254780797

254780797

hypothetical protein CLIBASIA_03440

GeneID in NCBI database:8209803Locus tag:CLIBASIA_03440
Protein GI in NCBI database:254780797Protein Accession:YP_003065210.1
Gene range:-(461744, 462439)Protein Length:231aa
Gene description:hypothetical protein
COG prediction:[L] Exonuclease III
KEGG prediction:hypothetical protein
SEED prediction:hypothetical protein
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
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-
MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI
cccccccEEEEEEccccccccccccccccccHHHHcHHHHHHHHHHccccEEEEEEcccccccHHcccHHHHHHHHHcccccccccEEEEEEEccccccEEEEccccHHcccccccccccEEEEEEEcccccEEEEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEcccccccccccccHHHHHHHHHccHHHHHHHHHcccccEEEEEEcc
cEEEEEcccccccHHHHccccccccccccccccHHHHHHHHHHHHHccccEEEEEEcccHHHHHHHccccccEEEEEcccccccEEEEEEEEEcccEEEEccccccccccccccccccEEEEEEEEccccccEEEHHEEHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEcccccHccccHHHHHHHHHHHHccccccccccccccccHEEEEEEcc
MILAQRIRIASWNinnlseksgvalfknsvirednDYALLQKYAEQLDADIVCLQeigsyeaikrvfpndkwdilysgsntdkhAMHTAIVIRKGAIHLLQksylpmdtegldskagKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDqknnlnmpfiiagdfnrkinhshsgikDELWQKInqdntlmrlphkknhnAIRTKILKI
MILAQRIRIaswninnlseksgvALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDtegldskagkrRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDntlmrlphkknhnairtkilki
MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI
***AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFC*************YMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI
MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI
MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI
MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI
MILAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILKI

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
254781003304 hypothetical protein CLIBASIA_04520 [Candidatus Li 3e-66
254780995125 Endonuclease/exonuclease/phosphatase [Candidatus L 3e-14
254780996109 hypothetical protein CLIBASIA_04485 [Candidatus Li 1e-13
254780288281 exodeoxyribonuclease III protein [Candidatus Liber 0.008
>gi|254781003|ref|YP_003065416.1| hypothetical protein CLIBASIA_04520 [Candidatus Liberibacter asiaticus str. psy62] Length = 304 Back     alignment
 Score =  242 bits (618), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 118/235 (50%), Positives = 166/235 (70%), Gaps = 9/235 (3%)

Query: 3   LAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEA 62
           +AQ++R+ SWNIN LSE+ GV+L+KNSV R  +DY LL++YA+ LDADIV LQE+GSY A
Sbjct: 20  VAQKVRLVSWNINTLSEQEGVSLWKNSVKRTTSDYTLLRQYAKNLDADIVFLQEMGSYNA 79

Query: 63  IKRVFPNDKWDILYSGSNTDKHA-------MHTAIVIRKGAIHLLQKSYLPMDTEGLDSK 115
           + +VFP + W I YS      H+       +HTAI +RK  + +LQ+SY  +  +   S+
Sbjct: 80  VAKVFPKNTWCIFYSTERLINHSKRDSNNDIHTAIAVRKKNVRVLQQSYPLLGAKDSFSR 139

Query: 116 AGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKN 175
           AG RRAVE+L E++G+KIW+LDIHLKSFCFLDS+E++Y  SC +L+ QA WLK W+ QK 
Sbjct: 140 AGNRRAVELLVEINGKKIWVLDIHLKSFCFLDSLENTYSPSCSLLSQQAQWLKDWITQKK 199

Query: 176 NLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKNHNAIRTKILK 230
              +PF+IAGDFNRKIN  + G  D+ W+ I+ +++L+R P +K+      K L+
Sbjct: 200 ESLVPFVIAGDFNRKIN--YLGNNDDFWKTIDPNDSLIRFPKEKDSRCNANKNLR 252

>gi|254780995|ref|YP_003065408.1| Endonuclease/exonuclease/phosphatase [Candidatus Liberibacter asiaticus str. psy62] Length = 125 Back     alignment
 Score = 70.5 bits (171), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 41/61 (67%), Gaps = 2/61 (3%)

Query: 159 MLNLQATWLKQWVDQKNNLNMPFIIAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHK 218
           ML+ Q  WLK+W DQK    +PF+IAGDFNRKIN    G  D+ WQK++ D  L+R P +
Sbjct: 1   MLSQQGEWLKKWADQKIKTGIPFVIAGDFNRKIN--SIGDTDDFWQKMDPDGLLIRFPQE 58

Query: 219 K 219
           K
Sbjct: 59  K 59

>gi|254780996|ref|YP_003065409.1| hypothetical protein CLIBASIA_04485 [Candidatus Liberibacter asiaticus str. psy62] Length = 109 Back     alignment
 Score = 68.6 bits (166), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/110 (36%), Positives = 56/110 (50%), Gaps = 27/110 (24%)

Query: 67  FPNDKWDILYSGS-------------------------NTDKHAMHTAIVIRKGAIHLLQ 101
            P DKW I YSG                          +TD+  ++TAI IRK    +LQ
Sbjct: 1   MPEDKWYIFYSGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQ 60

Query: 102 KSY-LPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIE 150
            SY LP   E +  + G R+ VE+L E+D +K+WLL++HLKS C +  I+
Sbjct: 61  VSYPLPAPQE-ITPRMGNRKTVELLIEIDDQKVWLLNVHLKSSCVVKKIQ 109

>gi|254780288|ref|YP_003064701.1| exodeoxyribonuclease III protein [Candidatus Liberibacter asiaticus str. psy62] Length = 281 Back     alignment
 Score = 32.3 bits (72), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 46/203 (22%), Positives = 87/203 (42%), Gaps = 41/203 (20%)

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

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

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

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

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

IdentityAlignment graphLength Definition Round E-value
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
315122019315 hypothetical protein CKC_01345 [Candidatus Liberibacter 1 2e-87
254781003304 hypothetical protein CLIBASIA_04520 [Candidatus Liberib 1 2e-62
114328405358 hypothetical protein GbCGDNIH1_1741 [Granulibacter beth 1 2e-22
88860700316 hypothetical protein PTD2_05565 [Pseudoalteromonas tuni 1 4e-20
71278943301 endonuclease/exonuclease/phosphatase family protein [Co 1 1e-16
148982124291 hypothetical protein VSWAT3_19371 [Vibrionales bacteriu 1 3e-16
221134816321 endonuclease/exonuclease/phosphatase [Glaciecola sp. HT 1 3e-16
90412878320 hypothetical protein P3TCK_26405 [Photobacterium profun 1 1e-15
295689871288 endonuclease/exonuclease/phosphatase [Caulobacter segni 1 1e-15
54309887319 hypothetical protein PBPRA2733 [Photobacterium profundu 1 2e-15
>gi|315122019|ref|YP_004062508.1| hypothetical protein CKC_01345 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 315 Back     alignment and organism information
 Score =  326 bits (835), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 156/230 (67%), Positives = 188/230 (81%), Gaps = 7/230 (3%)

Query: 3   LAQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEA 62
            AQRIRIASWNIN LSEKSG+ L KNSV+RED DY LL++YAE+L+ADIVCLQE+GSY A
Sbjct: 35  FAQRIRIASWNINTLSEKSGMPLLKNSVVREDADYDLLRRYAERLNADIVCLQEMGSYAA 94

Query: 63  IKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAV 122
           IKRVFP D W+ILYSG+++D+H +HTAIV RKG +H+L+KSYL MDT  LDSKAGKRR+V
Sbjct: 95  IKRVFPEDTWEILYSGNDSDEHTVHTAIVARKGTVHVLEKSYLSMDTNKLDSKAGKRRSV 154

Query: 123 EILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFI 182
           EILFEV+G KIWLLDIHLKSFCF+DS++D+Y  SCY LNLQ  WL +W+ QK   N+PFI
Sbjct: 155 EILFEVNGIKIWLLDIHLKSFCFVDSLKDAYTLSCYTLNLQVNWLNKWIHQKKRSNIPFI 214

Query: 183 IAGDFNRKINHSHSGIKDELWQKINQDNTLMRLPHKKN-----HNAIRTK 227
           IAGDFNRKIN  H G  DELW KI++D  L+R+P+KK      H +IR +
Sbjct: 215 IAGDFNRKIN--HFGDNDELWGKISKDTILIRVPNKKRSWCNAHKSIRKR 262


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|254781003|ref|YP_003065416.1| hypothetical protein CLIBASIA_04520 [Candidatus Liberibacter asiaticus str. psy62] Length = 304 Back     alignment and organism information
>gi|114328405|ref|YP_745562.1| hypothetical protein GbCGDNIH1_1741 [Granulibacter bethesdensis CGDNIH1] Length = 358 Back     alignment and organism information
>gi|88860700|ref|ZP_01135337.1| hypothetical protein PTD2_05565 [Pseudoalteromonas tunicata D2] Length = 316 Back     alignment and organism information
>gi|71278943|ref|YP_268710.1| endonuclease/exonuclease/phosphatase family protein [Colwellia psychrerythraea 34H] Length = 301 Back     alignment and organism information
>gi|148982124|ref|ZP_01816600.1| hypothetical protein VSWAT3_19371 [Vibrionales bacterium SWAT-3] Length = 291 Back     alignment and organism information
>gi|221134816|ref|ZP_03561119.1| endonuclease/exonuclease/phosphatase [Glaciecola sp. HTCC2999] Length = 321 Back     alignment and organism information
>gi|90412878|ref|ZP_01220878.1| hypothetical protein P3TCK_26405 [Photobacterium profundum 3TCK] Length = 320 Back     alignment and organism information
>gi|295689871|ref|YP_003593564.1| endonuclease/exonuclease/phosphatase [Caulobacter segnis ATCC 21756] Length = 288 Back     alignment and organism information
>gi|54309887|ref|YP_130907.1| hypothetical protein PBPRA2733 [Photobacterium profundum SS9] Length = 319 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
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
pfam03372255 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phos 2e-08
>gnl|CDD|146159 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase family Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
TIGR00195281 exoDNase_III exodeoxyribonuclease III; InterPro: IPR000 99.9
TIGR00633279 xth exodeoxyribonuclease III (xth); InterPro: IPR004808 99.9
TIGR03395283 sphingomy sphingomyelin phosphodiesterase. Members of t 99.89
PRK11756268 exonuclease III; Provisional 99.87
COG3568259 ElsH Metal-dependent hydrolase [General function predic 99.85
COG0708261 XthA Exonuclease III [DNA replication, recombination, a 99.83
pfam03372255 Exo_endo_phos Endonuclease/Exonuclease/phosphatase fami 99.81
PRK13911250 hypothetical protein; Provisional 99.77
KOG2338 495 consensus 99.76
COG2374798 Predicted extracellular nuclease [General function pred 99.64
PRK05421254 hypothetical protein; Provisional 99.59
smart00128310 IPPc Inositol polyphosphate phosphatase, catalytic doma 99.51
PTZ00297 1452 pantothenate kinase; Provisional 99.16
KOG0566 1080 consensus 99.14
KOG3873 422 consensus 99.78
KOG2756349 consensus 99.78
smart00476276 DNaseIc deoxyribonuclease I. Deoxyribonuclease I cataly 99.76
COG5239 378 CCR4 mRNA deadenylase, exonuclease subunit and related 99.09
KOG0620 361 consensus 98.9
COG3021309 Uncharacterized protein conserved in bacteria [Function 98.83
COG5411 460 Phosphatidylinositol 5-phosphate phosphatase [Signal tr 98.17
KOG0565145 consensus 95.27
KOG1976 391 consensus 97.72
PTZ00312 356 inositol-1,4,5-triphosphate 5-phosphatase; Provisional 96.96
KOG1294335 consensus 90.85
>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
>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
>TIGR03395 sphingomy sphingomyelin phosphodiesterase Back     alignment and domain information
>PRK11756 exonuclease III; Provisional Back     alignment and domain information
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only] Back     alignment and domain information
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>pfam03372 Exo_endo_phos Endonuclease/Exonuclease/phosphatase family Back     alignment and domain information
>PRK13911 hypothetical protein; Provisional Back     alignment and domain information
>KOG2338 consensus Back     alignment and domain information
>COG2374 Predicted extracellular nuclease [General function prediction only] Back     alignment and domain information
>PRK05421 hypothetical protein; Provisional Back     alignment and domain information
>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues Back     alignment and domain information
>PTZ00297 pantothenate kinase; Provisional Back     alignment and domain information
>KOG0566 consensus Back     alignment and domain information
>KOG3873 consensus Back     alignment and domain information
>KOG2756 consensus Back     alignment and domain information
>smart00476 DNaseIc deoxyribonuclease I 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 Back     alignment and domain information
>COG3021 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>COG5411 Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms] Back     alignment and domain information
>KOG0565 consensus Back     alignment and domain information
>KOG1976 consensus Back     alignment and domain information
>PTZ00312 inositol-1,4,5-triphosphate 5-phosphatase; Provisional Back     alignment and domain information
>KOG1294 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
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
1ako_A268 Exonuclease Iii From Escherichia Coli Length = 268 1e-18
2uyr_X306 Crystal Structure Of Bacillus Cereus Sphingomyelina 3e-12
2ddr_A306 Crystal Structure Of Sphingomyelinase From Bacillus 4e-12
2jc4_A256 3'-5' Exonuclease (Nexo) From Neisseria Meningitidi 1e-10
1zwx_A301 Crystal Structure Of Smcl Length = 301 1e-09
3k55_A306 Structure Of Beta Hairpin Deletion Mutant Of Beta T 3e-09
3i5v_A313 Crystal Structure Of Beta Toxin 275-280 From Staphy 4e-09
3i41_A317 Crystal Structure Of Beta Toxin From Staphylococcus 4e-09
3mpr_A298 Crystal Structure Of EndonucleaseEXONUCLEASEPHOSPHA 3e-08
3g6s_A267 Crystal Structure Of The EndonucleaseEXONUCLEASEPHO 2e-07
2o3h_A285 Crystal Structure Of The Human C65a Ape Length = 28 1e-06
3l1w_A257 The Crystal Structure Of A Functionally Unknown Con 2e-06
2voa_A257 Structure Of An Ap Endonuclease From Archaeoglobus 5e-06
3g91_A265 1.2 Angstrom Structure Of The Exonuclease Iii Homol 1e-05
2isi_A317 Crystal Structure Of Ape1 From Homo Sapiens In A Ne 1e-05
1bix_A287 The Crystal Structure Of The Human Dna Repair Endon 1e-05
1e9n_A318 A Second Divalent Metal Ion In The Active Site Of A 1e-05
1dew_A279 Crystal Structure Of Human Ape1 Bound To Abasic Dna 1e-05
1de8_B276 Human ApurinicAPYRIMIDINIC ENDONUCLEASE-1 (Ape1) Bo 2e-05
3fzi_A265 1.9 Angstrom Structure Of The Thermophilic Exonucle 2e-05
2o3c_A282 Crystal Structure Of Zebrafish Ape Length = 282 3e-05
2jc5_A259 Apurinic Apyrimidinic (Ap) Endonuclease (Nape) From 6e-05
1atn_D260 Atomic Structure Of The Actin:dnase I Complex Lengt 5e-04
1dnk_A260 The X-Ray Structure Of The Dnase I-D(Ggtatacc)2 Com 6e-04
3g00_A265 Mth0212 In Complex With A 9bp Blunt End Dsdna At 1. 8e-04
2v0r_A240 Crystal Structure Of A Hairpin Exchange Variant (Lt 0.004
gi|157829928|pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli Length = 268 Back     alignment and structure
 Score = 97.3 bits (240), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 31/214 (14%), Positives = 67/214 (31%), Gaps = 29/214 (13%)

Query: 7   IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRV 66
           ++  S+NIN L                      L+   E+   D++ LQE    +    +
Sbjct: 1   MKFVSFNINGL----------------RARPHQLEAIVEKHQPDVIGLQE---TKVHDDM 41

Query: 67  FPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILF 126
           FP ++   L           H  + +      +  +   P      D +  +RR +    
Sbjct: 42  FPLEEVAKLGYNVFYHGQKGHYGVALLTKETPIAVRRGFP-----GDDEEAQRRIIMAEI 96

Query: 127 EVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKNNLNMPFIIAGD 186
                 + ++     +  F       +             L+ +++ +   + P +I GD
Sbjct: 97  PSLLGNVTVI-----NGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGD 151

Query: 187 FNRKINHSHSGIKDELWQKINQDNTLMRLPHKKN 220
            N        GI +E  ++  +      LP ++ 
Sbjct: 152 MNISPTDLDIGIGEENRKRWLRTGKCSFLPEERE 185


>gi|189096065|pdb|2UYR|X Chain X, Crystal Structure Of Bacillus Cereus Sphingomyelinase Mutant :n57a Length = 306 Back     alignment and structure
>gi|99032047|pdb|2DDR|A Chain A, Crystal Structure Of Sphingomyelinase From Bacillus Cereus With Calcium Ion Length = 306 Back     alignment and structure
gi|134104765|pdb|2JC4|A Chain A, 3'-5' Exonuclease (Nexo) From Neisseria Meningitidis Length = 256 Back     alignment and structure
>gi|75765927|pdb|1ZWX|A Chain A, Crystal Structure Of Smcl Length = 301 Back     alignment and structure
>gi|320089760|pdb|3K55|A Chain A, Structure Of Beta Hairpin Deletion Mutant Of Beta Toxin From Staphylococcus Aureus Length = 306 Back     alignment and structure
>gi|302566051|pdb|3I5V|A Chain A, Crystal Structure Of Beta Toxin 275-280 From Staphylococcus Aureus Length = 313 Back     alignment and structure
>gi|300508421|pdb|3I41|A Chain A, Crystal Structure Of Beta Toxin From Staphylococcus Aureus F277a, P278a Mutant Length = 317 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
>gi|223674122|pdb|3G6S|A Chain A, Crystal Structure Of The EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM Bacteroides Vulgatus. Northeast Structural Genomics Consortium Target Bvr56d Length = 267 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|283807250|pdb|3L1W|A Chain A, The Crystal Structure Of A Functionally Unknown Conserved Protein From Enterococcus Faecalis V583 Length = 257 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|290789984|pdb|3G91|A Chain A, 1.2 Angstrom Structure Of The Exonuclease Iii Homologue Mth0212 Length = 265 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|290789945|pdb|3FZI|A Chain A, 1.9 Angstrom Structure Of The Thermophilic Exonuclease Iii Homologue Mth0212 Length = 265 Back     alignment and structure
>gi|162329921|pdb|2O3C|A Chain A, Crystal Structure Of Zebrafish Ape Length = 282 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|229691|pdb|1ATN|D Chain D, Atomic Structure Of The Actin:dnase I Complex Length = 260 Back     alignment and structure
>gi|493974|pdb|1DNK|A Chain A, The X-Ray Structure Of The Dnase I-D(Ggtatacc)2 Complex At 2.3 Angstroms Resolution Length = 260 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|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

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1. 1e-10
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; INPP 7e-10
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpi 9e-08
3nr8_B316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; stru 1e-07
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM prote 1e-07
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.coli, D 1e-07
3g6s_A267 Putative endonuclease/exonuclease/phosphatase family pr 1e-07
1sr4_B261 CDT B, cytolethal distending toxin protein B; bacterial 2e-07
2xsw_A 357 72 kDa inositol polyphosphate 5-phosphatase; inositol s 7e-06
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, A 2e-05
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like folding, 4e-05
3l1w_A257 Uncharacterized protein; APC29019.2, conserved protein, 5e-05
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA bind 1e-04
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand specific 3 4e-04
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, tran 6e-04
3ngq_A398 CCR4-NOT transcription complex subunit 6-like; alpha/be 0.001
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA repair, 0.003
2j63_A 467 AP-endonuclease; base excision repair, lyase; 2.48A {Le 1e-04
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A Length = 317 Back     alignment and structure
 Score = 61.9 bits (149), Expect = 1e-10
 Identities = 28/223 (12%), Positives = 65/223 (29%), Gaps = 28/223 (12%)

Query: 5   QRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIK 64
             +++ S N+  LS              +     L+ + +   + D+V   E     A  
Sbjct: 28  TDLKLVSHNVYMLSTVLYPN------WGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASD 81

Query: 65  RVFPNDKWDILYSGSNTDKHAMHTAIVIRKGA--------------IHLLQKSYLPMDTE 110
           ++  N K +  Y      +            +                + +K      + 
Sbjct: 82  KLLSNVKKEYPYQTPVLGRSQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEKIQHVFKSG 141

Query: 111 GLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQW 170
                   +  V    E +G+ + ++  H +S                +   Q   +  +
Sbjct: 142 CGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSRCGAGHDR----KIRAEQMKEISDF 197

Query: 171 VDQKNNLN-MPFIIAGDFNRKINHSHSGIKDELWQKINQDNTL 212
           V +KN        I GD N    +  +    ++ + +N ++ L
Sbjct: 198 VKKKNIPKDETVYIGGDLN---VNKGTPEFKDMLKNLNVNDVL 237


>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
3i41_A317 Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1. 99.93
1zwx_A301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpi 99.93
2ddr_A306 Sphingomyelin phosphodiesterase; DNAse I like folding, 99.92
3ngq_A398 CCR4-NOT transcription complex subunit 6-like; alpha/be 99.88
3mpr_A298 Putative endonuclease/exonuclease/phosphatase FAM prote 99.87
3l1w_A257 Uncharacterized protein; APC29019.2, conserved protein, 99.85
2a40_B260 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, A 99.84
3g6s_A267 Putative endonuclease/exonuclease/phosphatase family pr 99.79
2j63_A467 AP-endonuclease; base excision repair, lyase; 2.48A {Le 99.79
1wdu_A245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA bind 99.76
1vyb_A238 ORF2 contains A reverse transcriptase domain; endonucle 99.76
1sr4_B261 CDT B, cytolethal distending toxin protein B; bacterial 99.71
1ako_A268 Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Es 99.7
2f1n_A262 CDT B, cytolethal distending toxin subunit B; E.coli, D 99.69
3mtc_A313 Type II inositol-1,4,5-trisphosphate 5-phosphatas; INPP 99.69
3nr8_B316 Phosphatidylinositol-3,4,5-trisphosphate 5-phosph; stru 99.67
1i9z_A347 Synaptojanin, phosphatidylinositol phosphate phosphatas 99.66
2xsw_A 357 72 kDa inositol polyphosphate 5-phosphatase; inositol s 99.63
1hd7_A318 DNA-(apurinic or apyrimidinic site) lyase; DNA repair, 99.59
2jc4_A256 Exodeoxyribonuclease III; hydrolase, repair phosphodies 99.58
2imq_X282 Salivary nitrophorin; ferrous heme, beta-sandwich, tran 99.52
2o3h_A285 DNA-(apurinic or apyrimidinic site) lyase; APE, endonuc 99.51
2ei9_A240 Non-LTR retrotransposon R1BMKS ORF2 protein; four layer 99.49
3g91_A265 MTH0212, exodeoxyribonuclease; double-strand specific 3 99.47
2voa_A257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endo 99.4
2jc5_A259 Exodeoxyribonuclease; hydrolase, repair phosphodiestera 99.17
>3i41_A Beta-hemolysin; beta toxin, sphingomyelinase, toxin; 1.75A {Staphylococcus aureus RN4220} PDB: 3i46_A 3i48_A Back     alignment and structure
Probab=99.93  E-value=1e-24  Score=149.03  Aligned_cols=177  Identities=15%  Similarity=0.077  Sum_probs=107.6

Q ss_pred             CCEEEEEEEEHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCC--CCCEEEEEECCC
Q ss_conf             654899887310076777556667666687999999999997518989999727998899987262--322167740357
Q gi|254780797|r    4 AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPN--DKWDILYSGSNT   81 (231)
Q Consensus         4 ~~~lrv~twNi~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~DVi~LQEv~~~~~~~~~~~~--~~~~~~~~~~~~   81 (231)
                      .+.||||||||..+.....      .......+.+.|++.|...+|||||||||.+......+...  ..|.+.....+.
T Consensus        27 ~~~lrv~syNi~~~~~~~~------~~~~~~~R~~~i~~~i~~~~~DII~LQEV~~~~~~~~l~~~l~~~~~~~~~~~~~  100 (317)
T 3i41_A           27 DTDLKLVSHNVYMLSTVLY------PNWGQYKRADLIGQSSYIKNNDVVIFNEAFDNGASDKLLSNVKKEYPYQTPVLGR  100 (317)
T ss_dssp             -CCCCEEEEEEEECCTTTS------TTSCHHHHHHHHHHCSTTSSCSEEEEEEECSHHHHHHHHHHTTTTCCEECCCTTS
T ss_pred             CCCEEEEEEECCCCCCCCC------CCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECC
T ss_conf             9968999852888766667------8706889999999999766999899986767354999999888658946776046


Q ss_pred             -------------CCCC--CEEEEEEECCCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCEEEEEEEEEECCCCCC
Q ss_conf             -------------8765--0356886146410100001221467565544575049999984997899999751168888
Q gi|254780797|r   82 -------------DKHA--MHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFL  146 (231)
Q Consensus        82 -------------~~~~--~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~g~~~~v~n~HL~s~~~~  146 (231)
                                   ....  ...+++++.+....   ................|+++.+.+..++.+++|+|+||+++...
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~g~~ilSr~pi~~~---~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~v~ntHl~~~~~~  177 (317)
T 3i41_A          101 SQSGWDKTEGSYSSTVAEDGGVAIVSKYPIKEK---IQHVFKSGCGFDNDSNKGFVYTKIEKNGKNVHVIGTHTQSEDSR  177 (317)
T ss_dssp             CSTTCSEEEESCCSSCSBCCCCEEEESSCEEEE---EEEECSCCCSSGGGBCCEEEEEEEEETTEEEEEEEEECCCCCSS
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEE---EEEECCCCCCCCCCCCCCEEEEEEECCCEEEEEEEECCCCCCCC
T ss_conf             654333322444555424773799985883005---88973678884101474469999962997999997435556775


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCEEEEEECCCCCCC
Q ss_conf             75430025457887548999999999740-488789999136888462
Q gi|254780797|r  147 DSIEDSYISSCYMLNLQATWLKQWVDQKN-NLNMPFIIAGDFNRKINH  193 (231)
Q Consensus       147 ~~~~~~~~~~~~~~~~q~~~l~~~i~~~~-~~~~~vii~GDFN~~~~~  193 (231)
                      ...    ......|..|++.+..++.... ..+.|+|+|||||..+.+
T Consensus       178 ~~~----~~~~~~R~~q~~~i~~~~~~~~~~~~~~vil~GDfN~~~~~  221 (317)
T 3i41_A          178 CGA----GHDRKIRAEQMKEISDFVKKKNIPKDETVYIGGDLNVNKGT  221 (317)
T ss_dssp             SCT----THHHHHHHHHHHHHHHHHHHHTCCTTSCEEEEEECCCCTTS
T ss_pred             CHH----HHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCC
T ss_conf             205----67899999999999986655401466757984447889887



>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
>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
>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
>3l1w_A Uncharacterized protein; APC29019.2, conserved protein, enterococcus faecalis V583, PSI-2, MCSG, structural genomics; 1.60A {Enterococcus faecalis} 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
>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
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} 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
>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
>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
>1ako_A Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli K12} SCOP: d.151.1.1 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
>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
>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
>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
>2xsw_A 72 kDa inositol polyphosphate 5-phosphatase; inositol signalling, SGC stockholm, structural genomics CONS hydrolase; 1.90A {Homo sapiens} 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
>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
>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
>2ei9_A Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori} 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
>2voa_A AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Back     alignment and structure
>2jc5_A Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} Back     alignment and structure

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 231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
d2f1na1250 d.151.1.1 (A:1-250) Cytolethal distending toxin subunit 5e-08
d1zwxa1293 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C 6e-08
d2ddra1299 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C { 4e-07
d1sr4b_261 d.151.1.1 (B:) Cytolethal distending toxin subunit B {H 6e-06
d2imqx1280 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex 2e-05
d2a40b1260 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos tauru 1e-04
d1wdua_228 d.151.1.1 (A:) Endonuclease domain of TRAS1 retrotransp 0.001
>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 = 51.6 bits (122), Expect = 5e-08
 Identities = 27/208 (12%), Positives = 61/208 (29%), Gaps = 32/208 (15%)

Query: 7   IRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRV 66
            R+A+WN+             ++      +  + Q  + +   DI+ +QE GS  +    
Sbjct: 5   FRVATWNLQGA----------SATTESKWNINVRQLISGENAVDILAVQEAGSPPSTAVD 54

Query: 67  -----------FPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDTEGLDSK 115
                           W++  +      +   +A+    G ++L   S    D       
Sbjct: 55  TGRVIPSPGIPVRELIWNLSTNSRPQQVYIYFSAVDALGGRVNLALVSNRRADEVF--VL 112

Query: 116 AGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQWVDQKN 175
           +  R+    L  +          H  +    D+              +     +      
Sbjct: 113 SPVRQGGRPLLGIRIGNDAFFTAHAIAMRNNDAPALVE---------EVYNFFRDSRDPV 163

Query: 176 NLNMPFIIAGDFNRKINHSHSGIKDELW 203
           +  + ++I GDFNR+       +   + 
Sbjct: 164 HQALNWMILGDFNREPADLEMNLTVPVR 191


>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
>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
>d2a40b1 d.151.1.1 (B:1-260) Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} Length = 260 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 in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
d1zwxa1293 Sphingomyelin phosphodiesterase C {Listeria ivanovii [T 99.93
d2ddra1299 Sphingomyelin phosphodiesterase C {Bacillus cereus [Tax 99.93
d2a40b1260 Deoxyribonuclease I {Cow (Bos taurus) [TaxId: 9913]} 99.81
d1vyba_236 Endonuclease domain of LINE-1 reverse transcriptase hom 99.8
d2f1na1250 Cytolethal distending toxin subunit B {Escherichia coli 99.78
d1sr4b_261 Cytolethal distending toxin subunit B {Haemophilus ducr 99.72
d1wdua_228 Endonuclease domain of TRAS1 retrotransposon (ORF2) {Si 99.7
d2imqx1280 Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId 99.68
d1i9za_345 Synaptojanin, IPP5C domain {Fission yeast (Schizosaccha 99.65
d1hd7a_275 DNA repair endonuclease Hap1 {Human (Homo sapiens) [Tax 99.5
d1akoa_268 DNA-repair enzyme exonuclease III {Escherichia coli [Ta 99.27
>d1zwxa1 d.151.1.3 (A:41-333) Sphingomyelin phosphodiesterase C {Listeria ivanovii [TaxId: 1638]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: DNase I-like
superfamily: DNase I-like
family: Sphingomyelin phosphodiesterase-like
domain: Sphingomyelin phosphodiesterase C
species: Listeria ivanovii [TaxId: 1638]
Probab=99.93  E-value=4.9e-25  Score=149.44  Aligned_cols=178  Identities=16%  Similarity=0.112  Sum_probs=110.2

Q ss_pred             CEEEEEEEEHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCC--CCEEEEEECCCC
Q ss_conf             548998873100767775566676666879999999999975189899997279988999872623--221677403578
Q gi|254780797|r    5 QRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFPND--KWDILYSGSNTD   82 (231)
Q Consensus         5 ~~lrv~twNi~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~DVi~LQEv~~~~~~~~~~~~~--~~~~~~~~~~~~   82 (231)
                      +.|||+||||.++.....      ......++.+.|++.|...+|||||||||.+......+....  .|.+........
T Consensus         3 ~~lki~s~Nv~~~~~~~~------~~~~~~~r~~~i~~~i~~~~~DVi~LQEv~~~~~~~~l~~~~~~~~~~~~~~~~~~   76 (293)
T d1zwxa1           3 GNFKITSHNVYLFSRNIY------PNWGQMHRADLIAQADYMKNNDVVILNEAFDTSASHRLLNNLREMYPHQTPVIGRS   76 (293)
T ss_dssp             CSCEEEEEEEEECCTTTS------TTSCHHHHHHHHHTSGGGSSCSEEEEEEECSHHHHHHHHHHTTTTCCEECCCTTSC
T ss_pred             CCCEEEEEECCCCCCCCC------CCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEHHCCCC
T ss_conf             977899884685765558------98278999999999997569988999846774258999987765414000001134


Q ss_pred             CC-------------CCEEEEEEECCCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCEEEEEEEEEECCCCCCCCC
Q ss_conf             76-------------50356886146410100001221467565544575049999984997899999751168888754
Q gi|254780797|r   83 KH-------------AMHTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSI  149 (231)
Q Consensus        83 ~~-------------~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~g~~~~v~n~HL~s~~~~~~~  149 (231)
                      ..             ....|+++.++.. .......+............++++.+.+..+|..++|+++||+++......
T Consensus        77 ~~~~~~~~~~~~~~~~~~~g~~ilsr~p-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~Hl~~~~~~~~~  155 (293)
T d1zwxa1          77 KHGWDKTEGNYSNFALEDGGVAVVSQWP-IVEKSQHIFQRGGGADRLSNKGFAYVKIMKNGKPYHIIGTHTQADDSLISK  155 (293)
T ss_dssp             STTCSEEEC-----CCBCCCCEEEESSC-EEEEEEEECSCCCGGGGGBCCEEEEEEEEETTEEEEEEEEECCCCCTTSCH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEECCC-CCCCEEEEEECCCCCCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCCCCH
T ss_conf             5432211145443201266269996467-544215652024542001341489999963993479998441036775303


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH-CCCCCCEEEEEECCCCCCC
Q ss_conf             3002545788754899999999974-0488789999136888462
Q gi|254780797|r  150 EDSYISSCYMLNLQATWLKQWVDQK-NNLNMPFIIAGDFNRKINH  193 (231)
Q Consensus       150 ~~~~~~~~~~~~~q~~~l~~~i~~~-~~~~~~vii~GDFN~~~~~  193 (231)
                          ......|..|++++.+++.+. ...+.|+|||||||..+.+
T Consensus       156 ----~~~~~~r~~~~~~~~~~~~~~~~~~~~~vil~GDfN~~~~~  196 (293)
T d1zwxa1         156 ----DTSRAIRAEQMQEIQTFIAKKNIPKDEIIFIGGDLNVNYGT  196 (293)
T ss_dssp             ----HHHHHHHHHHHHHHHHHHHHHTCCTTSEEEEEEECCCCTTS
T ss_pred             ----HHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCC
T ss_conf             ----57799999989886545554036889848998066989885



>d2ddra1 d.151.1.3 (A:7-305) Sphingomyelin phosphodiesterase C {Bacillus cereus [TaxId: 1396]} 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
>d1vyba_ d.151.1.1 (A:) Endonuclease domain of LINE-1 reverse transcriptase homolog {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
>d1sr4b_ d.151.1.1 (B:) Cytolethal distending toxin subunit B {Haemophilus ducreyi [TaxId: 730]} 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
>d2imqx1 d.151.1.2 (X:3-282) Salivary nitrophorin {Bedbug (Cimex lectularius) [TaxId: 79782]} 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
>d1hd7a_ d.151.1.1 (A:) DNA repair endonuclease Hap1 {Human (Homo sapiens) [TaxId: 9606]} 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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 231 hypothetical protein CLIBASIA_03440 [Candidatus Li
1zwx_A_301 (A:) SMCL, sphingomyelinase-C; dnase1-like fold, b 7e-09
2ddr_A_306 (A:) Sphingomyelin phosphodiesterase; DNAse I like 4e-08
1i9z_A_18-321304 (A:18-321) Synaptojanin, phosphatidylinositol phos 6e-04
1ako_A_268 (A:) Exonuclease III; AP-endonuclease, DNA repair; 0.001
3g6s_A_267 (A:) Putative endonuclease/exonuclease/phosphatase 0.001
2jc5_A_259 (A:) Exodeoxyribonuclease; hydrolase, repair phosp 0.002
2j63_A_135-232_440-467126 (A:135-232,A:440-467) AP-endonuclease; base excisi 4e-04
>1zwx_A (A:) SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii}Length = 301 Back     alignment and structure
 Score = 55.4 bits (131), Expect = 7e-09
 Identities = 27/204 (13%), Positives = 52/204 (25%), Gaps = 23/204 (11%)

Query: 4   AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGS---- 59
               +I S N+   S        +       +   L+ +     + D+V L E       
Sbjct: 8   PGNFKITSHNVYLFSRNIYPNWGQ------MHRADLIAQADYMKNNDVVILNEAFDTSAS 61

Query: 60  ----------YEAIKRVFPNDKWDILYSGSNTDKHAMHTAIVIRKGAIHLLQKSYLPMDT 109
                     Y     V    K     +  N    A+    V       +++KS      
Sbjct: 62  HRLLNNLREMYPHQTPVIGRSKHGWDKTEGNYSNFALEDGGVAVVSQWPIVEKSQHIFQR 121

Query: 110 EGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFCFLDSIEDSYISSCYMLNLQATWLKQ 169
            G   +   +    +    +G+   ++  H ++    DS+     S              
Sbjct: 122 GGGADRLSNKGFAYVKIMKNGKPYHIIGTHTQAD---DSLISKDTSRAIRAEQMQEIQTF 178

Query: 170 WVDQKNNLNMPFIIAGDFNRKINH 193
              +    +    I GD N     
Sbjct: 179 IAKKNIPKDEIIFIGGDLNVNYGT 202


>2ddr_A (A:) Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus}Length = 306 Back     alignment and structure
>1i9z_A (A:18-321) Synaptojanin, phosphatidylinositol phosphate phosphatase; spsynaptojanin, IPP5C, IP3, IP2,, hydrolase; HET: 2IP; 1.80A {Schizosaccharomyces pombe}Length = 304 Back     alignment and structure
>1ako_A (A:) Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli}Length = 268 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
>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
>2j63_A (A:135-232,A:440-467) AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major}Length = 126 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target231 hypothetical protein CLIBASIA_03440 [Candidatus Liberib
2ddr_A_306 Sphingomyelin phosphodiesterase; DNAse I like fold 99.92
1zwx_A_301 SMCL, sphingomyelinase-C; dnase1-like fold, beta-h 99.91
1ako_A_268 Exonuclease III; AP-endonuclease, DNA repair; 1.70 99.81
3g6s_A_267 Putative endonuclease/exonuclease/phosphatase fami 99.75
2imq_X_282 Salivary nitrophorin; ferrous heme, beta-sandwich, 99.73
2jc4_A_256 Exodeoxyribonuclease III; hydrolase, repair phosph 99.71
3l1w_A_257 Uncharacterized protein; APC29019.2, conserved pro 99.71
1hd7_A_318 DNA-(apurinic or apyrimidinic site) lyase; DNA rep 99.7
2o3h_A_285 DNA-(apurinic or apyrimidinic site) lyase; APE, en 99.67
2voa_A_257 AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP 99.65
1i9z_A_18-321304 Synaptojanin, phosphatidylinositol phosphate phosp 99.6
2ei9_A_240 Non-LTR retrotransposon R1BMKS ORF2 protein; four 99.57
2jc5_A_259 Exodeoxyribonuclease; hydrolase, repair phosphodie 99.55
1vyb_A_238 ORF2 contains A reverse transcriptase domain; endo 99.52
1wdu_A_245 TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA 99.45
2f1n_A_262 CDT B, cytolethal distending toxin subunit B; E.co 98.76
2j63_A_135-232_440-467126 AP-endonuclease; base excision repair, lyase; 2.48 99.28
2a40_B_1-87_228-260120 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse 98.86
2a40_B_88-227140 Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse 98.18
2j63_A_1-134_233-439341 AP-endonuclease; base excision repair, lyase; 2.48 97.98
1sr4_B_106-228123 CDT B, cytolethal distending toxin protein B; bact 94.02
1sr4_B_1-105_229-261138 CDT B, cytolethal distending toxin protein B; bact 95.41
>2ddr_A (A:) Sphingomyelin phosphodiesterase; DNAse I like folding, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; 1.40A {Bacillus cereus} Back     alignment and structure
Probab=99.92  E-value=3.3e-23  Score=141.75  Aligned_cols=179  Identities=13%  Similarity=0.103  Sum_probs=107.1

Q ss_pred             CCEEEEEEEEHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHC---CCCCEEEEEECC
Q ss_conf             65489988731007677755666766668799999999999751898999972799889998726---232216774035
Q gi|254780797|r    4 AQRIRIASWNINNLSEKSGVALFKNSVIREDNDYALLQKYAEQLDADIVCLQEIGSYEAIKRVFP---NDKWDILYSGSN   80 (231)
Q Consensus         4 ~~~lrv~twNi~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~DVi~LQEv~~~~~~~~~~~---~~~~~~~~~~~~   80 (231)
                      ..+|||+||||+++....      ......+.+++.+++.|...+|||||||||...........   ...+... ....
T Consensus         7 ~~~lrV~T~Nv~~~~~~~------~~~~~~~~r~~~i~~~i~~~~~DVi~LQEv~~~~~~~~~~~~~~~~~~~~~-~~~~   79 (306)
T 2ddr_A            7 NDTLKVMTHNVYMLSTNL------YPNWGQTERADLIGAADYIKNQDVVILNEVFDNSASDRLLGNLKKEYPNQT-AVLG   79 (306)
T ss_dssp             CCEEEEEEEEEEECCTTT------CTTSCHHHHHHHHHHCSTTCSCSEEEEEEECCHHHHHHHHHHHTTTCCEEC-CCTT
T ss_pred             CCCEEEEEEECCCCCCCC------CCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEE-EEEE
T ss_conf             998799998678565677------887068899999999997679998999837776417999999887577403-4310


Q ss_pred             CCCCCC----------------EEEEEEECCCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEECCEEEEEEEEEECCCC
Q ss_conf             787650----------------3568861464101000012214675655445750499999849978999997511688
Q gi|254780797|r   81 TDKHAM----------------HTAIVIRKGAIHLLQKSYLPMDTEGLDSKAGKRRAVEILFEVDGRKIWLLDIHLKSFC  144 (231)
Q Consensus        81 ~~~~~~----------------~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~g~~~~v~n~HL~s~~  144 (231)
                      ......                ...++++........   ..............+..+.+.+..++..+.|+|+||+++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~g~~~~s~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~Hl~~~~  156 (306)
T 2ddr_A           80 RSSGSEWDKTLGNYSSSTPEDGGVAIVSKWPIAEKIQ---YVFAKGCGPDNLSNKGFVYTKIKKNDRFVHVIGTHLQAED  156 (306)
T ss_dssp             SCCSTTSSEEEESCCTTCSSCCCCEEEESSCEEEEEE---EECSCCC----CCCCEEEEEEEEETTEEEEEEEEECCCC-
T ss_pred             CCCCCCCCEEEECCCCCCCCCCEEEEEEEECCCCCCE---EEEECCCCCCCCCCEEEEEEEEECCCCEEEEEEECCCCCC
T ss_conf             3567765314421334411264379998752333300---2310235654223106999998069918999993243355


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCEEEEEECCCCCCCCCC
Q ss_conf             887543002545788754899999999-9740488789999136888462222
Q gi|254780797|r  145 FLDSIEDSYISSCYMLNLQATWLKQWV-DQKNNLNMPFIIAGDFNRKINHSHS  196 (231)
Q Consensus       145 ~~~~~~~~~~~~~~~~~~q~~~l~~~i-~~~~~~~~~vii~GDFN~~~~~~~~  196 (231)
                      ........    ...+..+..++.+.+ ......+.++|+|||||..+.....
T Consensus       157 ~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~GDfN~~~~~~~~  205 (306)
T 2ddr_A          157 SMCGKTSP----ASVRTNQLKEIQDFIKNKNIPNNEYVLIGGDMNVNKINAEN  205 (306)
T ss_dssp             ------CH----HHHHHHHHHHHHHHHHHHTCCTTSCEEEEEECCCCCTTTSS
T ss_pred             CCCCCCHH----HHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHH
T ss_conf             55221013----78998888877666654212566618998347889762554



>1zwx_A (A:) SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin, hydrolase; 1.90A {Listeria ivanovii} Back     alignment and structure
>1ako_A (A:) Exonuclease III; AP-endonuclease, DNA repair; 1.70A {Escherichia coli} 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} Back     alignment and structure
>2imq_X (X:) Salivary nitrophorin; ferrous heme, beta-sandwich, transport protein; HET: HEM; 1.30A {Cimex lectularius} Back     alignment and structure
>2jc4_A (A:) Exodeoxyribonuclease III; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: 1PE; 1.90A {Neisseria meningitidis} 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} Back     alignment and structure
>1hd7_A (A:) DNA-(apurinic or apyrimidinic site) lyase; DNA repair, endonuclease, APE1, HAP1, REF-1; 1.95A {Homo sapiens} 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_A Back     alignment and structure
>2voa_A (A:) AF_EXO, XTHA, exodeoxyribonuclease III; EXOIII, AP endonuclease, lyase; 1.7A {Archaeoglobus fulgidus} Back     alignment and structure
>1i9z_A (A:18-321) Synaptojanin, phosphatidylinositol phosphate phosphatase; spsynaptojanin, IPP5C, IP3, IP2,, hydrolase; HET: 2IP; 1.80A {Schizosaccharomyces pombe} Back     alignment and structure
>2ei9_A (A:) Non-LTR retrotransposon R1BMKS ORF2 protein; four layered alpha beta sandwich, gene regulation; 2.00A {Bombyx mori} Back     alignment and structure
>2jc5_A (A:) Exodeoxyribonuclease; hydrolase, repair phosphodiesterase, DNA repair, exonuclease, endonuclease; HET: BCN DIO GOL; 1.50A {Neisseria meningitidis} Back     alignment and structure
>1vyb_A (A:) ORF2 contains A reverse transcriptase domain; endonuclease, APE-1 type, retrotransposition, retrotransposon, transferase; 1.8A {Homo sapiens} Back     alignment and structure
>1wdu_A (A:) TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein; 2.40A {Bombyx mori} Back     alignment and structure
>2f1n_A (A:) CDT B, cytolethal distending toxin subunit B; E.coli, DNAse I, microbatch; 1.73A {Escherichia coli} Back     alignment and structure
>2j63_A (A:135-232,A:440-467) AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Back     alignment and structure
>2a40_B (B:1-87,B:228-260) Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3, structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus} Back     alignment and structure
>2a40_B (B:88-227) Deoxyribonuclease-1; WAVE, WH2, WAsp, actin, DNAse I, ARP2/3, structural protein; HET: HIC NAG ATP; 1.80A {Bos taurus} Back     alignment and structure
>2j63_A (A:1-134,A:233-439) AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania major} Back     alignment and structure
>1sr4_B (B:106-228) CDT B, cytolethal distending toxin protein B; bacterial, virulence, DNA damage, genotoxin, cytotoxins, cell cycle, apoptosis, lectin; 2.00A {Haemophilus ducreyi} Back     alignment and structure
>1sr4_B (B:1-105,B:229-261) CDT B, cytolethal distending toxin protein B; bacterial, virulence, DNA damage, genotoxin, cytotoxins, cell cycle, apoptosis, lectin; 2.00A {Haemophilus ducreyi} Back     alignment and structure