Citrus Sinensis ID: 027283

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-----
MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVR
ccccccccccccccccccccccccccccccccccccccccccEEEEEEHHHHHHHHHcccHHHHHHHHHccccEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccEEEEEccccccEEEEEEEEccccccEEEcccccccccccccccEEEEEEccEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHcccccEEEEcccccc
cccEEEEcccccccccccccccccccccccccccccccccccEEEEEEcccHHHHEccccHHHHHHHHHccccEEEEEEcccccccccccccccccccccccHHHHHHHHHHHHHHccccccccEHHHHccccccEEEEEEEcccccEEEEEccccccHHcccccEEEEEEEccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccc
mkrffkpiekecsakkpalspskkdgettetsseenskkdplkFVTWNANSLLLRVknnwpefsnfittfdpdvialqevrmpaagskdapknhqelkddtKASREEKLILMRAlssppfknyqIWWSLADSKYAGTALLVKKcfqpkkvsFSLEKTalkyepdgrVILAEFETFYLLntyapnngwkeeENSFQRRRKWDKRIQEFVLQcsgkpliwcgdlnvr
mkrffkpiekecsakkpalspskkdgettetsseenskkdplkfVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMpaagskdapknhqelkddtkasREEKLILMRalssppfkNYQIWWSLADSKYAGTALLVKKcfqpkkvsfslektalkyepdGRVILAEFETFYLLNTyapnngwkeeeNSFQRRRKWDKRIQEFvlqcsgkpliwcgdlnvr
MKRFFKPIEKECsakkpalspskkdgettetsseenskkDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVR
*****************************************LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEV****************************LILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDL***
******************************************KFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVR
MKRFFKPIEKEC***************************DPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMP******************KASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVR
********EK*****************************DPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLN**
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKRFFKPIEKECSAKKPALSPSKKDGETTETSSEENSKKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFKNYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVR
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 ?
Query225 2.2.26 [Sep-21-2011]
P43138 317 DNA-(apurinic or apyrimid yes no 0.804 0.570 0.294 1e-15
P28352 317 DNA-(apurinic or apyrimid yes no 0.804 0.570 0.294 2e-15
A2T6Y4 318 DNA-(apurinic or apyrimid yes no 0.791 0.559 0.288 8e-15
A1YFZ3 318 DNA-(apurinic or apyrimid N/A no 0.791 0.559 0.288 8e-15
A2T7I6 318 DNA-(apurinic or apyrimid N/A no 0.791 0.559 0.288 1e-14
P27695 318 DNA-(apurinic or apyrimid yes no 0.791 0.559 0.288 1e-14
A1YES6 318 DNA-(apurinic or apyrimid N/A no 0.786 0.556 0.296 2e-14
P51173 361 DNA-(apurinic or apyrimid yes no 0.662 0.412 0.286 3e-14
P23196 318 DNA-(apurinic or apyrimid yes no 0.791 0.559 0.279 8e-13
P27864 679 Recombination repair prot yes no 0.657 0.217 0.277 2e-11
>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 = 83.2 bits (204), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 105/221 (47%), Gaps = 40/221 (18%)

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-CSGKPLIWCGDLNV 224
            G        + R++WD+  ++F+    S KPL+ CGDLNV
Sbjct: 174 AG--RGLVRLEYRQRWDEAFRKFLKDLASRKPLVLCGDLNV 212
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|P27864|RRP1_DROME Recombination repair protein 1 OS=Drosophila melanogaster GN=Rrp1 PE=1 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 ?
Query225
225456791 357 PREDICTED: DNA-(apurinic or apyrimidinic 0.986 0.621 0.741 3e-94
449487730 361 PREDICTED: LOW QUALITY PROTEIN: DNA-(apu 0.995 0.620 0.745 3e-94
449469598 361 PREDICTED: DNA-(apurinic or apyrimidinic 0.995 0.620 0.745 6e-94
297816036 684 hypothetical protein ARALYDRAFT_347932 [ 0.991 0.326 0.752 5e-93
224133800 366 predicted protein [Populus trichocarpa] 0.995 0.612 0.748 5e-93
4678346 686 putative protein [Arabidopsis thaliana] 0.991 0.325 0.738 9e-93
42565714 364 endonuclease/exonuclease/phosphatase dom 0.991 0.612 0.738 2e-92
356508768 355 PREDICTED: exodeoxyribonuclease-like [Gl 0.96 0.608 0.716 1e-87
358348989 367 DNA-(apurinic or apyrimidinic site) lyas 0.986 0.604 0.706 4e-83
358348991278 DNA-(apurinic or apyrimidinic site) lyas 0.986 0.798 0.706 4e-83
>gi|225456791|ref|XP_002277389.1| PREDICTED: DNA-(apurinic or apyrimidinic site) lyase [Vitis vinifera] gi|297733638|emb|CBI14885.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  350 bits (897), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 166/224 (74%), Positives = 191/224 (85%), Gaps = 2/224 (0%)

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

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

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

Query: 181 YAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNV 224
           Y PNNGWK+EE SFQRRRKWDKR+ EFV+Q S KPLIWCGDLNV
Sbjct: 179 YVPNNGWKDEETSFQRRRKWDKRMLEFVVQSSDKPLIWCGDLNV 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|449487730|ref|XP_004157772.1| PREDICTED: LOW QUALITY PROTEIN: DNA-(apurinic or apyrimidinic site) lyase-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449469598|ref|XP_004152506.1| PREDICTED: DNA-(apurinic or apyrimidinic site) lyase-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297816036|ref|XP_002875901.1| hypothetical protein ARALYDRAFT_347932 [Arabidopsis lyrata subsp. lyrata] gi|297321739|gb|EFH52160.1| hypothetical protein ARALYDRAFT_347932 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|224133800|ref|XP_002321664.1| predicted protein [Populus trichocarpa] gi|222868660|gb|EEF05791.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|4678346|emb|CAB41156.1| putative protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|42565714|ref|NP_566904.2| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana] gi|53828525|gb|AAU94372.1| At3g48425 [Arabidopsis thaliana] gi|55733769|gb|AAV59281.1| At3g48425 [Arabidopsis thaliana] gi|332644894|gb|AEE78415.1| endonuclease/exonuclease/phosphatase domain-containing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356508768|ref|XP_003523126.1| PREDICTED: exodeoxyribonuclease-like [Glycine max] Back     alignment and taxonomy information
>gi|358348989|ref|XP_003638523.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] gi|355504458|gb|AES85661.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] Back     alignment and taxonomy information
>gi|358348991|ref|XP_003638524.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] gi|355504459|gb|AES85662.1| DNA-(apurinic or apyrimidinic site) lyase [Medicago truncatula] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query225
TAIR|locus:505006392 364 AT3G48425 [Arabidopsis thalian 0.995 0.615 0.684 2.2e-80
GENEDB_PFALCIPARUM|PFC0250c 617 PFC0250c "AP endonuclease (DNA 0.791 0.288 0.386 1.9e-29
UNIPROTKB|O97240 617 PFC0250c "AP endonuclease (DNA 0.791 0.288 0.386 1.9e-29
DICTYBASE|DDB_G0277701 361 apeA "DNA-(apurinic or apyrimi 0.444 0.277 0.377 9.2e-19
UNIPROTKB|Q9Z2J2 317 APE "Apurinic/apyrimidinic end 0.515 0.365 0.377 1.2e-17
TIGR_CMR|BA_3868 252 BA_3868 "exodeoxyribonuclease 0.435 0.388 0.339 8.9e-17
MGI|MGI:88042 317 Apex1 "apurinic/apyrimidinic e 0.515 0.365 0.377 1.2e-16
RGD|2126 317 Apex1 "APEX nuclease (multifun 0.515 0.365 0.377 1.2e-14
UNIPROTKB|J9PA46 318 APEX1 "Uncharacterized protein 0.515 0.364 0.377 2.8e-14
UNIPROTKB|G3V3M6263 APEX1 "DNA-(apurinic or apyrim 0.515 0.441 0.370 3e-14
TAIR|locus:505006392 AT3G48425 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 807 (289.1 bits), Expect = 2.2e-80, P = 2.2e-80
 Identities = 154/225 (68%), Positives = 173/225 (76%)

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 TYAPNNGWKEEENSFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNV 224
             TY+PNNGWK+EEN+FQRRRKWDKRI EF+ + S KPLIWCGDLNV
Sbjct:   181 TYSPNNGWKDEENAFQRRRKWDKRIVEFLNKTSDKPLIWCGDLNV 225
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
UNIPROTKB|Q9Z2J2 APE "Apurinic/apyrimidinic endonuclease" [Cricetulus griseus (taxid:10029)] Back     alignment and assigned GO terms
TIGR_CMR|BA_3868 BA_3868 "exodeoxyribonuclease III" [Bacillus anthracis str. Ames (taxid:198094)] 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|G3V3M6 APEX1 "DNA-(apurinic or apyrimidinic site) lyase" [Homo sapiens (taxid:9606)] 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 ?
Query225
cd09087 253 cd09087, Ape1-like_AP-endo, Human Ape1-like subfam 1e-51
cd09073251 cd09073, ExoIII_AP-endo, Escherichia coli exonucle 3e-28
COG0708 261 COG0708, XthA, Exonuclease III [DNA replication, r 2e-26
TIGR00633 255 TIGR00633, xth, exodeoxyribonuclease III (xth) 3e-22
TIGR00195 254 TIGR00195, exoDNase_III, exodeoxyribonuclease III 1e-21
cd09085252 cd09085, Mth212-like_AP-endo, Methanothermobacter 4e-15
cd09076236 cd09076, L1-EN, Endonuclease domain (L1-EN) of the 1e-13
PRK13911 250 PRK13911, PRK13911, exodeoxyribonuclease III; Prov 4e-13
cd08372241 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase 8e-12
cd09086 254 cd09086, ExoIII-like_AP-endo, Escherichia coli exo 6e-11
cd09088 309 cd09088, Ape2-like_AP-endo, Human Ape2-like subfam 2e-10
cd10281 253 cd10281, Nape_like_AP-endo, Neisseria meningitides 1e-08
pfam03372143 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease 0.001
pfam03372143 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease 0.002
>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 =  167 bits (425), Expect = 1e-51
 Identities = 61/185 (32%), Positives = 92/185 (49%), Gaps = 36/185 (19%)

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 GDLNV 224
           GDLNV
Sbjct: 147 GDLNV 151

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|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|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional Back     alignment and domain information
>gnl|CDD|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily Back     alignment and domain information
>gnl|CDD|197320 cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|197322 cd09088, Ape2-like_AP-endo, Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases Back     alignment and domain information
>gnl|CDD|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|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 225
COG0708 261 XthA Exonuclease III [DNA replication, recombinati 100.0
PRK13911 250 exodeoxyribonuclease III; Provisional 99.97
PRK11756 268 exonuclease III; Provisional 99.93
TIGR00195 254 exoDNase_III exodeoxyribonuclease III. The model b 99.92
TIGR00633 255 xth exodeoxyribonuclease III (xth). This family is 99.9
PRK05421263 hypothetical protein; Provisional 99.69
PF03372249 Exo_endo_phos: Endonuclease/Exonuclease/phosphatas 99.49
PRK15251271 cytolethal distending toxin subunit CdtB; Provisio 99.48
TIGR03395283 sphingomy sphingomyelin phosphodiesterase. Members 99.47
COG3568259 ElsH Metal-dependent hydrolase [General function p 99.29
KOG2756349 consensus Predicted Mg2+-dependent phosphodiestera 99.26
PLN03144 606 Carbon catabolite repressor protein 4 homolog; Pro 99.25
PTZ00297 1452 pantothenate kinase; Provisional 99.21
KOG2338 495 consensus Transcriptional effector CCR4-related pr 99.18
smart00476276 DNaseIc deoxyribonuclease I. Deoxyribonuclease I c 99.12
KOG3873 422 consensus Sphingomyelinase family protein [Signal 98.97
smart00128 310 IPPc Inositol polyphosphate phosphatase, catalytic 98.76
KOG1294 335 consensus Apurinic/apyrimidinic endonuclease and r 98.72
COG3021309 Uncharacterized protein conserved in bacteria [Fun 98.3
PF14529119 Exo_endo_phos_2: Endonuclease-reverse transcriptas 98.06
KOG0566 1080 consensus Inositol-1,4,5-triphosphate 5-phosphatas 97.37
COG5239 378 CCR4 mRNA deadenylase, exonuclease subunit and rel 96.87
KOG0620 361 consensus Glucose-repressible alcohol dehydrogenas 94.63
COG2374 798 Predicted extracellular nuclease [General function 93.03
PLN03191 621 Type I inositol-1,4,5-trisphosphate 5-phosphatase 86.16
PTZ00312 356 inositol-1,4,5-triphosphate 5-phosphatase; Provisi 81.55
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information 
Probab=100.00  E-value=9.9e-33  Score=236.42  Aligned_cols=150  Identities=29%  Similarity=0.536  Sum_probs=126.7

Q ss_pred             cEEEEEeCCcchhhhhcChhHHHHHHhhcCCcEEEEeeeeCCCCCCCCCCcccccccchhhhhHHHHHHHHHhhCCCCCC
Q 027283           42 LKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPFK  121 (225)
Q Consensus        42 lkIitwNv~g~~~~~~~~~~~l~~~i~~~~pDIv~LQEt~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~  121 (225)
                      |||+||||||++++.+    .+.+|+.+++|||+|||||+.....+|..                       .+   ...
T Consensus         1 mkI~SwNVNgiRar~~----~~~~~l~~~~pDVlclQEtK~~~~~fp~~-----------------------~~---~~~   50 (261)
T COG0708           1 MKIASWNVNGLRARLK----KLLDWLEEEQPDVLCLQETKAQDEQFPRE-----------------------EL---EAL   50 (261)
T ss_pred             CeeEEEehhhHHHHHH----HHHHHHHHhCCCEEEEEecccCcccCCHh-----------------------HH---hhC
Confidence            7999999999999984    59999999999999999999999888631                       12   237


Q ss_pred             CceEEEEcCCCCcceEEEEEccCCCcceEEecCCcccccCCCCCCEEEEEeCCEEEEEEEccCCCCCCccccHHHHHHHH
Q 027283          122 NYQIWWSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRKWD  201 (225)
Q Consensus       122 gy~~~~~~~~~g~~GvAIlsr~~i~p~~~~~~~~~~~~~~~~~gr~l~~~~~~~~v~~vY~P~~~~~~~~~~~~~r~~~~  201 (225)
                      ||+.++..+.+|++||||+||.+  |.++..+++. .+..+.+||+|.++++.++|+|+|+|+++.. +.+++.+|.+|+
T Consensus        51 GY~~~~~~gqKgysGVailsr~~--~~~v~~g~~~-~~~~d~e~R~I~a~~~~~~v~~~Y~PnG~~~-~~~k~~yKl~f~  126 (261)
T COG0708          51 GYHHVFNHGQKGYSGVAILSKKP--PDDVRRGFPG-EEEDDEEGRVIEAEFDGFRVINLYFPNGSSI-GLEKFDYKLRFL  126 (261)
T ss_pred             CceEEEecCcCCcceEEEEEccC--chhhhcCCCC-CccccccCcEEEEEECCEEEEEEEcCCCCCC-CCcchHHHHHHH
Confidence            99666666778899999999986  5567778773 1345678999999999999999999999972 236899999999


Q ss_pred             HHHHHHHHhc--CCCCEEEEeccCCC
Q 027283          202 KRIQEFVLQC--SGKPLIWCGDLNVR  225 (225)
Q Consensus       202 ~~L~~~l~~~--~~~p~Il~GDFN~~  225 (225)
                      +.|..+++++  .+.|+|+|||||+|
T Consensus       127 ~~l~~~l~~l~~~~~~~vl~GD~NIa  152 (261)
T COG0708         127 DALRNYLEELLKKGKPVVLCGDFNIA  152 (261)
T ss_pred             HHHHHHHHHHhhcCCCEEEecccccC
Confidence            9999999875  56899999999986

>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
>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
>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
>KOG2756 consensus Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms] Back     alignment and domain information
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional Back     alignment and domain information
>PTZ00297 pantothenate kinase; Provisional Back     alignment and domain information
>KOG2338 consensus Transcriptional effector CCR4-related protein [Transcription] Back     alignment and domain information
>smart00476 DNaseIc deoxyribonuclease I Back     alignment and domain information
>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
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] 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
>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
>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
>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 ?
Query225
2o3h_A 285 Crystal Structure Of The Human C65a Ape Length = 28 5e-14
1e9n_A 318 A Second Divalent Metal Ion In The Active Site Of A 5e-14
2isi_A 317 Crystal Structure Of Ape1 From Homo Sapiens In A Ne 5e-14
1bix_A 287 The Crystal Structure Of The Human Dna Repair Endon 5e-14
1dew_A 279 Crystal Structure Of Human Ape1 Bound To Abasic Dna 6e-14
1de8_B 276 Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bo 6e-14
2o3c_A 282 Crystal Structure Of Zebrafish Ape Length = 282 4e-11
2jc4_A 256 3'-5' Exonuclease (Nexo) From Neisseria Meningitidi 1e-06
3g91_A 265 1.2 Angstrom Structure Of The Exonuclease Iii Homol 3e-06
3fzi_A 265 1.9 Angstrom Structure Of The Thermophilic Exonucle 6e-06
3g00_A 265 Mth0212 In Complex With A 9bp Blunt End Dsdna At 1. 2e-05
2voa_A 257 Structure Of An Ap Endonuclease From Archaeoglobus 3e-04
>pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape Length = 285 Back     alignment and structure 
Iteration: 1

 Score = 74.3 bits (181), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 35/185 (18%)
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 GDLNV 224
           GDLNV
Sbjct: 176 GDLNV 180
>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|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis Length = 256 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|2VOA|A Chain A, Structure Of An Ap Endonuclease From Archaeoglobus Fulgidus Length = 257 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 ?
Query225
2o3h_A 285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 3e-31
1hd7_A 318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 2e-30
3g91_A 265 MTH0212, exodeoxyribonuclease; double-strand speci 2e-28
2jc5_A 259 Exodeoxyribonuclease; hydrolase, repair phosphodie 2e-26
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 2e-24
2j63_A 467 AP-endonuclease; base excision repair, lyase; 2.48 8e-23
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 1e-15
1ako_A 268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 3e-11
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 2e-09
2voa_A 257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 5e-09
2ddr_A 306 Sphingomyelin phosphodiesterase; DNAse I like fold 8e-09
1zwx_A 301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 2e-08
2jc4_A 256 Exodeoxyribonuclease III; hydrolase, repair phosph 5e-08
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 4e-07
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 3e-06
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 3e-04
3mpr_A 298 Putative endonuclease/exonuclease/phosphatase FAM 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 =  114 bits (288), Expect = 3e-31
 Identities = 61/216 (28%), Positives = 98/216 (45%), Gaps = 41/216 (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-SGKPLIWCGDLNV 224
               +  R++WD+  ++F+    S KPL+ CGDLNV
Sbjct: 147 VRLEY--RQRWDEAFRKFLKGLASRKPLVLCGDLNV 180
>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
>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
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} SCOP: d.151.1.1 Length = 268 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
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Length = 257 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
>2jc4_A Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis} Length = 256 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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query225
3g91_A 265 MTH0212, exodeoxyribonuclease; double-strand speci 99.93
2o3h_A 285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 99.91
2j63_A 467 AP-endonuclease; base excision repair, lyase; 2.48 99.91
1hd7_A 318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 99.91
2voa_A 257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 99.9
2jc4_A 256 Exodeoxyribonuclease III; hydrolase, repair phosph 99.9
2jc5_A 259 Exodeoxyribonuclease; hydrolase, repair phosphodie 99.9
1vyb_A238 ORF2 contains A reverse transcriptase domain; endo 99.88
1ako_A 268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 99.87
2ei9_A 240 Non-LTR retrotransposon R1BMKS ORF2 protein; four 99.86
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 99.84
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 99.76
3teb_A266 Endonuclease/exonuclease/phosphatase; PSI-biology, 99.71
3l1w_A257 Uncharacterized protein; APC29019.2, conserved pro 99.68
1zwx_A 301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 99.66
2ddr_A 306 Sphingomyelin phosphodiesterase; DNAse I like fold 99.63
3g6s_A267 Putative endonuclease/exonuclease/phosphatase fami 99.63
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxi 99.61
3mpr_A 298 Putative endonuclease/exonuclease/phosphatase FAM 99.54
1sr4_B261 CDT B, cytolethal distending toxin protein B; bact 99.52
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.co 99.48
3ngq_A 398 CCR4-NOT transcription complex subunit 6-like; alp 99.43
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse 99.37
4b8c_D 727 Glucose-repressible alcohol dehydrogenase transcr 98.97
1i9z_A 347 Synaptojanin, phosphatidylinositol phosphate phosp 98.93
2imq_X 282 Salivary nitrophorin; ferrous heme, beta-sandwich, 98.79
3mtc_A 313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; 98.76
2xsw_A 357 72 kDa inositol polyphosphate 5-phosphatase; inosi 98.74
4a9c_A 316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; 98.25
>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=99.93  E-value=2.5e-25  Score=188.78  Aligned_cols=150  Identities=27%  Similarity=0.534  Sum_probs=116.7

Q ss_pred             CcEEEEEeCCcchhhhhcChhHHHHHHhhcCCcEEEEeeeeCCCCCCCCCCcccccccchhhhhHHHHHHHHHhhCCCCC
Q 027283           41 PLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSSPPF  120 (225)
Q Consensus        41 ~lkIitwNv~g~~~~~~~~~~~l~~~i~~~~pDIv~LQEt~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~  120 (225)
                      +|||+||||+|++...++   .+.++|++.+|||||||||+.....+.                        ..+.  ..
T Consensus         3 ~l~i~s~Nv~g~~~~~~~---~l~~~i~~~~~DIv~LQEt~~~~~~~~------------------------~~~~--~~   53 (265)
T 3g91_A            3 VLKIISWNVNGLRAVHRK---GFLKWFMEEKPDILCLQEIKAAPEQLP------------------------RKLR--HV   53 (265)
T ss_dssp             EEEEEEEECSCHHHHHHH---THHHHHHHHCCSEEEEECCCSCGGGSC------------------------HHHH--CC
T ss_pred             ccEEEEEEcCCchhhhhh---hHHHHHHhcCCCEEEEEeccccccccC------------------------hhhh--cc
Confidence            699999999999887753   589999999999999999987664321                        0111  13


Q ss_pred             CCceEEEEcC-CCCcceEEEEEccCCCcceEEecCCcccccCCCCCCEEEEEeCCEEEEEEEccCCCCCCccccHHHHHH
Q 027283          121 KNYQIWWSLA-DSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEFETFYLLNTYAPNNGWKEEENSFQRRRK  199 (225)
Q Consensus       121 ~gy~~~~~~~-~~g~~GvAIlsr~~i~p~~~~~~~~~~~~~~~~~gr~l~~~~~~~~v~~vY~P~~~~~~~~~~~~~r~~  199 (225)
                      .||..++... .++++||||++|.+  +..+..++.  ....+.+||++.+++..+.|+|+|+|++...  ..++.+|..
T Consensus        54 ~gy~~~~~~~~~~~~~Gvail~k~~--~~~~~~~~~--~~~~d~~gr~i~~~~~~~~i~~vy~p~~~~~--~~~~~~r~~  127 (265)
T 3g91_A           54 EGYRSFFTPAERKGYSGVAMYTKVP--PSSLREGFG--VERFDTEGRIQIADFDDFLLYNIYFPNGAMS--EERLKYKLE  127 (265)
T ss_dssp             TTCEEEEECBSSTTSCCEEEEESSC--CSEEECCCS--CHHHHSBSCEEEEECSSCEEEEEECCCCTTC--HHHHHHHHH
T ss_pred             cCCcEEEccCCCCCcCEEEEEEecC--hHHhccCCC--CcccCCcCCEEEEEeCCEEEEEEEecCCCCC--chhHHHHHH
Confidence            6998877654 35578999999996  344444443  1234578999999999999999999998863  367778999


Q ss_pred             HHHHHHHHHHhc--CCCCEEEEeccCCC
Q 027283          200 WDKRIQEFVLQC--SGKPLIWCGDLNVR  225 (225)
Q Consensus       200 ~~~~L~~~l~~~--~~~p~Il~GDFN~~  225 (225)
                      |++.|.+++.+.  .+.|+|+|||||++
T Consensus       128 ~~~~l~~~~~~~~~~~~~~ii~GDfN~~  155 (265)
T 3g91_A          128 FYDAFLEDVNRERDSGRNVIICGDFNTA  155 (265)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEEEECCCC
T ss_pred             HHHHHHHHHHHHHcCCCCEEEECccccC
Confidence            999999998875  36899999999964
>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
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Back     alignment and structure
>1hd7_A DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} SCOP: d.151.1.1 PDB: 1e9n_A 3u8u_A 2isi_A Back     alignment and structure
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling, SGC stockholm, structural genomics CONS hydrolase; 1.90A {Homo sapiens} 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 225
d2f1na1250 d.151.1.1 (A:1-250) Cytolethal distending toxin su 2e-14
d1sr4b_261 d.151.1.1 (B:) Cytolethal distending toxin subunit 2e-09
d2imqx1 280 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug ( 2e-09
d1zwxa1293 d.151.1.3 (A:41-333) Sphingomyelin phosphodiestera 5e-09
d2ddra1 299 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesteras 2e-08
d1hd7a_ 275 d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human 2e-07
d2a40b1260 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos 1e-06
d1akoa_268 d.151.1.1 (A:) DNA-repair enzyme exonuclease III { 2e-06
d1vyba_236 d.151.1.1 (A:) Endonuclease domain of LINE-1 rever 3e-06
d1wdua_228 d.151.1.1 (A:) Endonuclease domain of TRAS1 retrot 3e-05
>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 = 68.1 bits (165), Expect = 2e-14
 Identities = 22/187 (11%), Positives = 52/187 (27%), Gaps = 18/187 (9%)

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 WCGDLNV 224
             GD N 
Sbjct: 171 ILGDFNR 177
>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} Length = 261 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
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Length = 293 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
>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
>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
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} Length = 228 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 ?
Query225
d1vyba_236 Endonuclease domain of LINE-1 reverse transcriptas 99.87
d1wdua_228 Endonuclease domain of TRAS1 retrotransposon (ORF2 99.78
d1hd7a_ 275 DNA repair endonuclease Hap1 {Human (Homo sapiens) 99.7
d2f1na1250 Cytolethal distending toxin subunit B {Escherichia 99.66
d1zwxa1293 Sphingomyelin phosphodiesterase C {Listeria ivanov 99.63
d2ddra1 299 Sphingomyelin phosphodiesterase C {Bacillus cereus 99.57
d1sr4b_261 Cytolethal distending toxin subunit B {Haemophilus 99.53
d2imqx1 280 Salivary nitrophorin {Bedbug (Cimex lectularius) [ 99.49
d2a40b1260 Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913 99.44
d1akoa_268 DNA-repair enzyme exonuclease III {Escherichia col 99.4
d1i9za_ 345 Synaptojanin, IPP5C domain {Fission yeast (Schizos 99.08
>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=2.5e-21  Score=157.63  Aligned_cols=141  Identities=25%  Similarity=0.363  Sum_probs=94.1

Q ss_pred             CCCCcEEEEEeCCcchhhhhcChhHHHHHHhhcCCcEEEEeeeeCCCCCCCCCCcccccccchhhhhHHHHHHHHHhhCC
Q 027283           38 KKDPLKFVTWNANSLLLRVKNNWPEFSNFITTFDPDVIALQEVRMPAAGSKDAPKNHQELKDDTKASREEKLILMRALSS  117 (225)
Q Consensus        38 ~~~~lkIitwNv~g~~~~~~~~~~~l~~~i~~~~pDIv~LQEt~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~  117 (225)
                      ..++|||+||||+|++...++  ..+.++|++++|||||||||+.......                         .+  
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            467899999999999877665  6899999999999999999986554321                         11  


Q ss_pred             CCCCCceEE-EEcCCCCcceEEEEEccCCCcceEEecCCcccccCCCCCCEEEEEe----CCEEEEEEEccCCCCCCccc
Q 027283          118 PPFKNYQIW-WSLADSKYAGTALLVKKCFQPKKVSFSLEKTALKYEPDGRVILAEF----ETFYLLNTYAPNNGWKEEEN  192 (225)
Q Consensus       118 ~~~~gy~~~-~~~~~~g~~GvAIlsr~~i~p~~~~~~~~~~~~~~~~~gr~l~~~~----~~~~v~~vY~P~~~~~~~~~  192 (225)
                       ...++..+ +.....+..|+||+++.++.-....+       ..+..++++.+.+    ..++++++|+|+...     
T Consensus        53 -~~~~~~~~~~~~~~~~~~g~~i~~k~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~-----  119 (236)
T d1vyba_          53 -KIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKI-------KRDKEGHYIMVKGSIQQEELTILNIYAPNTGA-----  119 (236)
T ss_dssp             -CCTTCCEEEEECCSSSSCCEEEEECTTCCCEEEEE-------EECTTSSEEEEEEEETTEEEEEEEEECCSSSH-----
T ss_pred             -hhcccceEEEeeccccccceeeEeecccccccccc-------cccccccceeeeeeeccCcceeEEeccccccc-----
Confidence             11233333 33344456799999999742111111       1234566665544    269999999987753     


Q ss_pred             cHHHHHHHHHHHHHHHHhcCCCCEEEEeccCCC
Q 027283          193 SFQRRRKWDKRIQEFVLQCSGKPLIWCGDLNVR  225 (225)
Q Consensus       193 ~~~~r~~~~~~L~~~l~~~~~~p~Il~GDFN~~  225 (225)
                           ..++.++...+....+.|+|+|||||.+
T Consensus       120 -----~~~~~~~~~~~~~~~~~~~Il~GDfN~~  147 (236)
T d1vyba_         120 -----PRFIKQVLSDLQRDLDSHTLIMGDFNTP  147 (236)
T ss_dssp             -----HHHHHHHHHHTTTTCCTTEEEEEECSSC
T ss_pred             -----HHHHHhhhhhhcccccceeEEeeccccc
Confidence                 1233344444444457899999999963
>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
>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
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} 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