, AP endonuclease; HET: PG4; 1.23A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A* 3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A Length = 265 Back     alignment and structure
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} Length = 259 Back     alignment and structure
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Length = 467 Back     alignment and structure
>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A Length = 238 Back     alignment and structure
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} SCOP: d.151.1.1 Length = 268 Back     alignment and structure
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b} Length = 266 Back     alignment and structure
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Length = 257 Back     alignment and structure
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis} Length = 256 Back     alignment and structure
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A* 3k55_A Length = 317 Back     alignment and structure
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X Length = 306 Back     alignment and structure
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3 Length = 301 Back     alignment and structure
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} SCOP: d.151.1.1 Length = 245 Back     alignment and structure
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein; alpha-beta protein, structural genomics, PSI-2; 2.50A {Bacteroides vulgatus atcc 8482} Length = 267 Back     alignment and structure
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron} Length = 298 Back     alignment and structure
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} Length = 257 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query287
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 100.0
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48 99.97
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 99.97
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 99.97
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 99.97
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 99.96
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosph 99.96
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 99.95
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 99.95
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four 99.9
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 99.86
4gew_A362 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 99.85
4fva_A256 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 99.82
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 99.8
4f1h_A250 Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA com 99.77
4gz1_A256 Tyrosyl-DNA phosphodiesterase 2; protein-DNA compl 99.76
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 99.74
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 99.69
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 99.68
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like fold 99.66
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM 99.62
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 99.61
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.co 99.54
1sr4_B261 CDT B, cytolethal distending toxin protein B; bact 99.53
3ngq_A 398 CCR4-NOT transcription complex subunit 6-like; alp 99.45
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse 99.34
4b8c_D727 Glucose-repressible alcohol dehydrogenase transcr 98.98
1i9z_A347 Synaptojanin, phosphatidylinositol phosphate phosp 98.84
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, 98.78
2xsw_A357 72 kDa inositol polyphosphate 5-phosphatase; inosi 98.76
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; 98.64
4a9c_A316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; 98.11
>3g91_A MTH0212, exodeoxyribonuclease; double-strand specific 3'-5' exonuclease, AP endonuclease; HET: PG4; 1.23A {Methanothermobacter thermautotrophicusorganism_taxid} PDB: 3fzi_A 3g0a_A 3g1k_A 3g2c_A 3g3c_A* 3g3y_A* 3g4t_A* 3g00_A 3g0r_A* 3g2d_A* 3g38_A 3g8v_A* 3ga6_A Back     alignment and structure
Probab=100.00  E-value=5.1e-33  Score=246.90  Aligned_cols=195  Identities=26%  Similarity=0.478  Sum_probs=155.2

Q ss_pred             CcEEEEEecCccchhhhcCchhHHHHHhhcCCCEEEEeeecCCCCCCCCCCccccccchhhhhhHHHHHHHHHhhCCCCC
Q 023088           41 PLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPF  120 (287)
Q Consensus        41 ~lkIiTwNv~gl~~~~~~~~~~l~~~l~~~~pDIv~LQEt~~~~~~~~~~~~~~~~l~d~~~~~~~~~~~~~~~L~~~~~  120 (287)
                      +|||+||||+|++.+.++   .+.++|++++|||||||||+.....++                        ..+.  ..
T Consensus         3 ~l~i~s~Nv~g~~~~~~~---~l~~~i~~~~~DIv~LQEt~~~~~~~~------------------------~~~~--~~   53 (265)
T 3g91_A            3 VLKIISWNVNGLRAVHRK---GFLKWFMEEKPDILCLQEIKAAPEQLP------------------------RKLR--HV   53 (265)
T ss_dssp             EEEEEEEECSCHHHHHHH---THHHHHHHHCCSEEEEECCCSCGGGSC------------------------HHHH--CC
T ss_pred             ccEEEEEEcCCchhhhhh---hHHHHHHhcCCCEEEEEeccccccccC------------------------hhhh--cc
Confidence            599999999999887652   599999999999999999998764332                        0111  12


Q ss_pred             CCceEEEEcc-CCCceeEEEEEecCCCcceEeecCcccccccCCCCCEEEEEeCCEEEEEEeeCCCCCCCchhhHHHHHH
Q 023088          121 KNYQIWWSLA-DSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRK  199 (287)
Q Consensus       121 ~gy~~~~~~~-~~~~~GVAIlsr~~i~p~~~~~~l~~~~~~~d~egR~l~~~~~~~~linvY~P~~~~~~~~~~~~~r~~  199 (287)
                      .||..++... .++++|||||+|.+  +..+..+++.  ...+.+||++.+++..+.|+|+|+|++...  ..++.+|.+
T Consensus        54 ~gy~~~~~~~~~~~~~Gvail~k~~--~~~~~~~~~~--~~~d~~gr~i~~~~~~~~i~~vy~p~~~~~--~~~~~~r~~  127 (265)
T 3g91_A           54 EGYRSFFTPAERKGYSGVAMYTKVP--PSSLREGFGV--ERFDTEGRIQIADFDDFLLYNIYFPNGAMS--EERLKYKLE  127 (265)
T ss_dssp             TTCEEEEECBSSTTSCCEEEEESSC--CSEEECCCSC--HHHHSBSCEEEEECSSCEEEEEECCCCTTC--HHHHHHHHH
T ss_pred             cCCcEEEccCCCCCcCEEEEEEecC--hHHhccCCCC--cccCCcCCEEEEEeCCEEEEEEEecCCCCC--chhHHHHHH
Confidence            6998777654 34578999999986  4455554431  235679999999999999999999998863  357778899


Q ss_pred             HHHHHHHHHHhC--CCCCEEEEecCCCCCCCccccCchhhhhhhcCCCCCCCCCCCCCCCCCHHHHHHHHHHHHcCCeee
Q 023088          200 WDKRIQEFVLQC--SGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEYLIFL  277 (287)
Q Consensus       200 f~~~L~~~l~~~--~~~pvIl~GDFN~~~~~~D~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~er~~l~~l~~~g~lvD  277 (287)
                      |++.|.+++.+.  .+.++|||||||+.+.++|..++..               +.+.+++++.+|.+|+.+++.| |+|
T Consensus       128 ~~~~l~~~~~~~~~~~~~~ii~GDfN~~~~~~d~~~~~~---------------~~~~~~~~~~~~~~~~~l~~~g-l~D  191 (265)
T 3g91_A          128 FYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKE---------------NSNVSGFLPVERAWIDKFIENG-YVD  191 (265)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEEEECCCCCSGGGBSCTGG---------------GTTSTTSCHHHHHHHHHHHHTT-EEE
T ss_pred             HHHHHHHHHHHHHcCCCCEEEECccccCCchhhccCHhh---------------cCCCCccCHHHHHHHHHHHhcC-cEE
Confidence            999999988764  3689999999999999999987641               2367899999999999999656 999


Q ss_pred             eeeccccCC
Q 023088          278 CFYELAVMK  286 (287)
Q Consensus       278 ~~R~~~p~~  286 (287)
                      +||.+||..
T Consensus       192 ~~r~~~p~~  200 (265)
T 3g91_A          192 TFRMFNSDP  200 (265)
T ss_dssp             THHHHCCCS
T ss_pred             eeHhhCCCC
Confidence            999999864
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Back     alignment and structure
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A Back     alignment and structure
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Back     alignment and structure
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_A Back     alignment and structure
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} Back     alignment and structure
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis} Back     alignment and structure
>1vyb_A ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens} SCOP: d.151.1.1 PDB: 2v0s_A 2v0r_A Back     alignment and structure
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} SCOP: d.151.1.1 Back     alignment and structure
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori} Back     alignment and structure
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} SCOP: d.151.1.1 Back     alignment and structure
>4gew_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; 2.35A {Caenorhabditis elegans} PDB: 4f1i_A Back     alignment and structure
>4fva_A 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosyl-DNA diesterase, hydrolase; HET: EDO; 2.07A {Caenorhabditis elegans} Back     alignment and structure
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b} Back     alignment and structure
>4f1h_A Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA complex; HET: DNA; 1.66A {Danio rerio} PDB: 4fpv_A* 4f1h_B* Back     alignment and structure
>4gz1_A Tyrosyl-DNA phosphodiesterase 2; protein-DNA complex, DNA repair, 5'-DNA END processing, endonuclease/exonuclease/phosphatase domain; HET: DNA EPE; 1.50A {Mus musculus} PDB: 4gyz_A* 4gz0_A* 4gz2_A* Back     alignment and structure
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} Back     alignment and structure
>3g6s_A Putative endonuclease/exonuclease/phosphatase family protein; alpha-beta protein, structural genomics, PSI-2; 2.50A {Bacteroides vulgatus atcc 8482} Back     alignment and structure
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3 Back     alignment and structure
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X Back     alignment and structure
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron} Back     alignment and structure
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus} PDB: 3i46_A 3i48_A 3i5v_A* 3k55_A Back     alignment and structure
>2f1n_A CDT B, cytolethal distending toxin subunit B; E.coli, DNAse I, microbatch; 1.73A {Escherichia coli} SCOP: d.151.1.1 Back     alignment and structure
>1sr4_B CDT B, cytolethal distending toxin protein B; bacterial, virulence, DNA damage, genotoxin, cytotoxins, cell cycle, apoptosis, lectin; 2.00A {Haemophilus ducreyi} SCOP: d.151.1.1 PDB: 2f2f_B Back     alignment and structure
>3ngq_A CCR4-NOT transcription complex subunit 6-like; alpha/beta sandwich fold, hydrolase; HET: 1PS; 1.80A {Homo sapiens} PDB: 3ngo_A 3ngn_A Back     alignment and structure
>2a40_B Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3, structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus} SCOP: d.151.1.1 PDB: 1dnk_A* 2a3z_B* 2a41_B* 2a42_B* 2d1k_B* 2dnj_A* 3cjc_D* 3dni_A* 1atn_D* Back     alignment and structure
>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C} Back     alignment and structure
>1i9z_A Synaptojanin, phosphatidylinositol phosphate phosphatase; spsynaptojanin, IPP5C, IP3, IP2,, hydrolase; HET: 2IP; 1.80A {Schizosaccharomyces pombe} SCOP: d.151.1.2 PDB: 1i9y_A* Back     alignment and structure
>2imq_X Salivary nitrophorin; ferrous heme, beta-sandwich, transport protein; HET: HEM; 1.30A {Cimex lectularius} SCOP: d.151.1.2 PDB: 1ntf_A* 1y21_A* 1yjh_A* 1si6_X* Back     alignment and structure
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling, SGC stockholm, structural genomics CONS hydrolase; 1.90A {Homo sapiens} Back     alignment and structure
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas; INPP5BA,phosphoinositide 5-phosphatase, inositol signalling, phosphatase, magnesium; HET: PIF; 2.40A {Homo sapiens} PDB: 3n9v_A Back     alignment and structure
>4a9c_A Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; SGC, signalling, structural genomics consortium stockholm, magnesium binding, hydrolase; HET: B5F; 2.10A {Homo sapiens} PDB: 3nr8_B* 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 287
d2f1na1250 d.151.1.1 (A:1-250) Cytolethal distending toxin su 1e-14
d2imqx1280 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug ( 1e-10
d1sr4b_261 d.151.1.1 (B:) Cytolethal distending toxin subunit 5e-10
d2ddra1299 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesteras 2e-09
d1zwxa1293 d.151.1.3 (A:41-333) Sphingomyelin phosphodiestera 6e-09
d1hd7a_275 d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human 6e-09
d2a40b1260 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos 8e-08
d1akoa_268 d.151.1.1 (A:) DNA-repair enzyme exonuclease III { 2e-07
d1wdua_228 d.151.1.1 (A:) Endonuclease domain of TRAS1 retrot 3e-07
d1vyba_236 d.151.1.1 (A:) Endonuclease domain of LINE-1 rever 5e-06
>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]} Length = 250 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: DNase I-like
superfamily: DNase I-like
family: DNase I-like
domain: Cytolethal distending toxin subunit B
species: Escherichia coli [TaxId: 562]

 Score = 69.7 bits (169), Expect = 1e-14
 Identities = 23/203 (11%), Positives = 58/203 (28%), Gaps = 18/203 (8%)

Query: 42  LKFVTWNANSLLLRVKNNWPE--FSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKD 99
            +  TWN        ++ W              D++A+QE   P + + D  +       
Sbjct: 5   FRVATWNLQGASATTESKWNINVRQLISGENAVDILAVQEAGSPPSTAVDTGRVIPSPGI 64

Query: 100 DTKASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTA 158
                   +LI   + +S P + Y  + ++         AL+     +  +V       +
Sbjct: 65  P-----VRELIWNLSTNSRPQQVYIYFSAVDALGGRVNLALVSN--RRADEV----FVLS 113

Query: 159 LKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEF-VLQCSGKPLI 217
              +    ++            +A         ++     +     ++           +
Sbjct: 114 PVRQGGRPLLGIRIGNDAFFTAHAIAMR---NNDAPALVEEVYNFFRDSRDPVHQALNWM 170

Query: 218 WCGDLNVSHEEIDVSHPEFFAAA 240
             GD N    +++++       A
Sbjct: 171 ILGDFNREPADLEMNLTVPVRRA 193
>d2imqx1 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId: 79782]} Length = 280 Back     information, alignment and structure
>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} Length = 261 Back     information, alignment and structure
>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} Length = 299 Back     information, alignment and structure
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Length = 293 Back     information, alignment and structure
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} Length = 275 Back     information, alignment and structure
>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} Length = 260 Back     information, alignment and structure
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} Length = 268 Back     information, alignment and structure
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} Length = 228 Back     information, alignment and structure
>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 236 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 ?
Query287
d1vyba_236 Endonuclease domain of LINE-1 reverse transcriptas 99.93
d1hd7a_275 DNA repair endonuclease Hap1 {Human (Homo sapiens) 99.87
d1wdua_228 Endonuclease domain of TRAS1 retrotransposon (ORF2 99.82
d1akoa_268 DNA-repair enzyme exonuclease III {Escherichia col 99.73
d1zwxa1293 Sphingomyelin phosphodiesterase C {Listeria ivanov 99.64
d2f1na1250 Cytolethal distending toxin subunit B {Escherichia 99.63
d2ddra1299 Sphingomyelin phosphodiesterase C {Bacillus cereus 99.58
d1sr4b_261 Cytolethal distending toxin subunit B {Haemophilus 99.54
d2imqx1280 Salivary nitrophorin {Bedbug (Cimex lectularius) [ 99.53
d2a40b1260 Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913 99.42
d1i9za_345 Synaptojanin, IPP5C domain {Fission yeast (Schizos 99.07
>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: DNase I-like
superfamily: DNase I-like
family: DNase I-like
domain: Endonuclease domain of LINE-1 reverse transcriptase homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=8.1e-25  Score=186.91  Aligned_cols=180  Identities=21%  Similarity=0.305  Sum_probs=119.3

Q ss_pred             CCCCcEEEEEecCccchhhhcCchhHHHHHhhcCCCEEEEeeecCCCCCCCCCCccccccchhhhhhHHHHHHHHHhhCC
Q 023088           38 KKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSS  117 (287)
Q Consensus        38 ~~~~lkIiTwNv~gl~~~~~~~~~~l~~~l~~~~pDIv~LQEt~~~~~~~~~~~~~~~~l~d~~~~~~~~~~~~~~~L~~  117 (287)
                      ..++|||+||||+|++...++  ..|.++|++++|||||||||+.......                         .+  
T Consensus         2 ~~~~~kv~s~Nv~g~~~~~~~--~~i~~~i~~~~~DIi~LQE~~~~~~~~~-------------------------~~--   52 (236)
T d1vyba_           2 SNSHITILTLNINGLNSAIKR--HRLASWIKSQDPSVCCIQETHLTCRDTH-------------------------RL--   52 (236)
T ss_dssp             CCCCEEEEEEECSCCCSHHHH--HHHHHHHHHHCCSEEEEECCCCCTTSGG-------------------------GC--
T ss_pred             CCCCeEEEEEEcCCccchhhH--HHHHHHHHHCCCeEEEEEcccCccccch-------------------------hh--
Confidence            457899999999999876654  6899999999999999999987654211                         11  


Q ss_pred             CCCCCceEEEEc-cCCCceeEEEEEecCCCcceEeecCcccccccCCCCCEEEEEe--C--CEEEEEEeeCCCCCCCchh
Q 023088          118 PPFKNYQIWWSL-ADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEF--E--TFYLLNTYAPNNGWKEEEN  192 (287)
Q Consensus       118 ~~~~gy~~~~~~-~~~~~~GVAIlsr~~i~p~~~~~~l~~~~~~~d~egR~l~~~~--~--~~~linvY~P~~~~~~~~~  192 (287)
                       ...++..++.. ...+++|+||+++.++.-  ....+     ..+..++++.+.+  .  .++++++|+|+...    .
T Consensus        53 -~~~~~~~~~~~~~~~~~~g~~i~~k~~~~~--~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~----~  120 (236)
T d1vyba_          53 -KIKGWRKIYQANGKQKKAGVAILVSDKTDF--KPTKI-----KRDKEGHYIMVKGSIQQEELTILNIYAPNTGA----P  120 (236)
T ss_dssp             -CCTTCCEEEEECCSSSSCCEEEEECTTCCC--EEEEE-----EECTTSSEEEEEEEETTEEEEEEEEECCSSSH----H
T ss_pred             -hhcccceEEEeeccccccceeeEeeccccc--ccccc-----cccccccceeeeeeeccCcceeEEeccccccc----H
Confidence             11344444333 445578999999986421  11111     2345677665544  2  69999999997653    1


Q ss_pred             hHHHHHHHHHHHHHHHHhCCCCCEEEEecCCCCCCCccccCchhhhhhhcCCCCCCCCCCCCCCCCCHHHHHHHHHHHHc
Q 023088          193 SFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKE  272 (287)
Q Consensus       193 ~~~~r~~f~~~L~~~l~~~~~~pvIl~GDFN~~~~~~D~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~er~~l~~l~~~  272 (287)
                            ++..++...+....+.|+|+|||||.++...|..+.                     ...... +..+...+..
T Consensus       121 ------~~~~~~~~~~~~~~~~~~Il~GDfN~~~~~~d~~~~---------------------~~~~~~-~~~~~~~~~~  172 (236)
T d1vyba_         121 ------RFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTR---------------------QKVNKD-TQELNSALHQ  172 (236)
T ss_dssp             ------HHHHHHHHHTTTTCCTTEEEEEECSSCSSGGGBTTC---------------------CCCCHH-HHHHHHHHHH
T ss_pred             ------HHHHhhhhhhcccccceeEEeeccccccchhhhccc---------------------ccchhh-HHHHHHHHHh
Confidence                  233334444444467899999999998877776532                     112333 3445555555


Q ss_pred             CCeeeeeeccccCC
Q 023088          273 YLIFLCFYELAVMK  286 (287)
Q Consensus       273 g~lvD~~R~~~p~~  286 (287)
                      .+++|+||.+++..
T Consensus       173 ~~~~d~~r~~~~~~  186 (236)
T d1vyba_         173 ADLIDIYRTLHPKS  186 (236)
T ss_dssp             TTEEEHHHHHCTTC
T ss_pred             hhcccccceeccCC
Confidence            55999999988753
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} Back     information, alignment and structure
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Back     information, alignment and structure
>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} Back     information, alignment and structure
>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} Back     information, alignment and structure
>d2imqx1 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId: 79782]} Back     information, alignment and structure
>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} Back     information, alignment and structure
>d1i9za_ d.151.1.2 (A:) Synaptojanin, IPP5C domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Back     information, alignment and structure