254780124

254780124

hypothetical protein CLIBASIA_00015

GeneID in NCBI database:8209099Locus tag:CLIBASIA_00015
Protein GI in NCBI database:254780124Protein Accession:YP_003064537.1
Gene range:+(948, 2114)Protein Length:388aa
Gene description:hypothetical protein
COG prediction:none
KEGG prediction:hypothetical protein
SEED prediction:Phage 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
TOPPRED1 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-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------39
MAHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQTQKSQLSEFEVLG
ccccccccccccccHHcccccccHHHHcccHHHHHHHHHHHHHHHHHHHHHHccccHHEEcccccccccHHHHHHHHHHHHHHHHHHHHHccccEEEEEccccccEEEccccccEEEEEEEEccEEEEEEEccccccEEEccccHHHHHHHHHHHHHcccHHHHHHcEEEEEEEcccccccccccEEEcHHHHHHHHHHHHHHHHHHccHHHHcccccccccccccccEEEEcccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEcccccccHHHHHHHHHHHHHHccccHHHHHHccHHHHHHHHccccccHHHHHHHHHHHcccccccEEEEcccHHHHHHHHHHHccccccc
cccHccccccHHHHHHcccccccccccccccccHHHHHccHHHHHHHHHHHccccccHHHccccHcccccccccHHHHHHHHHHHHHHHHHcccccEEEccEccccccccccccccEEEEEcccEEEEEEccccccEEEcccccHHHHHHHHHHHHHHcccEEccccEEEEEEccccccccccHHHEccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEccccccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccccccccccHHHHHHHHHHHccccccHHHcccHHHHHHHHHcccccHHHHHHHHHHHcccccccEEEccccccHHHHHHcHHHHHHHcc
mahhaflsassshrwlkcpiaptleskipqttsiyasegTFAHNLLAHCLEQgvdaetvshqkltfendtrivdteMASSVSMVLAYVRTfsgpflsetevplepfttepgatgtadiLIFNSTQWIIVdfkygagvpvkaennTQLMLYACGALhqygdifgrpealtltiiqprvrtgspinewvISADDLLEKAKEFKERGTLALSLKSKRAVSlehygvnddscrfcrakvrcpalsrhvlleatkdpstntTVELSKAYSSISLIKSYVKACEDEMFKRLnagdeiqgyqlvegrkgnrsfkDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITrgdgkpviaprdiptnkqtqksqlsefevlg
MAHHAFlsassshrwLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQprvrtgspineWVISADDLLEKAKEFkergtlalslkskravslehygvnddscrfCRAKVRCPALSRHvlleatkdpstnttvelskayssISLIKSYVKACEDEMFKRLNagdeiqgyqlvegrkgnrsfKDINRAQELltsvlgeeafKRILKTPKELEQLYKEQKVSDEFWEELQELitrgdgkpviaprdiptnkqtqksqlsefevlg
MahhaflsassshRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQTQKSQLSEFEVLG
*AHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQL*******DEFWEELQELITRGDGKPVIAPRDIP*********LSEFEVLG
***********SHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTN***************
************HRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQTQKSQLSEF**LG
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MAHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQTQKSQLSEFEVLG
MAHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQTQKSQLSEFEVLG
MAHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGDGKPVIAPRDIPTNKQTQKSQLSEFEVLG

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
254781191165 hypothetical protein CLIBASIA_05490 [Candidatus Li 5e-34
>gi|254781191|ref|YP_003065604.1| hypothetical protein CLIBASIA_05490 [Candidatus Liberibacter asiaticus str. psy62] Length = 165 Back     alignment
 Score =  136 bits (343), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 68/165 (41%), Positives = 110/165 (66%), Gaps = 2/165 (1%)

Query: 223 VNDDSCRFCRAKVRCPALSRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMF 282
           +++++CRFCRAK RC AL+   L   ++     +  +LS+  + + LI++++K  ++E  
Sbjct: 1   MDENACRFCRAKPRCGALAVKALSTFSEHMQILSNRQLSQVMNVLPLIETWMKGVKEEAL 60

Query: 283 KRLNAGDEIQGYQLVEGRKGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQ 342
             L++G+++  Y+L EGRKG+R++ + N+ ++LL   LG+EA+ R L +P E EQL K +
Sbjct: 61  NVLSSGEDLPNYELKEGRKGSRTYNNDNQVEQLLMRELGDEAYNRTLLSPTETEQLVKRK 120

Query: 343 KVSDEFWEELQELITRGDGKPVIAPRDIPTNKQTQKSQLSEFEVL 387
           KVS+  WE+LQ+ ITR DGK VI P D+P N    K+ +SEF VL
Sbjct: 121 KVSETTWEQLQKFITRKDGKQVIVPCDLPVNH--LKANISEFSVL 163

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

IdentityAlignment graphLength Definition Round E-value
Target388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
317120738388 hypothetical protein SC2_gp195 [Liberibacter phage SC2] 1 0.0
315122931388 hypothetical protein CKC_05935 [Candidatus Liberibacter 1 1e-169
315121963388 hypothetical protein CKC_01065 [Candidatus Liberibacter 1 1e-166
15839112425 hypothetical protein XF2522 [Xylella fastidiosa 9a5c] L 1 4e-51
15837288425 hypothetical protein XF0686 [Xylella fastidiosa 9a5c] L 1 4e-51
71898930426 phage-related protein [Xylella fastidiosa Ann-1] Length 1 6e-50
45569531418 hypothetical protein BMP-1p37 [Bordetella phage BMP-1] 1 2e-49
273810429426 gp10 [Xylella phage Xfas53] Length = 426 1 2e-49
45580782418 hypothetical protein BIP-1p37 [Bordetella phage BIP-1] 1 2e-49
41179398418 Bbp38 [Bordetella phage BPP-1] Length = 418 1 3e-49
>gi|317120738|gb|ADV02560.1| hypothetical protein SC2_gp195 [Liberibacter phage SC2] Length = 388 Back     alignment and organism information
 Score =  804 bits (2077), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/388 (99%), Positives = 387/388 (99%)

Query: 1   MAHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVS 60
           MAHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVS
Sbjct: 1   MAHHAFLSASSSHRWLKCPIAPTLESKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVS 60

Query: 61  HQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILI 120
           HQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFL ETEVPLEPFTTEPGATGTADILI
Sbjct: 61  HQKLTFENDTRIVDTEMASSVSMVLAYVRTFSGPFLLETEVPLEPFTTEPGATGTADILI 120

Query: 121 FNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTG 180
           FNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTG
Sbjct: 121 FNSTQWIIVDFKYGAGVPVKAENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTG 180

Query: 181 SPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPAL 240
           SPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPAL
Sbjct: 181 SPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYGVNDDSCRFCRAKVRCPAL 240

Query: 241 SRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGR 300
           SRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGR
Sbjct: 241 SRHVLLEATKDPSTNTTVELSKAYSSISLIKSYVKACEDEMFKRLNAGDEIQGYQLVEGR 300

Query: 301 KGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGD 360
           KGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGD
Sbjct: 301 KGNRSFKDINRAQELLTSVLGEEAFKRILKTPKELEQLYKEQKVSDEFWEELQELITRGD 360

Query: 361 GKPVIAPRDIPTNKQTQKSQLSEFEVLG 388
           GKPVIAPRDIPTNKQTQKSQLSEFEVLG
Sbjct: 361 GKPVIAPRDIPTNKQTQKSQLSEFEVLG 388


Species: Liberibacter phage SC2
Genus: 
Family: Podoviridae
Order: Caudovirales
Class: 
Phylum: 
Superkingdom: Viruses
>gi|315122931|ref|YP_004063420.1| hypothetical protein CKC_05935 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 388 Back     alignment and organism information
>gi|315121963|ref|YP_004062452.1| hypothetical protein CKC_01065 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 388 Back     alignment and organism information
>gi|15839112|ref|NP_299800.1| hypothetical protein XF2522 [Xylella fastidiosa 9a5c] Length = 425 Back     alignment and organism information
>gi|15837288|ref|NP_297976.1| hypothetical protein XF0686 [Xylella fastidiosa 9a5c] Length = 425 Back     alignment and organism information
>gi|71898930|ref|ZP_00681097.1| phage-related protein [Xylella fastidiosa Ann-1] Length = 426 Back     alignment and organism information
>gi|45569531|ref|NP_996600.1| hypothetical protein BMP-1p37 [Bordetella phage BMP-1] Length = 418 Back     alignment and organism information
>gi|273810429|ref|YP_003344900.1| gp10 [Xylella phage Xfas53] Length = 426 Back     alignment and organism information
>gi|45580782|ref|NP_996648.1| hypothetical protein BIP-1p37 [Bordetella phage BIP-1] Length = 418 Back     alignment and organism information
>gi|41179398|ref|NP_958707.1| Bbp38 [Bordetella phage BPP-1] Length = 418 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
Target388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
pfam10926363 pfam10926, DUF2800, Protein of unknown function (DUF280 6e-68
>gnl|CDD|151373 pfam10926, DUF2800, Protein of unknown function (DUF2800) Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
pfam10926363 DUF2800 Protein of unknown function (DUF2800). This is 100.0
TIGR03623874 probable DNA repair protein. Members of this protein fa 99.91
COG2887269 RecB family exonuclease [DNA replication, recombination 99.58
TIGR00372206 cas4 CRISPR-associated protein Cas4; InterPro: IPR01334 99.29
KOG1805 1100 consensus 98.96
pfam01930162 Cas_Cas4 Domain of unknown function DUF83. This domain 98.93
TIGR03491 457 RecB family nuclease, putative, TM0106 family. Members 98.63
PHA00619210 CRISPR-associated Cas4-like protein 98.42
COG1468190 CRISPR-associated protein Cas4 (RecB family exonuclease 98.3
pfam06023290 DUF911 Archaeal protein of unknown function (DUF911). T 98.27
COG4343281 CRISPR-associated protein, RecB family exonuclease [Def 97.13
TIGR027731192 addB_Gpos ATP-dependent nuclease subunit B; InterPro: I 99.64
COG38571108 AddB ATP-dependent nuclease, subunit B [DNA replication 99.6
TIGR027861096 addB_alphas double-strand break repair protein AddB; In 99.47
TIGR027841190 addA_alphas double-strand break repair helicase AddA; I 99.39
pfam09810329 Morph_protein1 Defects in morphology protein 1, mitocho 98.65
TIGR027741116 rexB_recomb ATP-dependent nuclease subunit B; InterPro: 99.03
PRK13909911 putative recombination protein RecB; Provisional 99.01
COG10741139 RecB ATP-dependent exoDNAse (exonuclease V) beta subuni 98.37
TIGR027851295 addA_Gpos recombination helicase AddA; InterPro: IPR014 98.14
TIGR006091324 recB exodeoxyribonuclease V, beta subunit; InterPro: IP 97.93
PHA01622204 CRISPR-associated Cas4-like protein 98.34
TIGR01896295 cas_AF1879 CRISPR-associated protein, Csa1 family; Inte 95.03
COG2251474 Predicted nuclease (RecB family) [General function pred 97.91
PRK10876 1181 recB exonuclease V subunit beta; Provisional 97.78
pfam08696209 Dna2 DNA replication factor Dna2. Dna2 is a DNA replica 97.76
PRK09709877 exonuclease VIII; Reviewed 92.54
>pfam10926 DUF2800 Protein of unknown function (DUF2800) Back     alignment and domain information
>TIGR03623 probable DNA repair protein Back     alignment and domain information
>COG2887 RecB family exonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00372 cas4 CRISPR-associated protein Cas4; InterPro: IPR013343 This entry consists of conserved proteins found in many prokaryotic genomes whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats) Back     alignment and domain information
>KOG1805 consensus Back     alignment and domain information
>pfam01930 Cas_Cas4 Domain of unknown function DUF83 Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>PHA00619 CRISPR-associated Cas4-like protein Back     alignment and domain information
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms] Back     alignment and domain information
>pfam06023 DUF911 Archaeal protein of unknown function (DUF911) Back     alignment and domain information
>COG4343 CRISPR-associated protein, RecB family exonuclease [Defense mechanisms] Back     alignment and domain information
>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B; InterPro: IPR014140 DNA repair is accomplished by several different systems in prokaryotes Back     alignment and domain information
>COG3857 AddB ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR02786 addB_alphas double-strand break repair protein AddB; InterPro: IPR014153 AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage Back     alignment and domain information
>TIGR02784 addA_alphas double-strand break repair helicase AddA; InterPro: IPR014151 AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages Back     alignment and domain information
>pfam09810 Morph_protein1 Defects in morphology protein 1, mitochondrial precursor Back     alignment and domain information
>TIGR02774 rexB_recomb ATP-dependent nuclease subunit B; InterPro: IPR014141 DNA repair is accomplished by several different systems in prokaryotes Back     alignment and domain information
>PRK13909 putative recombination protein RecB; Provisional Back     alignment and domain information
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR02785 addA_Gpos recombination helicase AddA; InterPro: IPR014152 AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages Back     alignment and domain information
>TIGR00609 recB exodeoxyribonuclease V, beta subunit; InterPro: IPR004586 Exodeoxyribonuclease V, or RecBCD holoenzyme, (3 Back     alignment and domain information
>PHA01622 CRISPR-associated Cas4-like protein Back     alignment and domain information
>TIGR01896 cas_AF1879 CRISPR-associated protein, Csa1 family; InterPro: IPR009260 This family consists of several archaeal strongly conserved proteins whose genes are associated with CRISPRs (Clustered, Regularly Interspaced Short Palidromic Repeats) Back     alignment and domain information
>COG2251 Predicted nuclease (RecB family) [General function prediction only] Back     alignment and domain information
>PRK10876 recB exonuclease V subunit beta; Provisional Back     alignment and domain information
>pfam08696 Dna2 DNA replication factor Dna2 Back     alignment and domain information
>PRK09709 exonuclease VIII; Reviewed 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

No homologous structure with e-value below 0.005

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
1qzv_F154 Plant photosystem I: subunit PSAF; photosynthesis,plant 0.002
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Back     alignment and structure
 Score = 38.4 bits (88), Expect = 0.002
 Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 12/39 (30%)

Query: 209 SLKSKRAVSLEHYGVNDDSCRFCRAKVRCPALSRHVLLE 247
           +LK  +A SL+ Y   DDS          PAL+    +E
Sbjct: 21  ALKKLQA-SLKLYA--DDSA---------PALAIKATME 47


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
3l0a_A266 Putative exonuclease; RER070207002219, structural genom 99.71
3h4r_A265 Exodeoxyribonuclease 8; exonuclease, recombination, hyd 99.59
1w36_B1180 RECB, exodeoxyribonuclease V beta chain; recombination, 98.78
1w36_C1122 RECC, exodeoxyribonuclease V gamma chain; recombination 97.04
>3l0a_A Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale} Back     alignment and structure
Probab=99.71  E-value=7.3e-16  Score=122.30  Aligned_cols=211  Identities=17%  Similarity=0.138  Sum_probs=117.5

Q ss_pred             CCCCCCHHHHHCCCHHH--------HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCCCCCCCCCHHHHH
Q ss_conf             61842367787183238--------86213899989889998999999999972457--653432201045645377578
Q gi|254780124|r    6 FLSASSSHRWLKCPIAP--------TLESKIPQTTSIYASEGTFAHNLLAHCLEQGV--DAETVSHQKLTFENDTRIVDT   75 (388)
Q Consensus         6 ~LSpSs~~rwl~CP~s~--------~Le~~~pd~~S~aA~~GT~~H~llE~~l~~~l--~~~~~~~~~~~~~~~~~~~~~   75 (388)
                      .||.|++.+|+.||...        ++....+.++++++..||++|.++|..++...  ..+.. ........+ ...-.
T Consensus        18 y~S~S~ik~~~~~~~~~~~~a~~~a~~~~~~~~~~t~al~~Gt~vH~~le~~~~~~~~~~~~~~-~~~~~~~~e-~~~~~   95 (266)
T 3l0a_A           18 YMSVSGYKDFAGTYGKMPCEFYGMEKLNGRWEDEKSTALLVGSYVDSYFEGSLDQFKKDNPEIF-TQKGELKAN-FKQAE   95 (266)
T ss_dssp             CEEHHHHHHHHCBTTBCCCHHHHHHHHHTSCCCCCCHHHHHHHHHHHHHHTCHHHHHHHCGGGB-CTTSSBCHH-HHHHH
T ss_pred             EECHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHCCCCCC-CCCCHHHHH-HHHHH
T ss_conf             1269899998439311002688999860777889987998718999986574553420184201-333144899-99999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCC--------------
Q ss_conf             899999999999850378736887755320004405899999999859979999811368876744--------------
Q gi|254780124|r   76 EMASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKA--------------  141 (388)
Q Consensus        76 e~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a--------------  141 (388)
                      .|.+.+...- .....   ...+.|+.+...+.+..+.|++|++..+ +  .|+|+||.+......              
T Consensus        96 ~m~~~~~~~~-~~~~~---~~~~~E~~~~~~~~gv~~kg~iD~i~~~-~--~ivDlKtt~~~~~~~~~~~~~~~~~~~~~  168 (266)
T 3l0a_A           96 EIIARIERDE-YFMKY---MSGQKQVIMTGELFGAKWKIKMDSYIPG-V--AIVDLKVMASITDLKWVKDIGYLDFVRYW  168 (266)
T ss_dssp             HHHHHHHTCH-HHHHH---TTSEEEEEEEEEETTEEEEEEEEEEETT-T--EEEEEEEESCSSCCEEETTTEEECHHHHT
T ss_pred             HHHHHHHHCC-HHHHH---CCCCCEEEEEEEECCEEEEEEEEEEECC-C--CEEEEEEEECCCCCCCCCCCCHHHHHHHC
T ss_conf             9999999670-03555---1577247899977585874067899568-9--72676774115632244321035577752


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             66879999999999843835676513899999830488775430258988999999999999999985776530477667
Q gi|254780124|r  142 ENNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHY  221 (388)
Q Consensus       142 ~~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~  221 (388)
                      ....||.+|+.+..+.++...   .   ..++..-......+..+.++.+.+..-.+.+...+..+....     .++..
T Consensus       169 ~Y~~Q~a~Y~~~l~~~~g~~~---~---~~~v~v~k~~p~~~~~~~~~~~~l~~~~~~v~~~i~~i~~~~-----~~~~~  237 (266)
T 3l0a_A          169 GYDIQGAVYQEIVRQNTGEKL---P---FFIAGATKQTEPDIRIIHVTDNYLQEALHMVEMNMPRILRVK-----NGEVE  237 (266)
T ss_dssp             THHHHHHHHHHHHHHHHSCCC---C---EEEEEEECSSSCCEEEEEECHHHHHHHHHHHHHHHHHHHHHH-----TTSSC
T ss_pred             CHHHHHHHHHHHHHHHHCCCC---C---EEEEEEECCCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHH-----CCCCC
T ss_conf             889999999999999868986---3---799999788887604897798999999999999999999997-----28968


Q ss_pred             CCCCCCCCCCCCCCCCCHHHH
Q ss_conf             888666672576445620134
Q gi|254780124|r  222 GVNDDSCRFCRAKVRCPALSR  242 (388)
Q Consensus       222 ~~~g~~CrfC~~k~~Cra~a~  242 (388)
                      +   ++|.+|+|   ||..-+
T Consensus       238 p---~~C~~CdY---Cr~~k~  252 (266)
T 3l0a_A          238 P---DRCELCDC---CRHNRV  252 (266)
T ss_dssp             C---CCCSCSHH---HHHHCC
T ss_pred             C---CCCCCCCC---CHHHHH
T ss_conf             9---98998987---720300



>3h4r_A Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12} Back     alignment and structure
>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B* Back     alignment and structure
>1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.25 PDB: 3k70_C* 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

No hit with e-value below 0.005

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

IdentityAlignment graphLength Definition Probability
Target388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
d1w36b3276 Exodeoxyribonuclease V beta chain (RecB), C-terminal do 98.56
>d1w36b3 c.52.1.24 (B:899-1174) Exodeoxyribonuclease V beta chain (RecB), C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Restriction endonuclease-like
superfamily: Restriction endonuclease-like
family: Exodeoxyribonuclease V beta chain (RecB), C-terminal domain
domain: Exodeoxyribonuclease V beta chain (RecB), C-terminal domain
species: Escherichia coli [TaxId: 562]
Probab=98.56  E-value=4.6e-08  Score=69.46  Aligned_cols=49  Identities=14%  Similarity=0.137  Sum_probs=36.6

Q ss_pred             EEEEEEEEEEEECCEEEEEEEECCCCCCC-C-------------CCCCHHHHHHHHHHHHHCC
Q ss_conf             58999999998599799998113688767-4-------------4668799999999998438
Q gi|254780124|r  111 GATGTADILIFNSTQWIIVDFKYGAGVPV-K-------------AENNTQLMLYACGALHQYG  159 (388)
Q Consensus       111 ~~~GtiD~I~~~dg~l~IiDyKtGk~~~v-~-------------a~~n~QL~lYALgA~~~~~  159 (388)
                      -+.|.||+|...+|.+.|+||||.+=-.. +             .....|+.||++++.+.+.
T Consensus       163 ~l~G~IDlvf~~~g~~~llDYKTn~Lg~~~~~Y~~~~l~~~m~~~~Y~lQ~~lY~~AL~R~L~  225 (276)
T d1w36b3         163 MLKGFIDLVFRHEGRYYLLDYKSNWLGEDSSAYTQQAMAAAMQAHRYDLQYQLYTLALHRYLR  225 (276)
T ss_dssp             EEEEEEEEEEBSSSCBCCEEEECCCCCSSGGGSBHHHHHHHHHHTTTHHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEEEEEECCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             377788999999999999980056568873435899999999987688999999999999999



Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 388 hypothetical protein CLIBASIA_00015 [Candidatus Li
3h4r_A_265 (A:) Exodeoxyribonuclease 8; exonuclease, recombin 1e-11
3l0a_A_266 (A:) Putative exonuclease; RER070207002219, struct 9e-06
>3h4r_A (A:) Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12}Length = 265 Back     alignment and structure
 Score = 65.0 bits (157), Expect = 1e-11
 Identities = 28/261 (10%), Positives = 55/261 (21%), Gaps = 34/261 (13%)

Query: 4   HAFLSASSSHRWLKCPIAPTLES--KIPQTTSIYASEGTFAHNLLAHC------------ 49
              +S S        P          +  T +     GT  H  +               
Sbjct: 10  GPGISKSQLDDIADTPALYLWRKNAPVDTTKTKTLDLGTAFHCRVLELEEFSNRFIVAPE 69

Query: 50  ---LEQGVDAETVSHQKLTFENDTRIVDTEMASSVS---MVLAYVRTFSGPFLSETEVPL 103
                     E  +           ++  E    +      +  +        S      
Sbjct: 70  FNRRTNAGKEEEKAFLMECASTGKTVITAEEGRKIELMYQSVMALPLGQWLVESAGHAES 129

Query: 104 EPFTT--EPGATGTADILIFNSTQWIIVDFKYGAGVP------VKAENNTQLMLYACGAL 155
             +    E G                I+D K  A +            + Q   Y+ G  
Sbjct: 130 SIYWEDPETGILCRCRPDKIIPEFHWIMDVKTTADIQRFKTAYYDYRYHVQDAFYSDGYE 189

Query: 156 HQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRA 215
            Q+G    +P  + L           P+  +++  +  L   +E+     L         
Sbjct: 190 AQFGV---QPTFVFLVASTTIECGRYPVEIFMMGEEAKLAGQQEYHR--NLRTLSDCLNT 244

Query: 216 VSLEHYGVNDDSCRFCRAKVR 236
                        R+ +    
Sbjct: 245 DEWPAI-KTLSLPRWAKEYAN 264


>3l0a_A (A:) Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale}Length = 266 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target388 hypothetical protein CLIBASIA_00015 [Candidatus Liberib
3l0a_A_266 Putative exonuclease; RER070207002219, structural 99.93
3h4r_A_265 Exodeoxyribonuclease 8; exonuclease, recombination 99.9
1w36_B_886-964_1014-1180246 RECB, exodeoxyribonuclease V beta chain; recombina 98.91
>3l0a_A (A:) Putative exonuclease; RER070207002219, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI-2; HET: PE4; 2.19A {Eubacterium rectale} Back     alignment and structure
Probab=99.93  E-value=3.6e-24  Score=177.86  Aligned_cols=225  Identities=14%  Similarity=0.078  Sum_probs=146.2

Q ss_pred             CCCCCCCHHHHHC------CCHHHHHH--CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             5618423677871------83238862--138999898899989999999999724576534322010456453775788
Q gi|254780124|r    5 AFLSASSSHRWLK------CPIAPTLE--SKIPQTTSIYASEGTFAHNLLAHCLEQGVDAETVSHQKLTFENDTRIVDTE   76 (388)
Q Consensus         5 A~LSpSs~~rwl~------CP~s~~Le--~~~pd~~S~aA~~GT~~H~llE~~l~~~l~~~~~~~~~~~~~~~~~~~~~e   76 (388)
                      ..||||++++|+.      ||.++.+.  .++|...+.++..||++|.++|...........   .......+.....+.
T Consensus        17 ~~~S~S~l~~~~~~~~~~~cp~~~~~~~~~~~~~~~~~a~~~Gt~iH~~le~~~~~~~~~~~---~~~~~~~~~~~~~~~   93 (266)
T 3l0a_A           17 EYXSVSGYKDFAGTYGKXPCEFYGXEKLNGRWEDEKSTALLVGSYVDSYFEGSLDQFKKDNP---EIFTQKGELKANFKQ   93 (266)
T ss_dssp             HCEEHHHHHHHHCBTTBCCCHHHHHHHHHTSCCCCCCHHHHHHHHHHHHHHTCHHHHHHHCG---GGBCTTSSBCHHHHH
T ss_pred             CCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCCCCHHHHHHHH
T ss_conf             65478689998449510007799999861767888987899978999998727676544173---100212056899999


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEEEEEEECCEEEEEEEECCCCCCCCCC--------------
Q ss_conf             999999999998503787368877553200044058999999998599799998113688767446--------------
Q gi|254780124|r   77 MASSVSMVLAYVRTFSGPFLSETEVPLEPFTTEPGATGTADILIFNSTQWIIVDFKYGAGVPVKAE--------------  142 (388)
Q Consensus        77 ~~~~v~~~~~~~r~~~~~~~ve~E~~~~~~~~~~~~~GtiD~I~~~dg~l~IiDyKtGk~~~v~a~--------------  142 (388)
                      ....+..+..... .......+.|+.+....++..+.|++|+|+   +.+.|+|||||+.+.....              
T Consensus        94 ~~~~~~~~~~~~~-~~~~~~~~~E~~~~~~~~g~~l~GriD~id---~~~~IiDyKT~~~~~~~~~~~~~~~~~~~~~~~  169 (266)
T 3l0a_A           94 AEEIIARIERDEY-FXKYXSGQKQVIXTGELFGAKWKIKXDSYI---PGVAIVDLKVXASITDLKWVKDIGYLDFVRYWG  169 (266)
T ss_dssp             HHHHHHHHHTCHH-HHHHTTSEEEEEEEEEETTEEEEEEEEEEE---TTTEEEEEEEESCSSCCEEETTTEEECHHHHTT
T ss_pred             HHHHHHHHHHCCH-HHHHCCCCEEEEEEEEECCEEEEEEEEEEE---CCCEEEEEEECCCCCHHHCCCCHHHHHHHHHCC
T ss_conf             9999999995704-566435763789999876937651467993---687599954336565221244112355788608


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             68799999999998438356765138999998304887754302589889999999999999999857765304776678
Q gi|254780124|r  143 NNTQLMLYACGALHQYGDIFGRPEALTLTIIQPRVRTGSPINEWVISADDLLEKAKEFKERGTLALSLKSKRAVSLEHYG  222 (388)
Q Consensus       143 ~n~QL~lYALgA~~~~~~~~~~~~~v~~~I~qpr~~~~~~vs~~~~s~eeL~~~~~~v~~~a~~~~~~~a~~~~~~~~~~  222 (388)
                      ...||.+|++++.+.++..      +.+.++..+......+.+.+++.+.+....+.+...+..+...     ..+.+++
T Consensus       170 y~~Ql~~Y~~~~~~~~~~~------~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~i~~~-----~~~~~~p  238 (266)
T 3l0a_A          170 YDIQGAVYQEIVRQNTGEK------LPFFIAGATKQTEPDIRIIHVTDNYLQEALHXVEXNXPRILRV-----KNGEVEP  238 (266)
T ss_dssp             HHHHHHHHHHHHHHHHSCC------CCEEEEEEECSSSCCEEEEEECHHHHHHHHHHHHHHHHHHHHH-----HTTSSCC
T ss_pred             HHHHHHHHHHHHHHHHCCC------CCEEEEEEECCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHH-----HCCCCCC
T ss_conf             3999999999999986898------7359999977898732388479899999999999999999999-----7598479


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             8866667257644562013467876
Q gi|254780124|r  223 VNDDSCRFCRAKVRCPALSRHVLLE  247 (388)
Q Consensus       223 ~~g~~CrfC~~k~~Cra~a~~~l~~  247 (388)
                      .++++|+||+|+..|...-..+...
T Consensus       239 ~~~~~C~~C~~~~~c~~~~~~~~~~  263 (266)
T 3l0a_A          239 DRCELCDCCRHNRVLKKPISIXDLT  263 (266)
T ss_dssp             CCCSCSHHHHHHCCCCSCCCHHHHH
T ss_pred             CCCCCCCCCCCCCHHCCCCCHHHHH
T ss_conf             9999798861011011201199983



>3h4r_A (A:) Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase; 2.80A {Escherichia coli k-12} Back     alignment and structure
>1w36_B (B:886-964,B:1014-1180) RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} Back     alignment and structure