254780288

254780288

exodeoxyribonuclease III protein

GeneID in NCBI database:8209270Locus tag:CLIBASIA_00865
Protein GI in NCBI database:254780288Protein Accession:YP_003064701.1
Gene range:+(176801, 177646)Protein Length:281aa
Gene description:exodeoxyribonuclease III protein
COG prediction:[L] Exonuclease III
KEGG prediction:xthA; exodeoxyribonuclease III protein; K01142 exodeoxyribonuclease III [EC:3.1.11.2]
SEED prediction:Exodeoxyribonuclease III (EC 3.1.11.2)
Pathway involved in KEGG:Base excision repair [PATH:las03410]
Subsystem involved in SEED:DNA repair, bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------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-
MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIPEPRKKQQDSTSQNMKPI
cccEEEEEEEcccHHHHHHHHHHHHHHHcccEEEEEEEEccHHHccHHHHHccccEEEEccccccccEEEEEccccccEEEccccccccccccEEEEEEEcccccEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHcccHHHHcccccccHHHHHHHHHHHHcccEEEEHHHccccccEEcccccccccccccccEEEEEEEcHHHHHHHHHcEEcccccccccccccccEEEEEEEcccccccccccHHccccc
cccEEEEEEEcccHHHcHHHHHHHHHHHcccEEEEEcccccHHHccHHHHHHcccEEEEEEEccEEEEEEEEcccccEEEEccccccHHHHccEEEEEEEEccEEEEEEEEEcccccccccccccHHHHHHHHHHHHHHHHccccccEEEEcccccccccccccccHHHcccccccHHHHHHHHHHHHcccHHHHHHHccccccEEEEEccccccccccccEEEEEEccHHHHHHHHHccccHHHcccccccccccEEEEEEccccccccccccccccccc
MSVVTVATWNVNSIRARIHNLAAWIkennpdiiclqetktedknfpfetLQSLNYHIetcgqksyngvailskyqpieivthlpgddldVQARFIEATFTINTQTLrignlylphgnpitstkyddkISWIKRFLRFASQRLeleeplifagdyniipqphdcynpiiwendaCFTLEVRQSFQKLQNmgftdairathdthhlysfwdyyadswsknkgiridhimlspeatSLLHSAridtkprgwtkpsdhtpvivsldipeprkkqqdstsqnmkpi
MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPItstkyddkiSWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIdtkprgwtkpsdhtpvivsldipeprkkqqdstsqnmkpi
MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIPEPRKKQQDSTSQNMKPI
*SVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLD*******************
MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIPE****************
*SVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIPE****************
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MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIPEPRKKQQDSTSQNMKPI
MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIPEPRKKQQDSTSQNMKPI
MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIVSLDIPEPRKKQQDSTSQNMKPI

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target281 exodeoxyribonuclease III protein [Candidatus Liberibact
254780797231 hypothetical protein CLIBASIA_03440 [Candidatus Li 0.010
>gi|254780797|ref|YP_003065210.1| hypothetical protein CLIBASIA_03440 [Candidatus Liberibacter asiaticus str. psy62] Length = 231 Back     alignment
 Score = 32.3 bits (72), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 46/203 (22%), Positives = 87/203 (42%), Gaps = 41/203 (20%)

Query: 4   VTVATWNVNSIRARIHNLAAW----IKENN-------------PDIICLQETKTED---K 43
           + +A+WN+N++  +   +A +    I+E+N              DI+CLQE  + +   +
Sbjct: 7   IRIASWNINNLSEK-SGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKR 65

Query: 44  NFPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEIVTHLPGD--DLDVQA---RFIEAT 98
            FP +    L     T     +  + I      +   ++LP D   LD +A   R +E  
Sbjct: 66  VFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEIL 125

Query: 99  FTINTQTLRIGNLYLPHGNPITSTKYDDKIS----------WIKRFLRFASQRLELEEPL 148
           F ++ + + + +++L     + S + D  IS          W+K+++    Q+  L  P 
Sbjct: 126 FEVDGRKIWLLDIHLKSFCFLDSIE-DSYISSCYMLNLQATWLKQWV---DQKNNLNMPF 181

Query: 149 IFAGDYN-IIPQPHDCYNPIIWE 170
           I AGD+N  I   H      +W+
Sbjct: 182 IIAGDFNRKINHSHSGIKDELWQ 204

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target281 exodeoxyribonuclease III protein [Candidatus Liberibact
315122848265 exodeoxyribonuclease III protein [Candidatus Liberibact 1 1e-131
222085777263 exodeoxyribonuclease III protein [Agrobacterium radioba 1 9e-89
327191803263 exodeoxyribonuclease III protein [Rhizobium etli CNPAF5 1 2e-87
241204407263 exodeoxyribonuclease III Xth [Rhizobium leguminosarum b 1 3e-87
190891504263 exodeoxyribonuclease III protein [Rhizobium etli CIAT 6 1 9e-87
116251798263 exodeoxyribonuclease III [Rhizobium leguminosarum bv. v 1 1e-86
163759458260 exodeoxyribonuclease III [Hoeflea phototrophica DFL-43] 1 1e-86
86357443263 exodeoxyribonuclease III protein [Rhizobium etli CFN 42 1 1e-85
218463283263 exodeoxyribonuclease III protein [Rhizobium etli Kim 5] 1 1e-85
218673944263 exodeoxyribonuclease III Xth [Rhizobium etli GR56] Leng 1 2e-85
>gi|315122848|ref|YP_004063337.1| exodeoxyribonuclease III protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 265 Back     alignment and organism information
 Score =  471 bits (1213), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 216/265 (81%), Positives = 242/265 (91%)

Query: 1   MSVVTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETC 60
           MS+VT+ATWNVNSIR RI N+  WI+ENNPDI+CLQETKTEDK FPFE +QSLNYHIETC
Sbjct: 1   MSLVTIATWNVNSIRVRIKNVITWIQENNPDIVCLQETKTEDKTFPFEAIQSLNYHIETC 60

Query: 61  GQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPIT 120
           GQKSYNGVAILSKYQPIE++  LPGDDLD QARFIEATFTIN+Q LRIGN+YLP+GNPI 
Sbjct: 61  GQKSYNGVAILSKYQPIEMIKKLPGDDLDEQARFIEATFTINSQILRIGNIYLPNGNPIA 120

Query: 121 STKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVR 180
           STKYD KISWIKRFL+FASQRLELEE LIFAGDYNI+PQP DC++ I+ +NDACFTLEVR
Sbjct: 121 STKYDYKISWIKRFLQFASQRLELEEALIFAGDYNIVPQPRDCHDSIMLQNDACFTLEVR 180

Query: 181 QSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSAR 240
           Q+FQKLQNMGFTDAIRAT+D HH+YSFWDY++DSW KNKG+RIDH+MLSPEAT+ LHSA 
Sbjct: 181 QAFQKLQNMGFTDAIRATNDAHHIYSFWDYFSDSWRKNKGMRIDHVMLSPEATTFLHSAY 240

Query: 241 IDTKPRGWTKPSDHTPVIVSLDIPE 265
           ID KPRG  KPSDHTPVIV+LDIPE
Sbjct: 241 IDKKPRGCVKPSDHTPVIVALDIPE 265


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222085777|ref|YP_002544307.1| exodeoxyribonuclease III protein [Agrobacterium radiobacter K84] Length = 263 Back     alignment and organism information
>gi|327191803|gb|EGE58803.1| exodeoxyribonuclease III protein [Rhizobium etli CNPAF512] Length = 263 Back     alignment and organism information
>gi|241204407|ref|YP_002975503.1| exodeoxyribonuclease III Xth [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 263 Back     alignment and organism information
>gi|190891504|ref|YP_001978046.1| exodeoxyribonuclease III protein [Rhizobium etli CIAT 652] Length = 263 Back     alignment and organism information
>gi|116251798|ref|YP_767636.1| exodeoxyribonuclease III [Rhizobium leguminosarum bv. viciae 3841] Length = 263 Back     alignment and organism information
>gi|163759458|ref|ZP_02166543.1| exodeoxyribonuclease III [Hoeflea phototrophica DFL-43] Length = 260 Back     alignment and organism information
>gi|86357443|ref|YP_469335.1| exodeoxyribonuclease III protein [Rhizobium etli CFN 42] Length = 263 Back     alignment and organism information
>gi|218463283|ref|ZP_03503374.1| exodeoxyribonuclease III protein [Rhizobium etli Kim 5] Length = 263 Back     alignment and organism information
>gi|218673944|ref|ZP_03523613.1| exodeoxyribonuclease III Xth [Rhizobium etli GR56] Length = 263 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target281 exodeoxyribonuclease III protein [Candidatus Liberibact
TIGR00195254 TIGR00195, exoDNase_III, exodeoxyribonuclease III 5e-60
TIGR00633255 TIGR00633, xth, exodeoxyribonuclease III (xth) 2e-58
PRK11756268 PRK11756, PRK11756, exonuclease III; Provisional 8e-50
pfam03372255 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phos 5e-34
PRK13911250 PRK13911, PRK13911, exodeoxyribonuclease III; Provision 1e-22
KOG1294335 KOG1294, KOG1294, KOG1294, Apurinic/apyrimidinic endonu 2e-11
COG3568259 COG3568, ElsH, Metal-dependent hydrolase [General funct 1e-07
COG3021309 COG3021, COG3021, Uncharacterized protein conserved in 4e-04
COG0708261 COG0708, XthA, Exonuclease III [DNA replication, recomb 2e-79
KOG2756349 KOG2756, KOG2756, KOG2756, Predicted Mg2+-dependent pho 4e-04
>gnl|CDD|161757 TIGR00195, exoDNase_III, exodeoxyribonuclease III Back     alignment and domain information
>gnl|CDD|161970 TIGR00633, xth, exodeoxyribonuclease III (xth) Back     alignment and domain information
>gnl|CDD|183300 PRK11756, PRK11756, exonuclease III; Provisional Back     alignment and domain information
>gnl|CDD|146159 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase family Back     alignment and domain information
>gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional Back     alignment and domain information
>gnl|CDD|36508 KOG1294, KOG1294, KOG1294, Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] Back     alignment and domain information
>gnl|CDD|33370 COG3568, ElsH, Metal-dependent hydrolase [General function prediction only] Back     alignment and domain information
>gnl|CDD|32837 COG3021, COG3021, Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>gnl|CDD|31052 COG0708, XthA, Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|37967 KOG2756, KOG2756, KOG2756, Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 281 exodeoxyribonuclease III protein [Candidatus Liberibact
TIGR00633279 xth exodeoxyribonuclease III (xth); InterPro: IPR004808 100.0
TIGR00195281 exoDNase_III exodeoxyribonuclease III; InterPro: IPR000 100.0
PRK11756268 exonuclease III; Provisional 100.0
COG0708261 XthA Exonuclease III [DNA replication, recombination, a 100.0
PRK13911250 hypothetical protein; Provisional 100.0
pfam03372255 Exo_endo_phos Endonuclease/Exonuclease/phosphatase fami 100.0
KOG1294335 consensus 100.0
COG3568259 ElsH Metal-dependent hydrolase [General function predic 99.97
TIGR03395283 sphingomy sphingomyelin phosphodiesterase. Members of t 99.93
KOG3873 422 consensus 99.93
PRK05421254 hypothetical protein; Provisional 99.82
KOG2756349 consensus 99.8
COG3021309 Uncharacterized protein conserved in bacteria [Function 99.75
PTZ00297 1452 pantothenate kinase; Provisional 99.59
COG5239378 CCR4 mRNA deadenylase, exonuclease subunit and related 99.57
COG2374798 Predicted extracellular nuclease [General function pred 99.47
KOG2338495 consensus 99.71
smart00476276 DNaseIc deoxyribonuclease I. Deoxyribonuclease I cataly 99.63
smart00128310 IPPc Inositol polyphosphate phosphatase, catalytic doma 99.42
KOG0566 1080 consensus 99.3
KOG0620361 consensus 99.55
KOG1294 335 consensus 97.86
COG5411 460 Phosphatidylinositol 5-phosphate phosphatase [Signal tr 97.62
KOG1976391 consensus 93.04
>TIGR00633 xth exodeoxyribonuclease III (xth); InterPro: IPR004808 All proteins in this family for which functions are known are 5' AP endonucleases that function in base excision repair and the repair of abasic sites in DNA Back     alignment and domain information
>TIGR00195 exoDNase_III exodeoxyribonuclease III; InterPro: IPR000097 DNA damaging agents such as the antitumor drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA Back     alignment and domain information
>PRK11756 exonuclease III; Provisional Back     alignment and domain information
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13911 hypothetical protein; Provisional Back     alignment and domain information
>pfam03372 Exo_endo_phos Endonuclease/Exonuclease/phosphatase family Back     alignment and domain information
>KOG1294 consensus Back     alignment and domain information
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only] Back     alignment and domain information
>TIGR03395 sphingomy sphingomyelin phosphodiesterase Back     alignment and domain information
>KOG3873 consensus Back     alignment and domain information
>PRK05421 hypothetical protein; Provisional Back     alignment and domain information
>KOG2756 consensus Back     alignment and domain information
>COG3021 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PTZ00297 pantothenate kinase; Provisional Back     alignment and domain information
>COG5239 CCR4 mRNA deadenylase, exonuclease subunit and related nucleases [RNA processing and modification] Back     alignment and domain information
>COG2374 Predicted extracellular nuclease [General function prediction only] Back     alignment and domain information
>KOG2338 consensus Back     alignment and domain information
>smart00476 DNaseIc deoxyribonuclease I Back     alignment and domain information
>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues Back     alignment and domain information
>KOG0566 consensus Back     alignment and domain information
>KOG0620 consensus Back     alignment and domain information
>KOG1294 consensus Back     alignment and domain information
>COG5411 Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms] Back     alignment and domain information
>KOG1976 consensus Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target281 exodeoxyribonuclease III protein [Candidatus Liberibact
2jc4_A256 3'-5' Exonuclease (Nexo) From Neisseria Meningitidi 2e-50
1ako_A268 Exonuclease Iii From Escherichia Coli Length = 268 3e-50
3g00_A265 Mth0212 In Complex With A 9bp Blunt End Dsdna At 1. 3e-46
2voa_A257 Structure Of An Ap Endonuclease From Archaeoglobus 3e-46
3fzi_A265 1.9 Angstrom Structure Of The Thermophilic Exonucle 4e-46
3g91_A265 1.2 Angstrom Structure Of The Exonuclease Iii Homol 4e-46
2jc5_A259 Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From 2e-42
2o3h_A285 Crystal Structure Of The Human C65a Ape Length = 28 8e-42
2isi_A317 Crystal Structure Of Ape1 From Homo Sapiens In A Ne 3e-41
1bix_A287 The Crystal Structure Of The Human Dna Repair Endon 3e-41
1e9n_A318 A Second Divalent Metal Ion In The Active Site Of A 3e-41
1dew_A279 Crystal Structure Of Human Ape1 Bound To Abasic Dna 6e-41
1de8_B276 Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bo 9e-41
2o3c_A282 Crystal Structure Of Zebrafish Ape Length = 282 1e-39
2j63_A467 Crystal Structure Of Ap Endonuclease Lmap From Leis 9e-23
1vyb_A238 Endonuclease Domain Of Human Line1 Orf2p Length = 2 6e-15
2v0r_A240 Crystal Structure Of A Hairpin Exchange Variant (Lt 4e-14
2v0s_A236 Crystal Structure Of A Hairpin Exchange Variant (Lr 1e-13
3mpr_A298 Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHA 3e-04
gi|134104765|pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis Length = 256 Back     alignment and structure
 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 91/260 (35%), Positives = 135/260 (51%), Gaps = 4/260 (1%)

Query: 4   VTVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQK 63
           + + TWNVNS+  R+  +   + +N PDI+ LQE K +   FP   LQ + +H    GQK
Sbjct: 1   MKITTWNVNSLNVRLPQVQNLLADNPPDILVLQELKLDQDKFPAAALQMMGWHCVWSGQK 60

Query: 64  SYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTK 123
           +YNGVAI+S+  P ++   LP    D Q R I AT +     +R+ N+Y  +G  + S K
Sbjct: 61  TYNGVAIVSRSVPQDVHFGLPALPDDPQRRVIAATVSG----VRVINVYCVNGEALDSPK 116

Query: 124 YDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSF 183
           +  K  W      F    +     L+  GD+NI P   DCY+P  W      +   RQ F
Sbjct: 117 FKYKEQWFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQWF 176

Query: 184 QKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDT 243
           Q L ++G TD++R  H     Y+++DY    + +  G+RIDHI++SP   + L   R+D 
Sbjct: 177 QNLLDLGLTDSLRQVHPEGAFYTWFDYRGAMFQRKLGLRIDHILVSPAMAAALKDVRVDL 236

Query: 244 KPRGWTKPSDHTPVIVSLDI 263
           + R   +PSDH PV    D 
Sbjct: 237 ETRALERPSDHAPVTAEFDW 256


gi|157829928|pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli Length = 268 Back     alignment and structure
>gi|290789946|pdb|3G00|A Chain A, Mth0212 In Complex With A 9bp Blunt End Dsdna At 1.7 Angstrom Length = 265 Back     alignment and structure
>gi|217035255|pdb|2VOA|A Chain A, Structure Of An Ap Endonuclease From Archaeoglobus Fulgidus Length = 257 Back     alignment and structure
>gi|290789945|pdb|3FZI|A Chain A, 1.9 Angstrom Structure Of The Thermophilic Exonuclease Iii Homologue Mth0212 Length = 265 Back     alignment and structure
>gi|290789984|pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue Mth0212 Length = 265 Back     alignment and structure
gi|157883966|pdb|2JC5|A Chain A, Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From Neisseria Meningitidis Length = 259 Back     alignment and structure
>gi|162329924|pdb|2O3H|A Chain A, Crystal Structure Of The Human C65a Ape Length = 285 Back     alignment and structure
>gi|118138505|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
>gi|157830335|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
gi|13399540|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
>gi|6980832|pdb|1DEW|A Chain A, Crystal Structure Of Human Ape1 Bound To Abasic Dna Length = 279 Back     alignment and structure
>gi|6980804|pdb|1DE8|B Chain B, Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bound To Abasic Dna Length = 276 Back     alignment and structure
>gi|162329921|pdb|2O3C|A Chain A, Crystal Structure Of Zebrafish Ape Length = 282 Back     alignment and structure
>gi|158428909|pdb|2J63|A Chain A, Crystal Structure Of Ap Endonuclease Lmap From Leishmania Major Length = 467 Back     alignment and structure
>gi|49259594|pdb|1VYB|A Chain A, Endonuclease Domain Of Human Line1 Orf2p Length = 238 Back     alignment and structure
>gi|152149537|pdb|2V0R|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Ltx) Of The Targeting Line-1 Retrotransposon Endonuclease Length = 240 Back     alignment and structure
>gi|152149539|pdb|2V0S|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Lr1) Of The Targeting Line-1 Retrotransposon Endonuclease Length = 236 Back     alignment and structure
>gi|296863686|pdb|3MPR|A Chain A, Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHATASE FA Protein From Bacteroides Thetaiotaomicron, Northeast Struct Genomics Consortium Target Btr318a Length = 298 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target281 exodeoxyribonuclease III protein [Candidatus Liberibact
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand specific 3 1e-60
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endo 3e-50
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA repair, 6e-49
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48A {Le 4e-47
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosphodies 4e-42
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Es 5e-42
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, endonuc 1e-36
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; INPP 1e-35
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodiestera 1e-34
3nr8_B316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; stru 5e-32
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, tran 6e-31
2xsw_A357 72 kDa inositol polyphosphate 5-phosphatase; inositol s 1e-29
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.coli, D 5e-25
3g6s_A267 Putative endonuclease/exonuclease/phosphatase family pr 1e-24
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA bind 3e-24
1vyb_A238 ORF2 contains A reverse transcriptase domain; endonucle 1e-23
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM prote 4e-23
3l1w_A257 Uncharacterized protein; APC29019.2, conserved protein, 8e-22
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1. 3e-20
1sr4_B261 CDT B, cytolethal distending toxin protein B; bacterial 9e-19
3ngq_A398 CCR4-NOT transcription complex subunit 6-like; alpha/be 6e-18
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four layer 2e-16
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like folding, 6e-16
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpi 5e-13
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, A 2e-10
>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
 Score =  228 bits (581), Expect = 1e-60
 Identities = 66/268 (24%), Positives = 112/268 (41%), Gaps = 12/268 (4%)

Query: 1   MSVVTVATWNVNSIRA-RIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYH--I 57
           M+V+ + +WNVN +RA        W  E  PDI+CLQE K   +  P +      Y    
Sbjct: 1   MAVLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRHVEGYRSFF 60

Query: 58  ETCGQKSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGN 117
               +K Y+GVA+ +K  P  +      +  D + R   A F        + N+Y P+G 
Sbjct: 61  TPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADF----DDFLLYNIYFPNGA 116

Query: 118 PITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTL 177
                +   K+ +   FL   ++  +    +I  GD+N   +  D   P    N + F  
Sbjct: 117 MSE-ERLKYKLEFYDAFLEDVNRERDSGRNVIICGDFNTAHREIDLARPKENSNVSGFLP 175

Query: 178 EVRQSFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLH 237
             R    K    G+ D  R  +     Y++W Y   +  +N G R+D+  ++ E    + 
Sbjct: 176 VERAWIDKFIENGYVDTFRMFNSDPGQYTWWSYRTRARERNVGWRLDYFFVNEEFKGKVK 235

Query: 238 SARIDTKPRGWTKPSDHTPVIVSLDIPE 265
            + I +   G    SDH P+ + +++ E
Sbjct: 236 RSWILSDVMG----SDHCPIGLEIELLE 259


>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Length = 257 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 2isi_A Length = 318 Back     alignment and structure
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Length = 467 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
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} SCOP: d.151.1.1 Length = 268 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 Length = 285 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} Length = 313 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
>3nr8_B Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; structural genomics consortium, SGC, trisphosphate 5-phosphatase 2, SHIP2, INPPL1, SHIP-2; 2.80A {Homo sapiens} Length = 316 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* Length = 282 Back     alignment and structure
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling, SGC stockholm, structural genomics CONS hydrolase; 1.90A {Homo sapiens} Length = 357 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 Length = 262 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
>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
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron} Length = 298 Back     alignment and structure
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} Length = 257 Back     alignment and structure
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A Length = 317 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 Length = 261 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 Length = 398 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
>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
>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* Length = 260 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target281 exodeoxyribonuclease III protein [Candidatus Liberibact
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48A {Le 100.0
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Es 100.0
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA repair, 100.0
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosphodies 100.0
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endo 100.0
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand specific 3 100.0
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, endonuc 100.0
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodiestera 100.0
1vyb_A238 ORF2 contains A reverse transcriptase domain; endonucle 100.0
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, tran 100.0
3nr8_B316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; stru 100.0
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; INPP 100.0
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA bind 100.0
2xsw_A357 72 kDa inositol polyphosphate 5-phosphatase; inositol s 100.0
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1. 100.0
3l1w_A257 Uncharacterized protein; APC29019.2, conserved protein, 100.0
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four layer 99.97
1i9z_A347 Synaptojanin, phosphatidylinositol phosphate phosphatas 99.97
3ngq_A398 CCR4-NOT transcription complex subunit 6-like; alpha/be 99.97
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like folding, 99.97
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM prote 99.97
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpi 99.97
3g6s_A267 Putative endonuclease/exonuclease/phosphatase family pr 99.97
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.coli, D 99.97
1sr4_B261 CDT B, cytolethal distending toxin protein B; bacterial 99.95
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, A 99.94
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Back     alignment and structure
Probab=100.00  E-value=0  Score=413.39  Aligned_cols=258  Identities=21%  Similarity=0.306  Sum_probs=199.5

Q ss_pred             CCCEEEEEEECCHHHHHHH----HHHHHHHHCCCEEEEEEEECCHHHCCHHHHH--HCCCEEEEE---ECCCCCCEEEEE
Q ss_conf             7007998710318888998----9999987289889998565794458977873--289789993---047765148987
Q gi|254780288|r    2 SVVTVATWNVNSIRARIHN----LAAWIKENNPDIICLQETKTEDKNFPFETLQ--SLNYHIETC---GQKSYNGVAILS   72 (281)
Q Consensus         2 ~~lrI~TwNinglr~r~~~----l~~~l~~~~pDIi~LQEvk~~~~~~~~~~~~--~~gy~~~~~---~~k~~~GvaIls   72 (281)
                      .||||+||||||||+++++    +.+||++++||||||||||+..+.++.+.+.  ..||.+++.   +++||+||||++
T Consensus       148 ~~mKIiSWNVNGlR~~~kk~~~~l~~~L~~~~pDIIcLQEtk~~~~~~~~~~~~~~~~gY~~~~~~~~~kkgysGvAi~s  227 (467)
T 2j63_A          148 RMYKFITWNVAGLRGLLKKNASALRAFMEAEKPDVLCLQETKLNVDEADANATLGVVDGYSFVDHPCAFKRGYSGTRTYM  227 (467)
T ss_dssp             TEEEEEEEECSCHHHHHHHCTTHHHHHHHHHCCSEEEEECCCCCTTCHHHHHTSSCCTTEEEEEECCSSSTTSCCEEEEE
T ss_pred             CEEEEEEEECCCHHHHHHCCHHHHHHHHHHCCCCEEEEEEEECCHHHCCHHHHHHCCCCCCEEEECCCCCCCCCCEEEEE
T ss_conf             44689999404777754306589999998569998999874246444697888751378516874246655304089998


Q ss_pred             EECCEEE------EEC-----------------CCCCCCCCCCCEECCCCC------CCCCEEEEEEEECCCCCCCCCCC
Q ss_conf             4031378------632-----------------555644323301011000------23207999631046678544310
Q gi|254780288|r   73 KYQPIEI------VTH-----------------LPGDDLDVQARFIEATFT------INTQTLRIGNLYLPHGNPITSTK  123 (281)
Q Consensus        73 k~~~~~v------~~~-----------------~~~~~~d~~~R~i~~~i~------~~~~~i~v~n~y~P~g~~~~~~~  123 (281)
                      |.++...      ..+                 +.....|.+||++.+.+.      .....+.|+|+|+|++.. +..+
T Consensus       228 K~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~D~egR~~~~~~~~~~~~~~~~~~~~l~n~y~pn~~~-~~~~  306 (467)
T 2j63_A          228 KNSTTVKGLHARCTRGFALPSEPQADAAAGSRVLVEGAGDEEGRVLTTFLSPDPDSASSSSRIALVNTYVANSGM-GLTR  306 (467)
T ss_dssp             ECCCCCCTSCCEEEESSCCCCC-----------CCCCCCCTTCCEEEEEECSSCCC----CCEEEEEEECCCCCT-TSTT
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCEEEEEECCCCCCC-CCHH
T ss_conf             177643343311112544567665444444333565556655525899841565333445888999864677655-4202


Q ss_pred             HHHHHH-HHHHHHHHHHHH------------------HCCCCHHHHHHHCCCCCCCCCCHH---HHHCCCCCCCCHHHHH
Q ss_conf             123677-776553322232------------------014760000110146867420000---1210487344634556
Q gi|254780288|r  124 YDDKIS-WIKRFLRFASQR------------------LELEEPLIFAGDYNIIPQPHDCYN---PIIWENDACFTLEVRQ  181 (281)
Q Consensus       124 ~~~k~~-~~~~l~~~l~~~------------------~~~~~~vIi~GDFN~a~~~~D~~~---~~~~~~~~~~~~~er~  181 (281)
                      +++|.+ |...+..++..+                  ...++++|||||||++|.+.|.++   +..+.+.+||+++||.
T Consensus       307 ~~~r~~~~d~~~~~~l~~L~~~~~~~~~~~~~~~~~~~~~~~~vIl~GDfNv~~~~~D~~~~~~~~~~~~~~g~~~eER~  386 (467)
T 2j63_A          307 LPYRVQSFDPSMREYLHRLDTWATENAAVPSAAAMGSGSSPHGFIWAGDLNVAERDYDRYYAGTFKSMQECSGFAPEERM  386 (467)
T ss_dssp             HHHHHHTHHHHHHHHHHHHHHHHTTTTC----------CCSCEEEEEEECCCCCSTTSBCCCSCHHHHTTSTTSCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf             67788999999999999998866531011013445552257746872443557521102222324303678778989999


Q ss_pred             HHHHCC-CCCHHHHCCCCCCCC-CCEECCCCCCCCCCCCCCCEEEEEEECHHHHHHHHCEEEECHHHCCCCCCCCCCEEE
Q ss_conf             532103-310000001337888-720035787675255777135699947789833320287122206867676221999
Q gi|254780288|r  182 SFQKLQ-NMGFTDAIRATHDTH-HLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKPRGWTKPSDHTPVIV  259 (281)
Q Consensus       182 ~~~~l~-~~gl~D~~r~~~~~~-~~yT~~~~~~~~~~~n~G~RID~il~s~~l~~~v~~~~I~~~~~~~~~~SDH~Pv~~  259 (281)
                      +|..++ +.||+|+||.+||.. +.||||+|+.++|.+|.||||||||+|+.|.++|.+|.|+.+.+    +|||+||++
T Consensus       387 ~~~~~l~~~glvDafR~~hP~~~~~YT~W~~r~~~r~~n~G~RIDyilvS~~L~~~V~~~~I~~~~~----gSDH~PV~l  462 (467)
T 2j63_A          387 SFRETMQRTNSVDIFRQLYPQAGPVYSFWSQRINGRPRNLGWRLDYFVVSSRLASYVVDCFPMPTVM----GSDHCPFQM  462 (467)
T ss_dssp             HHHHHHHHTTEEEHHHHHCTTBCSCCSBCCTTTTTTTTTCCBCCEEEEEEGGGGGGEEEEEECTTCC----SSSBCCEEE
T ss_pred             HHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECHHHHHHCEEEEECCCCC----CCCCCCEEE
T ss_conf             9999998679899443035998998388287778432598660259997769970230899868999----688046499


Q ss_pred             EEECC
Q ss_conf             99558
Q gi|254780288|r  260 SLDIP  264 (281)
Q Consensus       260 ~l~lp  264 (281)
                      +|..|
T Consensus       463 ~Lr~p  467 (467)
T 2j63_A          463 WMRHP  467 (467)
T ss_dssp             EEECC
T ss_pred             EEECC
T ss_conf             98689



>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli K12} SCOP: d.151.1.1 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 2isi_A 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
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} 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 Back     alignment and structure
>2o3h_A DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_A Back     alignment and structure
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} Back     alignment and structure
>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
>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
>3nr8_B Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; structural genomics consortium, SGC, trisphosphate 5-phosphatase 2, SHIP2, INPPL1, SHIP-2; 2.80A {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} 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
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling, SGC stockholm, structural genomics CONS hydrolase; 1.90A {Homo sapiens} Back     alignment and structure
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A Back     alignment and structure
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} Back     alignment and structure
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori} 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
>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
>2ddr_A Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} SCOP: d.151.1.3 PDB: 2dds_A 2ddt_A* 2uyr_X Back     alignment and structure
>3mpr_A Putative endonuclease/exonuclease/phosphatase FAM protein; structural genomics, PSI-2, protein structure initiative; HET: MSE PEG; 1.90A {Bacteroides thetaiotaomicron} Back     alignment and structure
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3 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
>2f1n_A CDT B, cytolethal distending toxin subunit B; E.coli, DNAse I, microbatch; 1.73A {Escherichia coli} SCOP: d.151.1.1 Back     alignment and structure
>1sr4_B CDT B, cytolethal distending toxin protein B; bacterial, virulence, DNA damage, genotoxin, cytotoxins, cell cycle, apoptosis, lectin; 2.00A {Haemophilus ducreyi} SCOP: d.151.1.1 PDB: 2f2f_B Back     alignment and structure
>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

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 281 exodeoxyribonuclease III protein [Candidatus Liberibact
d1akoa_268 d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Esche 1e-42
d1hd7a_275 d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Hom 6e-35
d2imqx1280 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex 2e-29
d2f1na1250 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit 1e-28
d1vyba_236 d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse tr 2e-24
d1i9za_345 d.151.1.2 (A:) Synaptojanin, IPP5C domain {Fission yeas 4e-24
d1sr4b_261 d.151.1.1 (B:) Cytolethal distending toxin subunit B {H 5e-21
d1wdua_228 d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransp 5e-19
d2ddra1299 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C { 6e-18
d1zwxa1293 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C 8e-15
d2a40b1260 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos tauru 6e-12
>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} Length = 268 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 enzyme exonuclease III
species: Escherichia coli [TaxId: 562]
 Score =  166 bits (421), Expect = 1e-42
 Identities = 80/264 (30%), Positives = 123/264 (46%), Gaps = 8/264 (3%)

Query: 6   VATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSY 65
             ++N+N +RAR H L A ++++ PD+I LQETK  D  FP E +  L Y++   GQK +
Sbjct: 3   FVSFNINGLRARPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLGYNVFYHGQKGH 62

Query: 66  NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGN-PITSTKY 124
            GVA+L+K  PI +    PGDD + Q R I A        + + N Y P G       K+
Sbjct: 63  YGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIKF 122

Query: 125 DDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYN------PIIWENDACFTLE 178
             K  + +    +    L+ + P++  GD NI P   D           +      F  E
Sbjct: 123 PAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPE 182

Query: 179 VRQSFQKLQNMGFTDAIRATHDTH-HLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLH 237
            R+   +L + G  D  R  +      +S++DY +  +  N+G+RID ++ S        
Sbjct: 183 EREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAECCV 242

Query: 238 SARIDTKPRGWTKPSDHTPVIVSL 261
              ID + R   KPSDH PV  + 
Sbjct: 243 ETGIDYEIRSMEKPSDHAPVWATF 266


>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} Length = 275 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
>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
>d1i9za_ d.151.1.2 (A:) Synaptojanin, IPP5C domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Length = 345 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
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} Length = 228 Back     information, alignment and structure
>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} Length = 299 Back     information, alignment and structure
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Length = 293 Back     information, alignment and structure
>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} Length = 260 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target281 exodeoxyribonuclease III protein [Candidatus Liberibact
d1hd7a_275 DNA repair endonuclease Hap1 {Human (Homo sapiens) [Tax 100.0
d1akoa_268 DNA-repair enzyme exonuclease III {Escherichia coli [Ta 100.0
d1vyba_236 Endonuclease domain of LINE-1 reverse transcriptase hom 100.0
d2imqx1280 Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId 100.0
d1wdua_228 Endonuclease domain of TRAS1 retrotransposon (ORF2) {Si 100.0
d1zwxa1293 Sphingomyelin phosphodiesterase C {Listeria ivanovii [T 100.0
d2ddra1299 Sphingomyelin phosphodiesterase C {Bacillus cereus [Tax 99.98
d2f1na1250 Cytolethal distending toxin subunit B {Escherichia coli 99.98
d1sr4b_261 Cytolethal distending toxin subunit B {Haemophilus ducr 99.96
d2a40b1260 Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} 99.96
d1i9za_345 Synaptojanin, IPP5C domain {Fission yeast (Schizosaccha 99.96
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {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: DNA repair endonuclease Hap1
species: Human (Homo sapiens) [TaxId: 9606]
Probab=100.00  E-value=0  Score=292.50  Aligned_cols=252  Identities=29%  Similarity=0.480  Sum_probs=176.4

Q ss_pred             CCCEEEEEEECCHHHHHH-HHHHHHHHHCCCEEEEEEEECCHHHCCHHHHHHCCCEEEE----EECCCCCCEEEEEEECC
Q ss_conf             700799871031888899-8999998728988999856579445897787328978999----30477651489874031
Q gi|254780288|r    2 SVVTVATWNVNSIRARIH-NLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIET----CGQKSYNGVAILSKYQP   76 (281)
Q Consensus         2 ~~lrI~TwNinglr~r~~-~l~~~l~~~~pDIi~LQEvk~~~~~~~~~~~~~~gy~~~~----~~~k~~~GvaIlsk~~~   76 (281)
                      ++|||+||||||+|++.+ .+.+||++++||||||||||+.++++..+.....+|.+..    .+.++..|++++++..+
T Consensus        17 ~~mki~S~NvnGlr~~~~~~~~~~i~~~~pDIi~LQE~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (275)
T d1hd7a_          17 ATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCP   96 (275)
T ss_dssp             CCEEEEEEECSSHHHHHHTTHHHHHHHHCCSEEEEECCCCCC-----------CCCEEEEECC-----CCCEEEEESSCC
T ss_pred             CCEEEEEEEECCHHHHHHCCHHHHHHHCCCCEEEEECCCCCHHHCCHHHHHCCCCCEEEEEEECCCCCCCCCCEECCCCC
T ss_conf             76799999825687613435899997589989998822058233888787165764356643202333344201215686


Q ss_pred             EEEEECCCCCCCCCCCCEECCCCCCCCCEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCC
Q ss_conf             37863255564432330101100023207999631046678544310123677776553322232014760000110146
Q gi|254780288|r   77 IEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYDDKISWIKRFLRFASQRLELEEPLIFAGDYNI  156 (281)
Q Consensus        77 ~~v~~~~~~~~~d~~~R~i~~~i~~~~~~i~v~n~y~P~g~~~~~~~~~~k~~~~~~l~~~l~~~~~~~~~vIi~GDFN~  156 (281)
                      ..+.........+.++.+.....  ....+....++.+.  . ...++.+.. ....+..........+.+++++||||+
T Consensus        97 ~~v~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~--~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~gd~n~  170 (275)
T d1hd7a_          97 LKVSYGIGDEEHDQEGRVIVAEF--DSFVLVTAYVPNAG--R-GLVRLEYRQ-RWDEAFRKFLKGLASRKPLVLCGDLNV  170 (275)
T ss_dssp             SEEEESCSCGGGSSSSCEEEEEC--SSCEEEEEECCCCC--G-GGTTHHHHH-HHHHHHHHHHHHHHHHSCEEEEEECSC
T ss_pred             EEEEECCCCCCCHHHHHEEEEEE--CCEEEEEEEEEECC--C-CCCCHHHHH-HHCCCCCCCCCCCCCCCCEEEECCCCC
T ss_conf             03664233453022321124553--13043102454046--6-541013333-310020000100124775376112245


Q ss_pred             CCCCCCCHHHHHCCCCCCCCHHHHHHHHHC-CCCCHHHHCCCCCC-CCCCEECCCCCCCCCCCCCCCEEEEEEECHHHHH
Q ss_conf             867420000121048734463455653210-33100000013378-8872003578767525577713569994778983
Q gi|254780288|r  157 IPQPHDCYNPIIWENDACFTLEVRQSFQKL-QNMGFTDAIRATHD-THHLYSFWDYYADSWSKNKGIRIDHIMLSPEATS  234 (281)
Q Consensus       157 a~~~~D~~~~~~~~~~~~~~~~er~~~~~l-~~~gl~D~~r~~~~-~~~~yT~~~~~~~~~~~n~G~RID~il~s~~l~~  234 (281)
                      ++.+.+..+........+....|...|..+ .+.||.|+||..+| .+..||||+++.+++.+|.|+||||||||+++.+
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~~~~D~~r~~~p~~~~~~t~~~~~~~~~~~~~g~RIDyi~vs~~l~~  250 (275)
T d1hd7a_         171 AHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLP  250 (275)
T ss_dssp             CCSGGGBSCHHHHTTSTTSCHHHHHHHHHHHHHTTCEEHHHHHCTTCTTCCSBCCSGGGHHHHTCCBCCEEEEECGGGGG
T ss_pred             CCCHHHHCCCHHHHCCCCCCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCEEECCCCCCCCCCCCCEEEEEEEECHHHHH
T ss_conf             72334404510121022222211045665540367653202403776873023233478641899767579996718861


Q ss_pred             HHHCEEEECHHHCCCCCCCCCCEEEEEEC
Q ss_conf             33202871222068676762219999955
Q gi|254780288|r  235 LLHSARIDTKPRGWTKPSDHTPVIVSLDI  263 (281)
Q Consensus       235 ~v~~~~I~~~~~~~~~~SDH~Pv~~~l~l  263 (281)
                      ++.++.|+..    ..+|||+||+++|+|
T Consensus       251 ~v~~~~i~~~----~~~SDH~PV~v~l~l  275 (275)
T d1hd7a_         251 ALCDSKIRSK----ALGSDHCPITLYLAL  275 (275)
T ss_dssp             GEEEEEECTT----CCSSSBCCEEEEECC
T ss_pred             HEEEEEECCC----CCCCCCCCEEEEEEC
T ss_conf             2558998789----999980057999979



>d1akoa_ d.151.1.1 (A:) DNA-repair enzyme exonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {Human (Homo sapiens) [TaxId: 9606]} 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
>d1wdua_ d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransposon (ORF2) {Silkworm (Bombyx mori) [TaxId: 7091]} 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
>d2f1na1 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit B {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} Back     information, alignment and structure
>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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 281 exodeoxyribonuclease III protein [Candidatus Liber
1ako_A_268 (A:) Exonuclease III; AP-endonuclease, DNA repair; 2e-43
2jc4_A_256 (A:) Exodeoxyribonuclease III; hydrolase, repair p 2e-39
2voa_A_257 (A:) AF_EXO, XTHA, exodeoxyribonuclease III; EXOII 3e-39
1hd7_A_318 (A:) DNA-(apurinic or apyrimidinic site) lyase; DN 2e-38
2o3h_A_285 (A:) DNA-(apurinic or apyrimidinic site) lyase; AP 2e-35
2jc5_A_259 (A:) Exodeoxyribonuclease; hydrolase, repair phosp 1e-34
3g6s_A_267 (A:) Putative endonuclease/exonuclease/phosphatase 5e-30
3l1w_A_257 (A:) Uncharacterized protein; APC29019.2, conserve 3e-29
2ei9_A_240 (A:) Non-LTR retrotransposon R1BMKS ORF2 protein; 2e-26
1zwx_A_301 (A:) SMCL, sphingomyelinase-C; dnase1-like fold, b 1e-25
1vyb_A_238 (A:) ORF2 contains A reverse transcriptase domain; 1e-25
1wdu_A_245 (A:) TRAS1 ORF2P; four-layered alpha/beta sandwich 1e-24
2imq_X_282 (X:) Salivary nitrophorin; ferrous heme, beta-sand 4e-23
2ddr_A_306 (A:) Sphingomyelin phosphodiesterase; DNAse I like 6e-22
1i9z_A_18-321304 (A:18-321) Synaptojanin, phosphatidylinositol phos 2e-20
2j63_A_1-134_233-439341 (A:1-134,A:233-439) AP-endonuclease; base excision 5e-37
2j63_A_135-232_440-467126 (A:135-232,A:440-467) AP-endonuclease; base excisi 5e-16
>1ako_A (A:) Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli}Length = 268 Back     alignment and structure
 Score =  170 bits (430), Expect = 2e-43
 Identities = 80/265 (30%), Positives = 122/265 (46%), Gaps = 8/265 (3%)

Query: 5   TVATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKS 64
              ++N+N +RAR H L A ++++ PD+I LQETK  D  FP E +  L Y++   GQK 
Sbjct: 2   KFVSFNINGLRARPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKLGYNVFYHGQKG 61

Query: 65  YNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPIT-STK 123
           + GVA+L+K  PI +    PGDD + Q R I A        + + N Y P G       K
Sbjct: 62  HYGVALLTKETPIAVRRGFPGDDEEAQRRIIMAEIPSLLGNVTVINGYFPQGESRDHPIK 121

Query: 124 YDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEV---- 179
           +  K  + +    +    L+ + P++  GD NI P   D             T +     
Sbjct: 122 FPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLP 181

Query: 180 --RQSFQKLQNMGFTDAIRA-THDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLL 236
             R+   +L + G  D  R     T   +S++DY +  +  N+G+RID ++ S       
Sbjct: 182 EEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAECC 241

Query: 237 HSARIDTKPRGWTKPSDHTPVIVSL 261
               ID + R   KPSDH PV  + 
Sbjct: 242 VETGIDYEIRSMEKPSDHAPVWATF 266


>2jc4_A (A:) Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis}Length = 256 Back     alignment and structure
>2voa_A (A:) AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus}Length = 257 Back     alignment and structure
>1hd7_A (A:) DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens}Length = 318 Back     alignment and structure
>2o3h_A (A:) DNA-(apurinic or apyrimidinic site) lyase; APE, endonuclease; 1.90A {Homo sapiens} PDB: 1bix_A 1dew_A* 1de8_B* 1de9_A* 2o3c_ALength = 285 Back     alignment and structure
>2jc5_A (A:) Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis}Length = 259 Back     alignment and structure
>3g6s_A (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
>3l1w_A (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
>2ei9_A (A:) Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori}Length = 240 Back     alignment and structure
>1zwx_A (A:) SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii}Length = 301 Back     alignment and structure
>1vyb_A (A:) ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens}Length = 238 Back     alignment and structure
>1wdu_A (A:) TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori}Length = 245 Back     alignment and structure