Citrus Sinensis ID: 025138

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-------
MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLVLLS
ccccccccccccccccccccccccccccccccccccccccccEEEEEEHHHHHHHHHcccHHHHHHHHHccccEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccEEEEEcccccccEEEEEEEccccccEEEEccccccccccccccEEEEEEccEEEEEEEccccccccccccHHHHHHHHHHHHHHHHHcccccEEEEcccccccccccccccccccccccccccHHHHHHccccc
cccEEEEcccccccccccccccccccccccccccccccccccEEEEEEcccHHHHHccccHHHHHHHHHccccEEEEEEEccccccccccccccccccccccHHHHHHHHHHHHHHccccccccHHHHcccccccEEEEEEEcccccEEEEEccccccHccccccEEEEEEcccEEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHEccHHcccccccccccHHHHHHHHccc
mkrffkpiekecsakkpalspskkdgettetsseenskkdplkFVTWNANSLLLRVknnwpefsnfittfdpdvialqevrmpaagskdapknhqelkddtKASREEKLILMRAlssppfknyqIWWSLADSKYAGTALLVKKcfqpkkvsFSLEKTalkyepdgrVILAEFETFYLLntyapnngwkeeENSFQRRRKWDKRIQEFVLQcsgkpliwcgdlnvsheeidvshpeFFAAAklngyvppnKEVLVLLS
mkrffkpiekecsakkpalspskkdgettetsseenskkdplkfVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMpaagskdapknhqelkddtkasREEKLILMRalssppfkNYQIWWSLADSKYAGTALLVKKcfqpkkvsfslektalkyepdGRVILAEFETFYLLNTyapnngwkeeeNSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLVLLS
MKRFFKPIEKECsakkpalspskkdgettetsseenskkDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLVLLS
*****************************************LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEV****************************LILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLVL**
******************************************KFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLVLLS
MKRFFKPIEKEC***************************DPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMP******************KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLVLLS
*********K****************************KDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKD******ELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFA*******V***********
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MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLVLLS
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 ?
Query257 2.2.26 [Sep-21-2011]
P43138317 DNA-(apurinic or apyrimid yes no 0.801 0.649 0.298 4e-20
P28352317 DNA-(apurinic or apyrimid yes no 0.801 0.649 0.298 7e-20
A2T6Y4318 DNA-(apurinic or apyrimid yes no 0.789 0.638 0.293 3e-19
A1YFZ3318 DNA-(apurinic or apyrimid N/A no 0.789 0.638 0.293 3e-19
A2T7I6318 DNA-(apurinic or apyrimid N/A no 0.789 0.638 0.293 4e-19
P27695318 DNA-(apurinic or apyrimid yes no 0.789 0.638 0.293 4e-19
A1YES6318 DNA-(apurinic or apyrimid N/A no 0.789 0.638 0.293 7e-19
P51173361 DNA-(apurinic or apyrimid yes no 0.622 0.443 0.295 1e-17
P23196318 DNA-(apurinic or apyrimid yes no 0.789 0.638 0.285 3e-17
P37454252 Exodeoxyribonuclease OS=B yes no 0.607 0.619 0.271 5e-15
>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 = 98.6 bits (244), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 121/248 (48%), Gaps = 42/248 (16%)

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+     K  
Sbjct: 174 AG--RGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNVAHEEIDLRNPK--GNKKNA 229

Query: 244 GYVPPNKE 251
           G+ P  ++
Sbjct: 230 GFTPQERQ 237
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|P37454|EXOA_BACSU Exodeoxyribonuclease OS=Bacillus subtilis (strain 168) GN=exoA 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 ?
Query257
449487730 361 PREDICTED: LOW QUALITY PROTEIN: DNA-(apu 0.976 0.695 0.760 1e-110
449469598 361 PREDICTED: DNA-(apurinic or apyrimidinic 0.976 0.695 0.760 1e-110
225456791357 PREDICTED: DNA-(apurinic or apyrimidinic 0.968 0.697 0.760 1e-110
297816036 684 hypothetical protein ARALYDRAFT_347932 [ 0.972 0.365 0.774 1e-110
4678346 686 putative protein [Arabidopsis thaliana] 0.972 0.364 0.762 1e-109
224133800 366 predicted protein [Populus trichocarpa] 0.976 0.685 0.767 1e-109
42565714 364 endonuclease/exonuclease/phosphatase dom 0.972 0.686 0.762 1e-108
356508768355 PREDICTED: exodeoxyribonuclease-like [Gl 0.945 0.684 0.731 1e-103
358348991278 DNA-(apurinic or apyrimidinic site) lyas 0.968 0.895 0.725 3e-98
358348989 367 DNA-(apurinic or apyrimidinic site) lyas 0.968 0.678 0.725 3e-98
>gi|449487730|ref|XP_004157772.1| PREDICTED: LOW QUALITY PROTEIN: DNA-(apurinic or apyrimidinic site) lyase-like [Cucumis sativus] Back     alignment and taxonomy information
 Score =  404 bits (1038), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 191/251 (76%), Positives = 218/251 (86%)

Query: 1   MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNW 60
           MKRFFKPIEKE S+KK ALSPS KDG+  ++ +    KK+PLKFVTWNANSLLLRVKN+W
Sbjct: 1   MKRFFKPIEKEGSSKKVALSPSLKDGDDGDSEASVPDKKEPLKFVTWNANSLLLRVKNDW 60

Query: 61  PEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPF 120
            EF+ F+T  DPD IA+QEVR+PAAGSK A KN  ELKDDT  SREEK +LMRALSSPPF
Sbjct: 61  SEFTKFVTNLDPDAIAIQEVRIPAAGSKGASKNQGELKDDTNTSREEKQMLMRALSSPPF 120

Query: 121 KNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNT 180
            NY++WWSL+DSKYAGTAL +KKCFQPKKV F+L++ A K+E DGRVILAEFETF LLNT
Sbjct: 121 ANYRVWWSLSDSKYAGTALFIKKCFQPKKVXFNLDRIASKHEVDGRVILAEFETFRLLNT 180

Query: 181 YAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAA 240
           Y+PNNGWKEEE SF+RRRKWDKR+ EFV+Q S KPLIWCGDLNVSHEEIDVSHP+FF+AA
Sbjct: 181 YSPNNGWKEEEKSFKRRRKWDKRMLEFVIQSSDKPLIWCGDLNVSHEEIDVSHPDFFSAA 240

Query: 241 KLNGYVPPNKE 251
           KLNGY+PPNKE
Sbjct: 241 KLNGYIPPNKE 251

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449469598|ref|XP_004152506.1| PREDICTED: DNA-(apurinic or apyrimidinic site) lyase-like [Cucumis sativus] Back     alignment and taxonomy information
>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
>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|224133800|ref|XP_002321664.1| predicted protein [Populus trichocarpa] gi|222868660|gb|EEF05791.1| predicted protein [Populus trichocarpa] 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|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
>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

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 ?
Query257
TAIR|locus:505006392 364 AT3G48425 [Arabidopsis thalian 0.976 0.689 0.714 2e-95
GENEDB_PFALCIPARUM|PFC0250c 617 PFC0250c "AP endonuclease (DNA 0.778 0.324 0.396 1.6e-34
UNIPROTKB|O97240 617 PFC0250c "AP endonuclease (DNA 0.778 0.324 0.396 1.6e-34
MGI|MGI:88042317 Apex1 "apurinic/apyrimidinic e 0.548 0.444 0.370 3.4e-23
RGD|2126317 Apex1 "APEX nuclease (multifun 0.548 0.444 0.370 3.4e-23
UNIPROTKB|J9PA46318 APEX1 "Uncharacterized protein 0.548 0.443 0.370 6.9e-23
UNIPROTKB|A1YFZ3318 APEX1 "DNA-(apurinic or apyrim 0.548 0.443 0.363 8.8e-23
UNIPROTKB|A2T6Y4318 APEX1 "DNA-(apurinic or apyrim 0.548 0.443 0.363 8.8e-23
UNIPROTKB|Q9Z2J2317 APE "Apurinic/apyrimidinic end 0.548 0.444 0.370 1.1e-22
UNIPROTKB|A1YES6318 APEX1 "DNA-(apurinic or apyrim 0.544 0.440 0.374 1.1e-22
TAIR|locus:505006392 AT3G48425 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 949 (339.1 bits), Expect = 2.0e-95, P = 2.0e-95
 Identities = 180/252 (71%), Positives = 199/252 (78%)

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 AKLNGYVPPNKE 251
             AKLNGYVPPNKE
Sbjct:   241 AKLNGYVPPNKE 252
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:
fgenesh1_pg.C_scaffold_5001324
annotation not avaliable (684 aa)
(Arabidopsis lyrata)
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 ?
Query257
cd09087253 cd09087, Ape1-like_AP-endo, Human Ape1-like subfam 1e-59
cd09073251 cd09073, ExoIII_AP-endo, Escherichia coli exonucle 5e-34
COG0708261 COG0708, XthA, Exonuclease III [DNA replication, r 4e-32
TIGR00633255 TIGR00633, xth, exodeoxyribonuclease III (xth) 2e-29
TIGR00195254 TIGR00195, exoDNase_III, exodeoxyribonuclease III 5e-27
cd09085252 cd09085, Mth212-like_AP-endo, Methanothermobacter 2e-20
PRK13911250 PRK13911, PRK13911, exodeoxyribonuclease III; Prov 8e-18
cd09088309 cd09088, Ape2-like_AP-endo, Human Ape2-like subfam 2e-14
cd09086254 cd09086, ExoIII-like_AP-endo, Escherichia coli exo 3e-14
cd09076236 cd09076, L1-EN, Endonuclease domain (L1-EN) of the 1e-13
cd08372241 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase 2e-13
cd10281253 cd10281, Nape_like_AP-endo, Neisseria meningitides 7e-13
PRK11756268 PRK11756, PRK11756, exonuclease III; Provisional 7e-04
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 =  188 bits (481), Expect = 1e-59
 Identities = 67/198 (33%), Positives = 103/198 (52%), Gaps = 36/198 (18%)

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 GDLNVSHEEIDVSHPEFF 237
           GDLNV+HEEID+++P+  
Sbjct: 147 GDLNVAHEEIDLANPKTN 164

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|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|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|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 257
COG0708261 XthA Exonuclease III [DNA replication, recombinati 100.0
PRK13911250 exodeoxyribonuclease III; Provisional 100.0
PRK11756268 exonuclease III; Provisional 99.96
TIGR00195254 exoDNase_III exodeoxyribonuclease III. The model b 99.95
TIGR00633255 xth exodeoxyribonuclease III (xth). This family is 99.93
PRK05421263 hypothetical protein; Provisional 99.67
PRK15251271 cytolethal distending toxin subunit CdtB; Provisio 99.58
TIGR03395283 sphingomy sphingomyelin phosphodiesterase. Members 99.57
COG3568259 ElsH Metal-dependent hydrolase [General function p 99.49
PF03372249 Exo_endo_phos: Endonuclease/Exonuclease/phosphatas 99.49
PLN03144 606 Carbon catabolite repressor protein 4 homolog; Pro 99.32
KOG2756349 consensus Predicted Mg2+-dependent phosphodiestera 99.25
PTZ00297 1452 pantothenate kinase; Provisional 99.23
smart00476276 DNaseIc deoxyribonuclease I. Deoxyribonuclease I c 99.2
KOG1294335 consensus Apurinic/apyrimidinic endonuclease and r 99.17
KOG2338 495 consensus Transcriptional effector CCR4-related pr 99.16
KOG3873 422 consensus Sphingomyelinase family protein [Signal 98.99
smart00128310 IPPc Inositol polyphosphate phosphatase, catalytic 98.72
COG3021309 Uncharacterized protein conserved in bacteria [Fun 98.68
PF14529119 Exo_endo_phos_2: Endonuclease-reverse transcriptas 98.15
COG5239 378 CCR4 mRNA deadenylase, exonuclease subunit and rel 97.06
KOG0566 1080 consensus Inositol-1,4,5-triphosphate 5-phosphatas 96.97
KOG0620 361 consensus Glucose-repressible alcohol dehydrogenas 94.12
COG2374798 Predicted extracellular nuclease [General function 90.8
PLN03191 621 Type I inositol-1,4,5-trisphosphate 5-phosphatase 89.36
PTZ00312 356 inositol-1,4,5-triphosphate 5-phosphatase; Provisi 81.16
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information 
Probab=100.00  E-value=1.2e-37  Score=272.46  Aligned_cols=180  Identities=28%  Similarity=0.532  Sum_probs=154.1

Q ss_pred             cEEEEEeCCcchhhhhcCchHHHHHHhhcCCcEEEEecccCCCCCCCCCCccccccchhhhhhHHHHHHHHHhhCCCCCC
Q 025138           42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFK  121 (257)
Q Consensus        42 lrIiTwNv~gl~~~~~~~~~~l~~~l~~~~~DIi~LQEt~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~  121 (257)
                      |||+||||||++.+.+    .+.+++.+++|||||||||+....++|..                       .+   ...
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            8999999999999884    59999999999999999999998887731                       12   127


Q ss_pred             CCeEEEEcCCCCcceEEEEEccCCCcceeeecCcccccCCCCCCCEEEEEeCCEEEEEEecCCCCCCCccccHHHHHHHH
Q 025138          122 NYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWD  201 (257)
Q Consensus       122 gY~~~~~~~~~~~~GVAIlsr~~l~p~~v~~~l~~~~~~~d~~gr~i~v~~~~~~i~~vY~P~~~~~~~~~~~~~r~~f~  201 (257)
                      ||+.++..+++|++||||+||.+  |..+..++++. ...+.+||+|.++++.+.|+|+|+|++... ..+++.+|.+|+
T Consensus        51 GY~~~~~~gqKgysGVailsr~~--~~~v~~g~~~~-~~~d~e~R~I~a~~~~~~v~~~Y~PnG~~~-~~~k~~yKl~f~  126 (261)
T COG0708          51 GYHHVFNHGQKGYSGVAILSKKP--PDDVRRGFPGE-EEDDEEGRVIEAEFDGFRVINLYFPNGSSI-GLEKFDYKLRFL  126 (261)
T ss_pred             CceEEEecCcCCcceEEEEEccC--chhhhcCCCCC-ccccccCcEEEEEECCEEEEEEEcCCCCCC-CCcchHHHHHHH
Confidence            99766666788999999999986  55777777641 235678999999999999999999999862 246799999999


Q ss_pred             HHHHHHHHcC--CCCCEEEEecCCCCCCCccCCCc-ccccCCCCCCCCHHHHhhhhh
Q 025138          202 KRIQEFVLQC--SGKPLIWCGDLNVSHEEIDVSHP-EFFAAAKLNGYVPPNKEVLVL  255 (257)
Q Consensus       202 ~~L~~~l~~~--~~~pvIl~GDFN~~~~~~D~~~~-~~~~~~~~~~~~~~~r~~~~~  255 (257)
                      +.|.+++.++  .+.|+|+|||||++|.+.|+++| +.+.+.+.+||+++||+.|..
T Consensus       127 ~~l~~~l~~l~~~~~~~vl~GD~NIap~~iDv~~~~~~~~n~~~~~f~~eeR~~~~~  183 (261)
T COG0708         127 DALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSGFLPEERAWFRR  183 (261)
T ss_pred             HHHHHHHHHHhhcCCCEEEecccccCCchhcccCchhhhhcCCCCCCCHHHHHHHHH
Confidence            9999999874  56899999999999999999999 777789999999999999864

>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
>PRK15251 cytolethal distending toxin subunit CdtB; Provisional Back     alignment and domain information
>TIGR03395 sphingomy sphingomyelin phosphodiesterase Back     alignment and domain information
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only] 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
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional Back     alignment and domain information
>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms] Back     alignment and domain information
>PTZ00297 pantothenate kinase; Provisional Back     alignment and domain information
>smart00476 DNaseIc deoxyribonuclease I Back     alignment and domain information
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] Back     alignment and domain information
>KOG2338 consensus Transcriptional effector CCR4-related protein [Transcription] Back     alignment and domain information
>KOG3873 consensus Sphingomyelinase family protein [Signal transduction mechanisms] 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
>COG2374 Predicted extracellular nuclease [General function prediction only] 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 ?
Query257
2o3h_A285 Crystal Structure Of The Human C65a Ape Length = 28 1e-18
1e9n_A318 A Second Divalent Metal Ion In The Active Site Of A 1e-18
2isi_A317 Crystal Structure Of Ape1 From Homo Sapiens In A Ne 1e-18
1bix_A287 The Crystal Structure Of The Human Dna Repair Endon 1e-18
1dew_A279 Crystal Structure Of Human Ape1 Bound To Abasic Dna 2e-18
1de8_B276 Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bo 2e-18
2o3c_A282 Crystal Structure Of Zebrafish Ape Length = 282 8e-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 8e-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|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape Length = 285 Back     alignment and structure 
Iteration: 1

 Score = 89.7 bits (221), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 64/212 (30%), Positives = 107/212 (50%), Gaps = 37/212 (17%)
Query: 42  LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDT 101
           LK  +WN + L   +K    +  +++    PD++ LQE +         P   QEL    
Sbjct: 29  LKIASWNVDGLRAWIKK---KGLDWVKEEAPDILCLQETK---CSENKLPAELQEL---- 78
Query: 102 KASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALK 160
                            P  ++Q W + +D + Y+G  LL ++C  P KVS+ +     +
Sbjct: 79  -----------------PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--E 117
Query: 161 YEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWC 219
           ++ +GRVI+AEF++F L+  Y PN G        + R++WD+  ++F+    S KPL+ C
Sbjct: 118 HDQEGRVIVAEFDSFVLVTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLC 175
Query: 220 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKE 251
           GDLNV+HEEID+ +P+     K  G+ P  ++
Sbjct: 176 GDLNVAHEEIDLRNPK--GNKKNAGFTPQERQ 205
>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
>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|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|1DEW|A Chain A, Crystal Structure Of Human Ape1 Bound To Abasic Dna Length = 279 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|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 ?
Query257
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 6e-37
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 4e-36
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 7e-34
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 1e-31
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 2e-30
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48 3e-28
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 8e-16
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 3e-15
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 3e-13
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosph 1e-11
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 6e-09
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like fold 3e-08
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 5e-08
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 2e-07
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 5e-07
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM 3e-04
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 3e-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 =  130 bits (330), Expect = 6e-37
 Identities = 67/227 (29%), Positives = 108/227 (47%), Gaps = 41/227 (18%)

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-SGKPLIWCGDLNVSHEEIDVSHPE 235
               +  R++WD+  ++F+    S KPL+ CGDLNV+HEEID+ +P+
Sbjct: 147 VRLEY--RQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPK 191
>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
>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
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Length = 467 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 ?
Query257
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 99.96
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48 99.94
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 99.94
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 99.94
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 99.94
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosph 99.93
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 99.93
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 99.91
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 99.9
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four 99.87
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 99.83
4gew_A362 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 99.83
4fva_A256 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 99.82
4f1h_A250 Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA com 99.77
4gz1_A256 Tyrosyl-DNA phosphodiesterase 2; protein-DNA compl 99.75
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 99.71
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 99.68
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 99.67
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like fold 99.65
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 99.64
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 99.63
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.co 99.58
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM 99.56
1sr4_B261 CDT B, cytolethal distending toxin protein B; bact 99.54
3ngq_A 398 CCR4-NOT transcription complex subunit 6-like; alp 99.49
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse 99.37
4b8c_D 727 Glucose-repressible alcohol dehydrogenase transcr 99.05
1i9z_A 347 Synaptojanin, phosphatidylinositol phosphate phosp 98.84
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, 98.8
2xsw_A 357 72 kDa inositol polyphosphate 5-phosphatase; inosi 98.77
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; 98.59
4a9c_A316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; 98.26
>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=99.96  E-value=4e-28  Score=211.45  Aligned_cols=178  Identities=27%  Similarity=0.550  Sum_probs=139.5

Q ss_pred             CCcEEEEEeCCcchhhhhcCchHHHHHHhhcCCcEEEEecccCCCCCCCCCCccccccchhhhhhHHHHHHHHHhhCCCC
Q 025138           40 DPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPP  119 (257)
Q Consensus        40 ~~lrIiTwNv~gl~~~~~~~~~~l~~~l~~~~~DIi~LQEt~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~  119 (257)
                      ..|||+||||+|++...+   ..+.++|++.+|||||||||+.....++                        ..+.  .
T Consensus         2 ~~l~i~s~Nv~g~~~~~~---~~l~~~i~~~~~DIv~LQEt~~~~~~~~------------------------~~~~--~   52 (265)
T 3g91_A            2 AVLKIISWNVNGLRAVHR---KGFLKWFMEEKPDILCLQEIKAAPEQLP------------------------RKLR--H   52 (265)
T ss_dssp             CEEEEEEEECSCHHHHHH---HTHHHHHHHHCCSEEEEECCCSCGGGSC------------------------HHHH--C
T ss_pred             CccEEEEEEcCCchhhhh---hhHHHHHHhcCCCEEEEEeccccccccC------------------------hhhh--c
Confidence            369999999999988765   2599999999999999999987754322                        0111  1


Q ss_pred             CCCCeEEEEcC-CCCcceEEEEEccCCCcceeeecCcccccCCCCCCCEEEEEeCCEEEEEEecCCCCCCCccccHHHHH
Q 025138          120 FKNYQIWWSLA-DSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRR  198 (257)
Q Consensus       120 ~~gY~~~~~~~-~~~~~GVAIlsr~~l~p~~v~~~l~~~~~~~d~~gr~i~v~~~~~~i~~vY~P~~~~~~~~~~~~~r~  198 (257)
                      ..||..++... ..+++||||++|.+  +..+..++..  ...+.++|++.+++..+.|+|+|+|++...  ..++.+|.
T Consensus        53 ~~gy~~~~~~~~~~~~~Gvail~k~~--~~~~~~~~~~--~~~d~~gr~i~~~~~~~~i~~vy~p~~~~~--~~~~~~r~  126 (265)
T 3g91_A           53 VEGYRSFFTPAERKGYSGVAMYTKVP--PSSLREGFGV--ERFDTEGRIQIADFDDFLLYNIYFPNGAMS--EERLKYKL  126 (265)
T ss_dssp             CTTCEEEEECBSSTTSCCEEEEESSC--CSEEECCCSC--HHHHSBSCEEEEECSSCEEEEEECCCCTTC--HHHHHHHH
T ss_pred             ccCCcEEEccCCCCCcCEEEEEEecC--hHHhccCCCC--cccCCcCCEEEEEeCCEEEEEEEecCCCCC--chhHHHHH
Confidence            26999777653 34677999999986  4444444432  234568999999999999999999998753  35778899


Q ss_pred             HHHHHHHHHHHcC--CCCCEEEEecCCCCCCCccCCCcccccCCCCCCCCHHHHhhhh
Q 025138          199 KWDKRIQEFVLQC--SGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEVLV  254 (257)
Q Consensus       199 ~f~~~L~~~l~~~--~~~pvIl~GDFN~~~~~~D~~~~~~~~~~~~~~~~~~~r~~~~  254 (257)
                      +|++.|.+++...  .+.|+|||||||+.+.+.|..+++  ...+.+||++++|+.|.
T Consensus       127 ~~~~~l~~~~~~~~~~~~~~ii~GDfN~~~~~~d~~~~~--~~~~~~~~~~~~~~~~~  182 (265)
T 3g91_A          127 EFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPK--ENSNVSGFLPVERAWID  182 (265)
T ss_dssp             HHHHHHHHHHHHHHHTTCCEEEEEECCCCCSGGGBSCTG--GGTTSTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCEEEECccccCCchhhccCHh--hcCCCCccCHHHHHHHH
Confidence            9999999988764  368999999999999999999988  45788999999998764
>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
>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
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} 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
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} 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
>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
>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
>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
>3teb_A Endonuclease/exonuclease/phosphatase; PSI-biology, MCSG, midwest center for structural genomics; 2.99A {Leptotrichia buccalis c-1013-b} 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
>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
>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
>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
>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
>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 257
d2f1na1250 d.151.1.1 (A:1-250) Cytolethal distending toxin su 6e-15
d2imqx1280 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug ( 7e-11
d1sr4b_261 d.151.1.1 (B:) Cytolethal distending toxin subunit 3e-10
d2ddra1299 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesteras 9e-10
d1hd7a_275 d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human 2e-09
d1zwxa1293 d.151.1.3 (A:41-333) Sphingomyelin phosphodiestera 3e-09
d2a40b1260 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos 9e-08
d1akoa_268 d.151.1.1 (A:) DNA-repair enzyme exonuclease III { 6e-07
d1wdua_228 d.151.1.1 (A:) Endonuclease domain of TRAS1 retrot 8e-07
d1vyba_236 d.151.1.1 (A:) Endonuclease domain of LINE-1 rever 3e-06
d1i9za_ 345 d.151.1.2 (A:) Synaptojanin, IPP5C domain {Fission 0.004
>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 = 70.1 bits (170), Expect = 6e-15
 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
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} Length = 275 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
>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
>d1i9za_ d.151.1.2 (A:) Synaptojanin, IPP5C domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Length = 345 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 ?
Query257
d1vyba_236 Endonuclease domain of LINE-1 reverse transcriptas 99.87
d1wdua_228 Endonuclease domain of TRAS1 retrotransposon (ORF2 99.79
d1hd7a_275 DNA repair endonuclease Hap1 {Human (Homo sapiens) 99.73
d2f1na1250 Cytolethal distending toxin subunit B {Escherichia 99.67
d1zwxa1293 Sphingomyelin phosphodiesterase C {Listeria ivanov 99.65
d2ddra1299 Sphingomyelin phosphodiesterase C {Bacillus cereus 99.59
d1akoa_268 DNA-repair enzyme exonuclease III {Escherichia col 99.5
d1sr4b_261 Cytolethal distending toxin subunit B {Haemophilus 99.5
d2imqx1280 Salivary nitrophorin {Bedbug (Cimex lectularius) [ 99.46
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=99.87  E-value=1.3e-21  Score=163.50  Aligned_cols=149  Identities=24%  Similarity=0.363  Sum_probs=98.8

Q ss_pred             CCCCcEEEEEeCCcchhhhhcCchHHHHHHhhcCCcEEEEecccCCCCCCCCCCccccccchhhhhhHHHHHHHHHhhCC
Q 025138           38 KKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSS  117 (257)
Q Consensus        38 ~~~~lrIiTwNv~gl~~~~~~~~~~l~~~l~~~~~DIi~LQEt~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~L~~  117 (257)
                      ..++|||+||||+|++...++  ..+.++|.+++|||||||||+.......                         .+  
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            457899999999999876554  7899999999999999999986543211                         11  


Q ss_pred             CCCCCCeEEEE-cCCCCcceEEEEEccCCCcceeeecCcccccCCCCCCCEEEEEe----CCEEEEEEecCCCCCCCccc
Q 025138          118 PPFKNYQIWWS-LADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEF----ETFYLLNTYAPNNGWKEEEN  192 (257)
Q Consensus       118 ~~~~gY~~~~~-~~~~~~~GVAIlsr~~l~p~~v~~~l~~~~~~~d~~gr~i~v~~----~~~~i~~vY~P~~~~~~~~~  192 (257)
                       ...++.+++. ....+.+|+||+++.++.  ......     ..+..++++.+++    ..+.++++|+|+...     
T Consensus        53 -~~~~~~~~~~~~~~~~~~g~~i~~k~~~~--~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~-----  119 (236)
T d1vyba_          53 -KIKGWRKIYQANGKQKKAGVAILVSDKTD--FKPTKI-----KRDKEGHYIMVKGSIQQEELTILNIYAPNTGA-----  119 (236)
T ss_dssp             -CCTTCCEEEEECCSSSSCCEEEEECTTCC--CEEEEE-----EECTTSSEEEEEEEETTEEEEEEEEECCSSSH-----
T ss_pred             -hhcccceEEEeeccccccceeeEeecccc--cccccc-----cccccccceeeeeeeccCcceeEEeccccccc-----
Confidence             1133443333 334456799999999632  111111     1234566665554    279999999987652     


Q ss_pred             cHHHHHHHHHHHHHHHHcCCCCCEEEEecCCCCCCCccCCC
Q 025138          193 SFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSH  233 (257)
Q Consensus       193 ~~~~r~~f~~~L~~~l~~~~~~pvIl~GDFN~~~~~~D~~~  233 (257)
                           .++...+...+....+.|+|+|||||..+...|...
T Consensus       120 -----~~~~~~~~~~~~~~~~~~~Il~GDfN~~~~~~d~~~  155 (236)
T d1vyba_         120 -----PRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRST  155 (236)
T ss_dssp             -----HHHHHHHHHHTTTTCCTTEEEEEECSSCSSGGGBTT
T ss_pred             -----HHHHHhhhhhhcccccceeEEeeccccccchhhhcc
Confidence                 123333444444445789999999998877776644
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} Back     information, alignment and structure
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} 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
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} 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
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} 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