Citrus Sinensis ID: 023207

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-----
MPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVSLELSEASSDSEKREKKNLDE
ccccccccHHHHHHHccccEEEEEcccccccccccccccccccEEEEccccccEEEEEEEEccccccEEEEccccccccccccccEEEEEcccEEEEEEEccccccHHHHcHHHHHHHHHHHHHHHHHHcccccEEEEcccccccccccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHcccEEEEccccccccccccEEEccccccccccccccEEEEEEccHHHHHHHHHcEEcccccccccccccccccEEEEEcccccccHHHHHccccc
ccHHHcccHHHHHHHccccEEEEEEcHcccccccccccccccHHHHHHccccccEEEEEEEcccccEEEEEcccccccccccccEEEEEEcccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHEccHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHccccEccHHEccccccccEEEEEEEcHHHHHHccccEEEEEEEcHHHHHHHHHccEccccEEcccccccccccEEEEEccccccccccccccccc
mpaagskdapknhqelkddtKASREEKLILMRAlssppfknyqIWWSLADSKYAGTALLVKKcfqpkkvsFSLEKTalkyepdgrVILAEFETFYLLntyapnngwkeeENSFQRRRKWDKRIQEFVLQcsgkpliwcgdlnvsheeidvshpeFFAAAklngyvppnkedwgqpgftiAERKRFGAILKEGRLIDAYRFLHkekdmdcgfswsgnpigkyrgkrmridYFIVSEELKDRIIACEMQghgielegfygsdhcpvslelseassdsEKREKKNLDE
mpaagskdapknhqelkddtkasREEKLILMRalssppfkNYQIWWSLADSKYAGTALLVKKcfqpkkvsfslektalkyepdGRVILAEFETFYLLNTyapnngwkeeeNSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKekdmdcgfswsgnpigkyrgkrMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVSLelseassdsekrekknlde
MPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVslelseassdseKREKKNLDE
****************************ILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV*********************
MPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVP**KEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVSLEL*****************
********************KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVSLEL*****************
MPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVSLELSEA**************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVSLELSEASSDSEKREKKNLDE
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 ?
Query285 2.2.26 [Sep-21-2011]
P51173361 DNA-(apurinic or apyrimid yes no 0.705 0.556 0.340 8e-27
P28352317 DNA-(apurinic or apyrimid yes no 0.715 0.643 0.329 9e-26
P43138317 DNA-(apurinic or apyrimid yes no 0.729 0.656 0.327 1e-25
A2T7I6318 DNA-(apurinic or apyrimid N/A no 0.729 0.654 0.323 4e-25
A2T6Y4318 DNA-(apurinic or apyrimid yes no 0.715 0.641 0.324 4e-25
A1YFZ3318 DNA-(apurinic or apyrimid N/A no 0.715 0.641 0.324 4e-25
P27695318 DNA-(apurinic or apyrimid yes no 0.715 0.641 0.324 5e-25
A1YES6318 DNA-(apurinic or apyrimid N/A no 0.712 0.638 0.331 1e-24
P23196318 DNA-(apurinic or apyrimid yes no 0.771 0.691 0.308 1e-24
P45951536 Apurinic endonuclease-red no no 0.680 0.361 0.344 1e-23
>sp|P51173|APEA_DICDI DNA-(apurinic or apyrimidinic site) lyase OS=Dictyostelium discoideum GN=apeA PE=2 SV=2 Back     alignment and function desciption
 Score =  120 bits (302), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 120/229 (52%), Gaps = 28/229 (12%)

Query: 40  KNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLN 98
           K Y+  +  AD K + GT +L KK  +P  ++F +     K++ +GRVI  E++ FY++N
Sbjct: 154 KGYEYHFIEADQKGHHGTGVLTKK--KPNAITFGI--GIAKHDNEGRVITLEYDQFYIVN 209

Query: 99  TYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSG-KPLIWCGDLNVSHEEIDVSHPEFFA 157
           TY PN G +  +    R ++WD   Q ++ + +  KP+IWCGDLNV+H EID+ +P    
Sbjct: 210 TYIPNAGTRGLQRLDYRIKEWDVDFQAYLEKLNATKPIIWCGDLNVAHTEIDLKNP---- 265

Query: 158 AAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNP 217
                      K +    GFTI ER  F   L++G  +D+YR  +  K+    F WS   
Sbjct: 266 -----------KTNKKSAGFTIEERTSFSNFLEKG-YVDSYRHFNPGKEGSYTF-WSYLG 312

Query: 218 IGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPVSL 266
            G+ +    R+DYF+VS+ L D I         +      GSDHCP+ +
Sbjct: 313 GGRSKNVGWRLDYFVVSKRLMDSIKISPFHRTSV-----MGSDHCPIGV 356

Dictyostelium discoideum (taxid: 44689)
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|P43138|APEX1_RAT DNA-(apurinic or apyrimidinic site) lyase OS=Rattus norvegicus GN=Apex1 PE=1 SV=2 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|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|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|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 ?
Query285
224133800366 predicted protein [Populus trichocarpa] 0.964 0.751 0.850 1e-137
225456791357 PREDICTED: DNA-(apurinic or apyrimidinic 0.971 0.775 0.819 1e-134
297816036 684 hypothetical protein ARALYDRAFT_347932 [ 0.989 0.412 0.790 1e-132
4678346 686 putative protein [Arabidopsis thaliana] 0.989 0.411 0.783 1e-132
42565714364 endonuclease/exonuclease/phosphatase dom 0.989 0.774 0.783 1e-131
449487730361 PREDICTED: LOW QUALITY PROTEIN: DNA-(apu 0.957 0.756 0.805 1e-130
449469598361 PREDICTED: DNA-(apurinic or apyrimidinic 0.957 0.756 0.805 1e-130
356508768355 PREDICTED: exodeoxyribonuclease-like [Gl 0.957 0.769 0.787 1e-129
115488172379 Os12g0279600 [Oryza sativa Japonica Grou 0.943 0.709 0.781 1e-128
357160291369 PREDICTED: DNA-(apurinic or apyrimidinic 0.961 0.742 0.774 1e-127
>gi|224133800|ref|XP_002321664.1| predicted protein [Populus trichocarpa] gi|222868660|gb|EEF05791.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  493 bits (1269), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 234/275 (85%), Positives = 253/275 (92%)

Query: 1   MPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLV 60
           MPAAGSK APKN  E+KDDT +SREEK ILMRALSS PF NY +WWSLADSKYAGTALLV
Sbjct: 89  MPAAGSKGAPKNSGEIKDDTNSSREEKKILMRALSSSPFGNYNVWWSLADSKYAGTALLV 148

Query: 61  KKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWD 120
           KKCFQP KVSF+L++TA K+EPDGRVILAEF+TF LLNTYAPNNGWKEEE SFQRRRKWD
Sbjct: 149 KKCFQPVKVSFALDQTASKHEPDGRVILAEFKTFRLLNTYAPNNGWKEEEKSFQRRRKWD 208

Query: 121 KRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIA 180
           KR+ E V+Q S KPLIWCGDLNVSHEEIDVSHPEFF+AAK+NGYVPPNKED GQPGFT++
Sbjct: 209 KRMLEVVVQLSDKPLIWCGDLNVSHEEIDVSHPEFFSAAKVNGYVPPNKEDCGQPGFTLS 268

Query: 181 ERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDR 240
           ERKRFGAILKEG+LIDAYRFLHKE+DM+ GFSWSGNPIGKYRGKRMRID+FIVSE+LKDR
Sbjct: 269 ERKRFGAILKEGKLIDAYRFLHKERDMERGFSWSGNPIGKYRGKRMRIDFFIVSEKLKDR 328

Query: 241 IIACEMQGHGIELEGFYGSDHCPVSLELSEASSDS 275
           II CEM GHGIELEGFYGSDHCPVSLELS AS DS
Sbjct: 329 IIQCEMHGHGIELEGFYGSDHCPVSLELSPASPDS 363

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|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|449487730|ref|XP_004157772.1| PREDICTED: LOW QUALITY PROTEIN: DNA-(apurinic or apyrimidinic site) lyase-like [Cucumis sativus] 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|356508768|ref|XP_003523126.1| PREDICTED: exodeoxyribonuclease-like [Glycine max] Back     alignment and taxonomy information
>gi|115488172|ref|NP_001066573.1| Os12g0279600 [Oryza sativa Japonica Group] gi|77554323|gb|ABA97119.1| exodeoxyribonuclease III family protein, expressed [Oryza sativa Japonica Group] gi|113649080|dbj|BAF29592.1| Os12g0279600 [Oryza sativa Japonica Group] gi|215687325|dbj|BAG91875.1| unnamed protein product [Oryza sativa Japonica Group] gi|222616909|gb|EEE53041.1| hypothetical protein OsJ_35763 [Oryza sativa Japonica Group] Back     alignment and taxonomy information
>gi|357160291|ref|XP_003578718.1| PREDICTED: DNA-(apurinic or apyrimidinic site) lyase-like [Brachypodium distachyon] 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 ?
Query285
TAIR|locus:505006392364 AT3G48425 [Arabidopsis thalian 0.926 0.725 0.806 5.2e-120
GENEDB_PFALCIPARUM|PFC0250c617 PFC0250c "AP endonuclease (DNA 0.877 0.405 0.402 1.2e-42
UNIPROTKB|O97240617 PFC0250c "AP endonuclease (DNA 0.877 0.405 0.402 1.2e-42
DICTYBASE|DDB_G0277701361 apeA "DNA-(apurinic or apyrimi 0.635 0.501 0.357 8.4e-26
MGI|MGI:88042317 Apex1 "apurinic/apyrimidinic e 0.680 0.611 0.348 8.7e-24
RGD|2126317 Apex1 "APEX nuclease (multifun 0.680 0.611 0.348 1.1e-23
UNIPROTKB|Q9Z2J2317 APE "Apurinic/apyrimidinic end 0.680 0.611 0.348 1.4e-23
UNIPROTKB|J9PA46318 APEX1 "Uncharacterized protein 0.680 0.610 0.348 1.8e-23
UNIPROTKB|A1YFZ3318 APEX1 "DNA-(apurinic or apyrim 0.680 0.610 0.343 1.8e-23
UNIPROTKB|A2T6Y4318 APEX1 "DNA-(apurinic or apyrim 0.680 0.610 0.343 1.8e-23
TAIR|locus:505006392 AT3G48425 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1181 (420.8 bits), Expect = 5.2e-120, P = 5.2e-120
 Identities = 213/264 (80%), Positives = 238/264 (90%)

Query:     1 MPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLV 60
             MPAAG K  PKNH+EL DDTK  REEK IL RALSSPPF NY +WWSLADSKYAGTALLV
Sbjct:    83 MPAAGGKGKPKNHEELSDDTKVLREEKQILTRALSSPPFGNYGVWWSLADSKYAGTALLV 142

Query:    61 KKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWD 120
             KKCF+P+KV F+L+K A K+EPDGRVILAEFETF LLNTY+PNNGWK+EEN+FQRRRKWD
Sbjct:   143 KKCFKPRKVYFNLDKLASKHEPDGRVILAEFETFRLLNTYSPNNGWKDEENAFQRRRKWD 202

Query:   121 KRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIA 180
             KRI EF+ + S KPLIWCGDLNVSHEEIDVSHPEFFA AKLNGYVPPNKED GQPGFT +
Sbjct:   203 KRIVEFLNKTSDKPLIWCGDLNVSHEEIDVSHPEFFATAKLNGYVPPNKEDCGQPGFTPS 262

Query:   181 ERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDR 240
             ER RFGA +KEGRL+DAYR+LHKE++M+ GFSWSGNPIGKYRGKRMRIDYF+VSE+LKDR
Sbjct:   263 ERGRFGATIKEGRLVDAYRYLHKEQEMESGFSWSGNPIGKYRGKRMRIDYFLVSEQLKDR 322

Query:   241 IIACEMQGHGIELEGFYGSDHCPV 264
             I++C+M G GIELEGF+GSDHCPV
Sbjct:   323 IVSCKMHGRGIELEGFHGSDHCPV 346
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
DICTYBASE|DDB_G0277701 apeA "DNA-(apurinic or apyrimidinic site) lyase" [Dictyostelium discoideum (taxid:44689)] 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|Q9Z2J2 APE "Apurinic/apyrimidinic endonuclease" [Cricetulus griseus (taxid:10029)] 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

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query285
cd09087253 cd09087, Ape1-like_AP-endo, Human Ape1-like subfam 3e-80
cd09073251 cd09073, ExoIII_AP-endo, Escherichia coli exonucle 7e-47
COG0708261 COG0708, XthA, Exonuclease III [DNA replication, r 9e-43
TIGR00633255 TIGR00633, xth, exodeoxyribonuclease III (xth) 8e-42
TIGR00195254 TIGR00195, exoDNase_III, exodeoxyribonuclease III 3e-36
cd09085252 cd09085, Mth212-like_AP-endo, Methanothermobacter 4e-33
PRK13911250 PRK13911, PRK13911, exodeoxyribonuclease III; Prov 1e-28
cd09086254 cd09086, ExoIII-like_AP-endo, Escherichia coli exo 1e-26
cd10281253 cd10281, Nape_like_AP-endo, Neisseria meningitides 4e-22
cd09088309 cd09088, Ape2-like_AP-endo, Human Ape2-like subfam 2e-21
cd09076236 cd09076, L1-EN, Endonuclease domain (L1-EN) of the 4e-18
cd08372241 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase 6e-17
PRK11756268 PRK11756, PRK11756, exonuclease III; Provisional 1e-10
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 =  242 bits (621), Expect = 3e-80
 Identities = 91/258 (35%), Positives = 136/258 (52%), Gaps = 41/258 (15%)

Query: 14  QELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFS 72
           QE    TK   E  +           K Y  +W+ A+ K Y+GTA+L KK   P  V++ 
Sbjct: 34  QE----TKLQ-EGDVPKELKEL---LKGYHQYWNAAEKKGYSGTAILSKKK--PLSVTYG 83

Query: 73  LEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-S 131
           +     +++ +GRVI AEFE FYL+NTY PN+G   E     RR++WD   + ++ +  S
Sbjct: 84  IGIE--EHDQEGRVITAEFENFYLVNTYVPNSGRGLE--RLDRRKEWDVDFRAYLKKLDS 139

Query: 132 GKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKE 191
            KP+IWCGDLNV+HEEID+++P+                     GFT  ER+ F  +L+ 
Sbjct: 140 KKPVIWCGDLNVAHEEIDLANPKTNK---------------KSAGFTPEERESFTELLEA 184

Query: 192 GRLIDAYRFLHKEKDMDCGFSWSGNPIG-KYRGKRMRIDYFIVSEELKDRIIACEMQGHG 250
           G  +D +R LH +K+    +++       + +    R+DYF+VSE LKDR++   +    
Sbjct: 185 G-FVDTFRHLHPDKEGA--YTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVDSFI---- 237

Query: 251 IELEGFYGSDHCPVSLEL 268
                  GSDHCP+ LEL
Sbjct: 238 --RSDIMGSDHCPIGLEL 253

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|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|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|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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 285
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 100.0
PRK05421263 hypothetical protein; Provisional 99.85
COG3568259 ElsH Metal-dependent hydrolase [General function p 99.85
KOG1294335 consensus Apurinic/apyrimidinic endonuclease and r 99.84
TIGR03395283 sphingomy sphingomyelin phosphodiesterase. Members 99.78
PTZ00297 1452 pantothenate kinase; Provisional 99.74
PRK15251271 cytolethal distending toxin subunit CdtB; Provisio 99.71
PF03372249 Exo_endo_phos: Endonuclease/Exonuclease/phosphatas 99.67
PLN03144606 Carbon catabolite repressor protein 4 homolog; Pro 99.66
KOG3873 422 consensus Sphingomyelinase family protein [Signal 99.63
PF14529119 Exo_endo_phos_2: Endonuclease-reverse transcriptas 99.58
COG3021309 Uncharacterized protein conserved in bacteria [Fun 99.51
KOG2756349 consensus Predicted Mg2+-dependent phosphodiestera 99.47
smart00476276 DNaseIc deoxyribonuclease I. Deoxyribonuclease I c 99.23
KOG2338495 consensus Transcriptional effector CCR4-related pr 99.01
smart00128310 IPPc Inositol polyphosphate phosphatase, catalytic 98.96
COG5239378 CCR4 mRNA deadenylase, exonuclease subunit and rel 98.73
KOG0620361 consensus Glucose-repressible alcohol dehydrogenas 98.57
COG2374798 Predicted extracellular nuclease [General function 97.77
KOG0566 1080 consensus Inositol-1,4,5-triphosphate 5-phosphatas 97.65
PLN03191621 Type I inositol-1,4,5-trisphosphate 5-phosphatase 97.52
COG5411 460 Phosphatidylinositol 5-phosphate phosphatase [Sign 96.81
KOG1294 335 consensus Apurinic/apyrimidinic endonuclease and r 92.14
PTZ00312356 inositol-1,4,5-triphosphate 5-phosphatase; Provisi 86.88
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information 
Probab=100.00  E-value=2.8e-50  Score=339.41  Aligned_cols=238  Identities=29%  Similarity=0.479  Sum_probs=195.4

Q ss_pred             hhhhhhhcCCCeEEEehhhhhHhhhcCCCC--CCCceEEEeccCCCceeEEEEEeccCCcceeeeccCcCCCCCCCCCcE
Q 023207            9 APKNHQELKDDTKASREEKLILMRALSSPP--FKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRV   86 (285)
Q Consensus         9 ~~~~l~~~~~DIv~LQE~~~~~~~~l~~~~--~~gy~~~~~~~~~~~~GvaIlsr~~~~~~~~~~~l~~~~~~~d~~gR~   86 (285)
                      +++||.+++|||||||||+.. ...+....  ..||+.++..+++||+|||||||.+  |..+..++++. ...|.+||+
T Consensus        18 ~~~~l~~~~pDVlclQEtK~~-~~~fp~~~~~~~GY~~~~~~gqKgysGVailsr~~--~~~v~~g~~~~-~~~d~e~R~   93 (261)
T COG0708          18 LLDWLEEEQPDVLCLQETKAQ-DEQFPREELEALGYHHVFNHGQKGYSGVAILSKKP--PDDVRRGFPGE-EEDDEEGRV   93 (261)
T ss_pred             HHHHHHHhCCCEEEEEecccC-cccCCHhHHhhCCceEEEecCcCCcceEEEEEccC--chhhhcCCCCC-ccccccCcE
Confidence            889999999999999999974 22332222  3699766666889999999999986  44566777641 235678999


Q ss_pred             EEEEeCCEEEEEEEeeCCCCCcchhhHHHHHHHHHHHHHHHHh--cCCCCEEEEcccCccCCCCcCCCh-hhhhhhhcCC
Q 023207           87 ILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ--CSGKPLIWCGDLNVSHEEIDVSHP-EFFAAAKLNG  163 (285)
Q Consensus        87 l~~~~~~~~v~~vy~p~~~~~~~~~~~~~r~~~~~~l~~~l~~--~~~~p~Il~GDFN~~~~~~D~~~~-~~~~~~~~~~  163 (285)
                      |.+.++.+.|+|+|+|+++... .+++.+|++|++.|..++.+  ..+.|+|+|||||.+|..+|.+++ +.|.      
T Consensus        94 I~a~~~~~~v~~~Y~PnG~~~~-~~k~~yKl~f~~~l~~~l~~l~~~~~~~vl~GD~NIap~~iDv~~~~~~~~------  166 (261)
T COG0708          94 IEAEFDGFRVINLYFPNGSSIG-LEKFDYKLRFLDALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWL------  166 (261)
T ss_pred             EEEEECCEEEEEEEcCCCCCCC-CcchHHHHHHHHHHHHHHHHHhhcCCCEEEecccccCCchhcccCchhhhh------
Confidence            9999999999999999998722 35688999999999999876  367999999999999999999987 4442      


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHhhhhcCCeeeeeeccCCCCCCceeeeeeCCCCCCc-CCccceEEEEEeChhhHhhhe
Q 023207          164 YVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKY-RGKRMRIDYFIVSEELKDRII  242 (285)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~r~~l~~~l~~~~l~D~~r~~~p~~~~~~~~T~~~~~~~~~-~~~~~RID~i~~s~~l~~~v~  242 (285)
                             |.+.++|+++||++|..+++.| |+|+||.++|...   .||||+++.+.+ .+.|+|||||++|+.+..+++
T Consensus       167 -------n~~~~~f~~eeR~~~~~ll~~G-~~D~~R~~~p~~~---~YTwW~YR~~~~~~n~G~RID~~l~S~~L~~~~~  235 (261)
T COG0708         167 -------NEGNSGFLPEERAWFRRLLNAG-FVDTFRLFHPEPE---KYTWWDYRANAARRNRGWRIDYILVSPALADRLK  235 (261)
T ss_pred             -------cCCCCCCCHHHHHHHHHHHHcc-hhhhhHhhCCCCC---cccccccccchhhhcCceeEEEEEeCHHHHHHHH
Confidence                   3477899999999999999987 9999999999884   599999876633 468999999999999999999


Q ss_pred             eeEEccCccccCCCCCCCcccEEEEEee
Q 023207          243 ACEMQGHGIELEGFYGSDHCPVSLELSE  270 (285)
Q Consensus       243 ~~~i~~~~~~~~~~~~SDH~PV~~~l~~  270 (285)
                      +|.|.....  ....+|||+||+++|++
T Consensus       236 ~a~I~~~~r--g~e~pSDHaPV~~e~~~  261 (261)
T COG0708         236 DAGIDREVR--GWEKPSDHAPVWVELDL  261 (261)
T ss_pred             hcCccHHHh--cCCCCCCcCcEEEEecC
Confidence            999997421  12466999999999864

>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
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only] Back     alignment and domain information
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] Back     alignment and domain information
>TIGR03395 sphingomy sphingomyelin phosphodiesterase Back     alignment and domain information
>PTZ00297 pantothenate kinase; Provisional Back     alignment and domain information
>PRK15251 cytolethal distending toxin subunit CdtB; Provisional 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
>KOG3873 consensus Sphingomyelinase family protein [Signal transduction mechanisms] Back     alignment and domain information
>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B Back     alignment and domain information
>COG3021 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms] Back     alignment and domain information
>smart00476 DNaseIc deoxyribonuclease I Back     alignment and domain information
>KOG2338 consensus Transcriptional effector CCR4-related protein [Transcription] Back     alignment and domain information
>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues Back     alignment and domain information
>COG5239 CCR4 mRNA deadenylase, exonuclease subunit and related nucleases [RNA processing and modification] 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
>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
>PLN03191 Type I inositol-1,4,5-trisphosphate 5-phosphatase 2; Provisional Back     alignment and domain information
>COG5411 Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms] Back     alignment and domain information
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] 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 ?
Query285
2o3h_A285 Crystal Structure Of The Human C65a Ape Length = 28 5e-25
1bix_A287 The Crystal Structure Of The Human Dna Repair Endon 6e-25
2isi_A317 Crystal Structure Of Ape1 From Homo Sapiens In A Ne 6e-25
1e9n_A318 A Second Divalent Metal Ion In The Active Site Of A 6e-25
1dew_A279 Crystal Structure Of Human Ape1 Bound To Abasic Dna 7e-25
1de8_B276 Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bo 7e-25
2o3c_A282 Crystal Structure Of Zebrafish Ape Length = 282 2e-19
3g91_A265 1.2 Angstrom Structure Of The Exonuclease Iii Homol 8e-15
3fzi_A265 1.9 Angstrom Structure Of The Thermophilic Exonucle 2e-14
3g00_A265 Mth0212 In Complex With A 9bp Blunt End Dsdna At 1. 5e-14
2j63_A467 Crystal Structure Of Ap Endonuclease Lmap From Leis 7e-08
2voa_A257 Structure Of An Ap Endonuclease From Archaeoglobus 2e-07
2jc5_A259 Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From 6e-07
4b5h_A259 Substate Bound Inactive Mutant Of Neisseria Ap Endo 2e-06
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape Length = 285 Back     alignment and structure 
Iteration: 1

 Score =  111 bits (277), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 124/229 (54%), Gaps = 30/229 (13%)
Query: 38  PFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYL 96
           P  ++Q W + +D + Y+G  LL ++C  P KVS+ +     +++ +GRVI+AEF++F L
Sbjct: 79  PGLSHQYWSAPSDKEGYSGVGLLSRQC--PLKVSYGIGDE--EHDQEGRVIVAEFDSFVL 134
Query: 97  LNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQ-CSGKPLIWCGDLNVSHEEIDVSHPEF 155
           +  Y PN G        + R++WD+  ++F+    S KPL+ CGDLNV+HEEID+ +P+ 
Sbjct: 135 VTAYVPNAG--RGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKG 192
Query: 156 FAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSG 215
                       NK++    GFT  ER+ FG +L+   L D++R L+        F W+ 
Sbjct: 193 ------------NKKN---AGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTF-WTY 236
Query: 216 NPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYGSDHCPV 264
               + +    R+DYF++S  L   +   +++   +      GSDHCP+
Sbjct: 237 MMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKAL------GSDHCPI 279
>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|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|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|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|2J63|A Chain A, Crystal Structure Of Ap Endonuclease Lmap From Leishmania Major Length = 467 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 ?
Query285
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 1e-51
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 1e-50
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 2e-50
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 6e-49
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 7e-42
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48 8e-40
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 2e-29
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 4e-26
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosph 2e-23
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 2e-08
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 3e-06
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four 4e-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 =  169 bits (431), Expect = 1e-51
 Identities = 83/265 (31%), Positives = 132/265 (49%), Gaps = 51/265 (19%)

Query: 14  QELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSK-YAGTALLVKKCFQPKKVSFS 72
           QE    TK S  +   L   L   P  ++Q W + +D + Y+G  LL ++   P KVS+ 
Sbjct: 62  QE----TKCSENK---LPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQ--CPLKVSYG 112

Query: 73  LEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC-S 131
           +     +++ +GRVI+AEF++F L+  Y PN G       +  R++WD+  ++F+    S
Sbjct: 113 IGDE--EHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEY--RQRWDEAFRKFLKGLAS 168

Query: 132 GKPLIWCGDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKE 191
            KPL+ CGDLNV+HEEID+ +P+             NK      GFT  ER+ FG +L+ 
Sbjct: 169 RKPLVLCGDLNVAHEEIDLRNPK------------GNK---KNAGFTPQERQGFGELLQA 213

Query: 192 GRLIDAYRFLHKEKDMDCGFS-WSGNPIGKYRGK-R-----MRIDYFIVSEELKDRIIAC 244
             L D++R L+        ++ W+      Y    R      R+DYF++S  L   +   
Sbjct: 214 VPLADSFRHLYPNTPYA--YTFWT------YMMNARSKNVGWRLDYFLLSHSLLPALCDS 265

Query: 245 EMQGHGIELEGFYGSDHCPVSLELS 269
           ++           GSDHCP++L L+
Sbjct: 266 KI------RSKALGSDHCPITLYLA 284
>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
>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
>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
>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
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori} Length = 240 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query285
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand speci 100.0
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48 100.0
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 100.0
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodie 100.0
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosph 100.0
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 100.0
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 100.0
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 100.0
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 100.0
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four 99.96
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 99.95
4gew_A362 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 99.95
4fva_A256 5'-tyrosyl-DNA phosphodiesterase; 5'-phosphotyrosy 99.94
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 99.94
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 99.93
4gz1_A256 Tyrosyl-DNA phosphodiesterase 2; protein-DNA compl 99.92
4f1h_A250 Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA com 99.92
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 99.92
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM 99.9
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 99.88
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like fold 99.85
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 99.83
4b8c_D727 Glucose-repressible alcohol dehydrogenase transcr 99.77
1sr4_B261 CDT B, cytolethal distending toxin protein B; bact 99.74
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.co 99.74
3ngq_A398 CCR4-NOT transcription complex subunit 6-like; alp 99.69
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse 99.63
1i9z_A347 Synaptojanin, phosphatidylinositol phosphate phosp 99.48
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, 99.44
2xsw_A357 72 kDa inositol polyphosphate 5-phosphatase; inosi 99.14
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; 98.84
4a9c_A316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; 98.56
>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=2.1e-38  Score=273.81  Aligned_cols=235  Identities=27%  Similarity=0.480  Sum_probs=181.5

Q ss_pred             ChhhhhhhcCCCeEEEehhhhhHhhhcCCC--CCCCceEEEecc-CCCceeEEEEEeccCCcceeeeccCcCCCCCCCCC
Q 023207            8 DAPKNHQELKDDTKASREEKLILMRALSSP--PFKNYQIWWSLA-DSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDG   84 (285)
Q Consensus         8 ~~~~~l~~~~~DIv~LQE~~~~~~~~l~~~--~~~gy~~~~~~~-~~~~~GvaIlsr~~~~~~~~~~~l~~~~~~~d~~g   84 (285)
                      ++.++|++.+|||||||||+... ..+...  ...||..++... ..+++|||||+|.++  ..+..++..  ...+.++
T Consensus        21 ~l~~~i~~~~~DIv~LQEt~~~~-~~~~~~~~~~~gy~~~~~~~~~~~~~Gvail~k~~~--~~~~~~~~~--~~~d~~g   95 (265)
T 3g91_A           21 GFLKWFMEEKPDILCLQEIKAAP-EQLPRKLRHVEGYRSFFTPAERKGYSGVAMYTKVPP--SSLREGFGV--ERFDTEG   95 (265)
T ss_dssp             THHHHHHHHCCSEEEEECCCSCG-GGSCHHHHCCTTCEEEEECBSSTTSCCEEEEESSCC--SEEECCCSC--HHHHSBS
T ss_pred             hHHHHHHhcCCCEEEEEeccccc-cccChhhhcccCCcEEEccCCCCCcCEEEEEEecCh--HHhccCCCC--cccCCcC
Confidence            68999999999999999998642 222111  136998777643 356789999999863  334443321  1235689


Q ss_pred             cEEEEEeCCEEEEEEEeeCCCCCcchhhHHHHHHHHHHHHHHHHhc--CCCCEEEEcccCccCCCCcCCChhhhhhhhcC
Q 023207           85 RVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQC--SGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN  162 (285)
Q Consensus        85 R~l~~~~~~~~v~~vy~p~~~~~~~~~~~~~r~~~~~~l~~~l~~~--~~~p~Il~GDFN~~~~~~D~~~~~~~~~~~~~  162 (285)
                      |++.+.+..+.|+|+|+|++...  ..++.+|.+|++.|.+++...  .+.|+|||||||+.+...|..++..       
T Consensus        96 r~i~~~~~~~~i~~vy~p~~~~~--~~~~~~r~~~~~~l~~~~~~~~~~~~~~ii~GDfN~~~~~~d~~~~~~-------  166 (265)
T 3g91_A           96 RIQIADFDDFLLYNIYFPNGAMS--EERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKE-------  166 (265)
T ss_dssp             CEEEEECSSCEEEEEECCCCTTC--HHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEEECCCCCSGGGBSCTGG-------
T ss_pred             CEEEEEeCCEEEEEEEecCCCCC--chhHHHHHHHHHHHHHHHHHHHcCCCCEEEECccccCCchhhccCHhh-------
Confidence            99999999999999999998863  345667889999998888753  3689999999999998888766532       


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHhhhhcCCeeeeeeccCCCCCCceeeeeeCCCCCCc-CCccceEEEEEeChhhHhhh
Q 023207          163 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKY-RGKRMRIDYFIVSEELKDRI  241 (285)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~r~~l~~~l~~~~l~D~~r~~~p~~~~~~~~T~~~~~~~~~-~~~~~RID~i~~s~~l~~~v  241 (285)
                              +.+..++++.+++++..+++.+ |+|+||..+|..   ..|||++...+.+ .+.++||||||+++.+..++
T Consensus       167 --------~~~~~~~~~~~~~~~~~l~~~g-l~D~~r~~~p~~---~~yT~~~~~~~~~~~~~~~rID~il~s~~~~~~~  234 (265)
T 3g91_A          167 --------NSNVSGFLPVERAWIDKFIENG-YVDTFRMFNSDP---GQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKV  234 (265)
T ss_dssp             --------GTTSTTSCHHHHHHHHHHHHTT-EEETHHHHCCCS---CCCSBCCSSTTTTTTTCCBCCEEEEEEGGGGGGE
T ss_pred             --------cCCCCccCHHHHHHHHHHHhcC-cEEeeHhhCCCC---CCCCCcCCCCCccccCceEEEEEEEECHHHHhhh
Confidence                    2356788999999999999655 999999999887   4799998654432 35678999999999998889


Q ss_pred             eeeEEccCccccCCCCCCCcccEEEEEeeCCCC
Q 023207          242 IACEMQGHGIELEGFYGSDHCPVSLELSEASSD  274 (285)
Q Consensus       242 ~~~~i~~~~~~~~~~~~SDH~PV~~~l~~~~~~  274 (285)
                      .++.|...      ..+|||+||++++.....+
T Consensus       235 ~~~~i~~~------~~~SDH~Pv~~~~~~~~~~  261 (265)
T 3g91_A          235 KRSWILSD------VMGSDHCPIGLEIELLEHH  261 (265)
T ss_dssp             EEEEECTT------CCSSSBCCEEEEEECCCCC
T ss_pred             cEEEEeCC------CCCCCcceEEEEhhhhhhc
Confidence            99999863      4789999999999875444
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Back     alignment and structure
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} 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
>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
>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
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} 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
>4f1h_A Tyrosyl-DNA phosphodiesterase 2; hydrolase-DNA complex; HET: DNA; 1.66A {Danio rerio} PDB: 4fpv_A* 4f1h_B* 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
>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
>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
>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
>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C} 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
>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
>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
>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 285
d1hd7a_275 d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human 7e-17
d1akoa_268 d.151.1.1 (A:) DNA-repair enzyme exonuclease III { 1e-14
d2imqx1280 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug ( 3e-14
d1wdua_228 d.151.1.1 (A:) Endonuclease domain of TRAS1 retrot 1e-10
d2f1na1250 d.151.1.1 (A:1-250) Cytolethal distending toxin su 5e-09
d1vyba_236 d.151.1.1 (A:) Endonuclease domain of LINE-1 rever 5e-08
d2ddra1299 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesteras 7e-07
d2a40b1260 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos 1e-06
d1zwxa1293 d.151.1.3 (A:41-333) Sphingomyelin phosphodiestera 1e-04
d1sr4b_261 d.151.1.1 (B:) Cytolethal distending toxin subunit 7e-04
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} Length = 275 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: DNA repair endonuclease Hap1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.3 bits (186), Expect = 7e-17
 Identities = 71/251 (28%), Positives = 111/251 (44%), Gaps = 29/251 (11%)

Query: 19  DTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTAL 78
           +TK S  +   L   L   P  ++Q W + +D +      L+ +   P KVS+ +     
Sbjct: 53  ETKCSENK---LPAELQELPGLSHQYWSAPSDKEGYSGVGLLSR-QCPLKVSYGIGDEEH 108

Query: 79  KYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWC 138
             E    V  AEF++F L+  Y PN G       +++R     R        S KPL+ C
Sbjct: 109 DQEGRVIV--AEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKG-LASRKPLVLC 165

Query: 139 GDLNVSHEEIDVSHPEFFAAAKLNGYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAY 198
           GDLNV+HEEID+ +P+                     GFT  ER+ FG +L+   L D++
Sbjct: 166 GDLNVAHEEIDLRNPKGN---------------KKNAGFTPQERQGFGELLQAVPLADSF 210

Query: 199 RFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRIIACEMQGHGIELEGFYG 258
           R L+        F W+     + +    R+DYF++S  L   +   ++           G
Sbjct: 211 RHLYPNTPYAYTF-WTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKI------RSKALG 263

Query: 259 SDHCPVSLELS 269
           SDHCP++L L+
Sbjct: 264 SDHCPITLYLA 274
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} Length = 268 Back     information, alignment and structure
>d2imqx1 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId: 79782]} Length = 280 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
>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]} Length = 250 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
>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} Length = 299 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
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Length = 293 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

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query285
d1vyba_236 Endonuclease domain of LINE-1 reverse transcriptas 99.97
d1hd7a_275 DNA repair endonuclease Hap1 {Human (Homo sapiens) 99.94
d1wdua_228 Endonuclease domain of TRAS1 retrotransposon (ORF2 99.92
d1akoa_268 DNA-repair enzyme exonuclease III {Escherichia col 99.87
d2f1na1250 Cytolethal distending toxin subunit B {Escherichia 99.84
d1zwxa1293 Sphingomyelin phosphodiesterase C {Listeria ivanov 99.82
d2ddra1299 Sphingomyelin phosphodiesterase C {Bacillus cereus 99.82
d2imqx1280 Salivary nitrophorin {Bedbug (Cimex lectularius) [ 99.78
d1sr4b_261 Cytolethal distending toxin subunit B {Haemophilus 99.74
d2a40b1260 Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913 99.68
d1i9za_345 Synaptojanin, IPP5C domain {Fission yeast (Schizos 99.55
>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=99.97  E-value=1.3e-29  Score=211.97  Aligned_cols=208  Identities=22%  Similarity=0.291  Sum_probs=135.8

Q ss_pred             ChhhhhhhcCCCeEEEehhhhhHhhhcCCCCCCCceEEEe-ccCCCceeEEEEEeccCCcceeeeccCcCCCCCCCCCcE
Q 023207            8 DAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWS-LADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRV   86 (285)
Q Consensus         8 ~~~~~l~~~~~DIv~LQE~~~~~~~~l~~~~~~gy~~~~~-~~~~~~~GvaIlsr~~~~~~~~~~~l~~~~~~~d~~gR~   86 (285)
                      .+.++|++++|||||||||+....... .....++.+++. .....+.|+||+++.++........       .+..+++
T Consensus        24 ~i~~~i~~~~~DIi~LQE~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~g~~i~~k~~~~~~~~~~~-------~~~~~~~   95 (236)
T d1vyba_          24 RLASWIKSQDPSVCCIQETHLTCRDTH-RLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIK-------RDKEGHY   95 (236)
T ss_dssp             HHHHHHHHHCCSEEEEECCCCCTTSGG-GCCCTTCCEEEEECCSSSSCCEEEEECTTCCCEEEEEE-------ECTTSSE
T ss_pred             HHHHHHHHCCCeEEEEEcccCccccch-hhhhcccceEEEeeccccccceeeEeeccccccccccc-------ccccccc
Confidence            577899999999999999975322221 122334443333 2345577999999997532211111       2335666


Q ss_pred             EEEEe--C--CEEEEEEEeeCCCCCcchhhHHHHHHHHHHHHHHHHhcCCCCEEEEcccCccCCCCcCCChhhhhhhhcC
Q 023207           87 ILAEF--E--TFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVSHEEIDVSHPEFFAAAKLN  162 (285)
Q Consensus        87 l~~~~--~--~~~v~~vy~p~~~~~~~~~~~~~r~~~~~~l~~~l~~~~~~p~Il~GDFN~~~~~~D~~~~~~~~~~~~~  162 (285)
                      +.+.+  .  .+.++|+|+|+...    .      .+...+...+....+.|+|||||||.+....|....         
T Consensus        96 ~~~~~~~~~~~~~~~~~y~~~~~~----~------~~~~~~~~~~~~~~~~~~Il~GDfN~~~~~~d~~~~---------  156 (236)
T d1vyba_          96 IMVKGSIQQEELTILNIYAPNTGA----P------RFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTR---------  156 (236)
T ss_dssp             EEEEEEETTEEEEEEEEECCSSSH----H------HHHHHHHHHTTTTCCTTEEEEEECSSCSSGGGBTTC---------
T ss_pred             eeeeeeeccCcceeEEeccccccc----H------HHHHhhhhhhcccccceeEEeeccccccchhhhccc---------
Confidence            65544  2  69999999987653    1      122233333333457899999999997765554321         


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHhhhhcCCeeeeeeccCCCCCCceeeeeeCCCCCCcCCccceEEEEEeChhhHhhhe
Q 023207          163 GYVPPNKEDWGQPGFTIAERKRFGAILKEGRLIDAYRFLHKEKDMDCGFSWSGNPIGKYRGKRMRIDYFIVSEELKDRII  242 (285)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~r~~l~~~l~~~~l~D~~r~~~p~~~~~~~~T~~~~~~~~~~~~~~RID~i~~s~~l~~~v~  242 (285)
                                  .......+ .+...+...++.|+||..++..   ..+||+....    +..+||||||+|+.+..++.
T Consensus       157 ------------~~~~~~~~-~~~~~~~~~~~~d~~r~~~~~~---~~~~~~~~~~----~~~~RiD~il~s~~~~~~~~  216 (236)
T d1vyba_         157 ------------QKVNKDTQ-ELNSALHQADLIDIYRTLHPKS---TEYTFFSAPH----HTYSKIDHIVGSKALLSKCK  216 (236)
T ss_dssp             ------------CCCCHHHH-HHHHHHHHTTEEEHHHHHCTTC---CCCSEEETTT----TEEECCEEEEEEGGGGGGEE
T ss_pred             ------------ccchhhHH-HHHHHHHhhhcccccceeccCC---ccccccCCCC----CCCceeEEEEEChHHHhhce
Confidence                        11223333 3444444456999999888765   3578776432    34589999999999988888


Q ss_pred             eeEEccCccccCCCCCCCcccEEEEEe
Q 023207          243 ACEMQGHGIELEGFYGSDHCPVSLELS  269 (285)
Q Consensus       243 ~~~i~~~~~~~~~~~~SDH~PV~~~l~  269 (285)
                      .+++..       ...|||+||+++|.
T Consensus       217 ~~~i~~-------~~~SDH~pv~~~lk  236 (236)
T d1vyba_         217 RTEIIT-------NYLSDHSAIKLELR  236 (236)
T ss_dssp             EEEEEC-------CSSSSSCEEEEEEC
T ss_pred             EEEECC-------CCCCCcccEEEEeC
Confidence            999886       46799999999984
>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
>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
>d2imqx1 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId: 79782]} 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
>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