254780134

254780134

phage-related integrase/recombinase

GeneID in NCBI database:8209109Locus tag:CLIBASIA_00065
Protein GI in NCBI database:254780134Protein Accession:YP_003064547.1
Gene range:+(8544, 9590)Protein Length:348aa
Gene description:phage-related integrase/recombinase
COG prediction:[L] Integrase
KEGG prediction:phage-related integrase/recombinase
SEED prediction:integrase
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-------35
MTPSLRLPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYINSPRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSRRISSVVDSDDP
ccccccccccEEEEEcccccEEEEEEEccccEEEccccccHHHHHHHHHHHHccccHHHHHcccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccHHHccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHcccccHHHHHHHHHHHHcccHHHHHcccHHHccccEEEEEEcccccEEEEEccHHHHHHHHHccccccEEEEccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
ccccccccccEEEEEEEccEEEEEEEcccccEEcccccccHHHHHHHHHHHHcccccHHHccccccccHHHHHHHHHHHHcccHHHHcHHHHHHHHHHHHHHHHHcccccHHHccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHcccccHHHHHHHHHHHHcccHHHHHHccHHHccccEEEEEEcccccEEEEcccHHHHHHHHHccccccEEEEccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
mtpslrlppfvtkertrhGKIIYYFRkghgrrirlpyphestfipaymsaltgstpkreyinsprkkptTLKWLISEYRksahwgslavnsrisFESYFDQIIRKSGDFDYRKITTKHIrsgvesrkhtpssAIQFLTSMRVLFKWAVRQEYvainpclsverpkrktegirpwtkeDMQQFKSFwsegsqprLAFEFLLYsglrcsdscrAGVQHLQNNIfsiktqktgtiITVELPDGFMKLLamtpigketffinndkqkmnATQFSIWFKAKatkagvnksahgvrkfSATISADAGATAHELMATYgwktvdqaetytkgADRIrlgiknsrrissvvdsddp
mtpslrlppfvtkertrhgkiiyyfrkghgrriRLPYPHESTFIPAYMSALTgstpkreyinsprkkpttLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIrksgdfdyrKITTKhirsgvesrkhtpssaIQFLTSMRVLFKWAVRQEYVainpclsverpkrktegirpwtkeDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQnnifsiktqktgtIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETytkgadrirlgiknsrrissvvdsddp
MTPSLRLPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYINSPRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSRRIssvvdsddP
******L**FVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSAL******************TLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKR*TEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIR******************
MTPSLRLPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYINSPRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIR***********SAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSR***********
***SLRLPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYINSPRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSRRISSVV*****
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MTPSLRLPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYINSPRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSRRISSVVDSDDP
MTPSLRLPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYINSPRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSRRISSVVDSDDP
MTPSLRLPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYINSPRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSRRISSVVDSDDP

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

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

IdentityAlignment graphLength Definition Round E-value
Target348 phage-related integrase/recombinase [Candidatus Liberib
240850345347 phage-related integrase/recombinase [Bartonella grahami 1 5e-59
323136183341 integrase family protein [Methylocystis sp. ATCC 49242] 1 8e-57
319405810345 phage-related integrase/recombinase [Bartonella sp. AR 1 8e-56
163868166345 phage-related integrase/recombinase [Bartonella triboco 1 3e-55
85716638371 Integrase /recombinase [Nitrobacter sp. Nb-311A] Length 1 2e-52
49475466345 integrase /recombinase [Bartonella henselae str. Housto 1 1e-51
307942454356 integrase family protein [Roseibium sp. TrichSKD4] Leng 1 4e-51
319409101347 phage-related integrase/recombinase [Bartonella schoenb 1 5e-50
319408877347 phage-related integrase/recombinase [Bartonella schoenb 1 6e-50
240850538345 phage-related integrase/recombinase [Bartonella grahami 1 3e-49
>gi|240850345|ref|YP_002971738.1| phage-related integrase/recombinase [Bartonella grahamii as4aup] Length = 347 Back     alignment and organism information
 Score =  233 bits (593), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 129/341 (37%), Positives = 192/341 (56%), Gaps = 13/341 (3%)

Query: 8   PPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHEST-FIPAYMSALTGSTPKREYINSPRK 66
           PP + KE TRHGKII+Y R GHG+RIR+   + +  F+  Y SAL     + + +  P+ 
Sbjct: 6   PPHLVKEVTRHGKIIWYVRIGHGKRIRIRGTYGTQEFVDNYKSALA----ELQGLILPKS 61

Query: 67  KPTTL-----KWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRS 121
           K   L      WL+ +Y  S HW SLA  ++   E    ++    G+  YR+I   HI +
Sbjct: 62  KTGKLVEGSFAWLLKQYFNSVHWHSLAKATKRQRELILMKVCDAIGNIPYREIKKSHITA 121

Query: 122 GVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPK-RKTEGIRPWTKEDMQ 180
           GVE RK  P++A  FL ++  LF WA+ QE +  NP L ++RP     +G   WT+ED++
Sbjct: 122 GVERRKEKPTAAQNFLKALNGLFNWAIDQELLENNPALGIKRPPLNNKDGFAVWTEEDVE 181

Query: 181 QFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELP-- 238
           ++   WS GS  R+  + LLY+GLR  D+ R G + +++NI  +KT+K+     V LP  
Sbjct: 182 KYYHHWSHGSHERVWIDVLLYTGLRRGDAVRIGWKDVKDNIIHLKTEKSKFQTDVFLPIL 241

Query: 239 DGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISA 298
               + L + PIG ETF    +  K+    F   F+     AG+ KSAHG+RK +AT +A
Sbjct: 242 PELAETLKIGPIGNETFICGKNGNKLVKESFGNLFREACNAAGIKKSAHGLRKLAATRAA 301

Query: 299 DAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKNSRRI 339
           ++GAT  +L A +GW   + A  YTK ADR RL I+  +++
Sbjct: 302 NSGATVSQLKAIFGWTDDNMASLYTKSADRKRLAIEAIKKL 342


Species: Bartonella grahamii
Genus: Bartonella
Family: Bartonellaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|323136183|ref|ZP_08071265.1| integrase family protein [Methylocystis sp. ATCC 49242] Length = 341 Back     alignment and organism information
>gi|319405810|emb|CBI79435.1| phage-related integrase/recombinase [Bartonella sp. AR 15-3] Length = 345 Back     alignment and organism information
>gi|163868166|ref|YP_001609374.1| phage-related integrase/recombinase [Bartonella tribocorum CIP 105476] Length = 345 Back     alignment and organism information
>gi|85716638|ref|ZP_01047608.1| Integrase /recombinase [Nitrobacter sp. Nb-311A] Length = 371 Back     alignment and organism information
>gi|49475466|ref|YP_033507.1| integrase /recombinase [Bartonella henselae str. Houston-1] Length = 345 Back     alignment and organism information
>gi|307942454|ref|ZP_07657805.1| integrase family protein [Roseibium sp. TrichSKD4] Length = 356 Back     alignment and organism information
>gi|319409101|emb|CBI82745.1| phage-related integrase/recombinase [Bartonella schoenbuchensis R1] Length = 347 Back     alignment and organism information
>gi|319408877|emb|CBI82534.1| phage-related integrase/recombinase [Bartonella schoenbuchensis R1] Length = 347 Back     alignment and organism information
>gi|240850538|ref|YP_002971937.1| phage-related integrase/recombinase [Bartonella grahamii as4aup] Length = 345 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
Target348 phage-related integrase/recombinase [Candidatus Liberib
cd00801357 cd00801, INT_P4, Bacteriophage P4 integrase 1e-09
COG4974300 COG4974, XerD, Site-specific recombinase XerD [DNA repl 6e-07
cd00798284 cd00798, INT_XerDC, XerD and XerC integrases, DNA break 4e-06
cd01182162 cd01182, INT_REC_C, DNA breaking-rejoining enzymes, int 5e-09
cd00397164 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-t 4e-07
pfam00589170 pfam00589, Phage_integrase, Phage integrase family 8e-11
TIGR02224295 TIGR02224, recomb_XerC, tyrosine recombinase XerC 4e-08
TIGR02225291 TIGR02225, recomb_XerD, tyrosine recombinase XerD 8e-06
cd01185299 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA 1e-05
cd00799287 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic 3e-04
PRK00283299 PRK00283, xerD, site-specific tyrosine recombinase XerD 2e-04
>gnl|CDD|29502 cd00801, INT_P4, Bacteriophage P4 integrase Back     alignment and domain information
>gnl|CDD|34580 COG4974, XerD, Site-specific recombinase XerD [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|29499 cd00798, INT_XerDC, XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains Back     alignment and domain information
>gnl|CDD|29503 cd01182, INT_REC_C, DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|29495 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|144254 pfam00589, Phage_integrase, Phage integrase family Back     alignment and domain information
>gnl|CDD|162771 TIGR02224, recomb_XerC, tyrosine recombinase XerC Back     alignment and domain information
>gnl|CDD|162772 TIGR02225, recomb_XerD, tyrosine recombinase XerD Back     alignment and domain information
>gnl|CDD|29506 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains Back     alignment and domain information
>gnl|CDD|29500 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 348 phage-related integrase/recombinase [Candidatus Liberib
TIGR02225305 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011 100.0
PRK00236295 xerC site-specific tyrosine recombinase XerC; Reviewed 100.0
TIGR02224313 recomb_XerC tyrosine recombinase XerC; InterPro: IPR011 100.0
PRK01287361 xerC site-specific tyrosine recombinase XerC; Reviewed 100.0
PRK00283296 xerD site-specific tyrosine recombinase XerD; Reviewed 100.0
cd00798284 INT_XerDC XerD and XerC integrases, DNA breaking-rejoin 100.0
cd01185299 INT_Tn4399 Tn4399 and related integrases, DNA breaking- 100.0
COG4974300 XerD Site-specific recombinase XerD [DNA replication, r 100.0
PRK05084360 xerS site-specific tyrosine recombinase XerS; Reviewed 100.0
PRK02436247 xerD site-specific tyrosine recombinase XerD-like prote 100.0
cd01187299 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integr 100.0
cd01193242 INT_IntI IntI (E2) integrases, site-specific tyrosine r 100.0
cd01196263 INT_VanD VanD integrase, IntD, and related integrases, 100.0
cd01190260 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integr 100.0
TIGR02249320 integrase_gron integron integrase; InterPro: IPR011946 100.0
COG4973299 XerC Site-specific recombinase XerC [DNA replication, r 100.0
cd00799287 INT_Cre Cre recombinase, C-terminal catalytic domain. C 100.0
cd00801357 INT_P4 Bacteriophage P4 integrase. P4-like integrases a 100.0
PRK09692413 integrase; Provisional 100.0
cd00796206 INT_Rci Rci recombinase, C-terminal catalytic domain. R 100.0
COG0582309 XerC Integrase [DNA replication, recombination, and rep 99.78
COG4342291 Uncharacterized protein conserved in archaea [Function 98.83
PHA00730322 int integrase 98.64
PRK09870200 tyrosine recombinase; Provisional 99.97
cd01197180 INT_FimBE_C FimB and FimE and related proteins, DNA bre 99.97
PRK09871198 tyrosine recombinase; Provisional 99.97
cd01192177 INT_P22_C P22-like integrases, site-specific recombinas 99.96
cd01188188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejo 99.96
cd00800162 INT_Lambda_C Lambda integrase, C-terminal catalytic dom 99.96
cd01186180 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, inte 99.96
cd00797158 HP1_INT_C Phage HP1 integrase, C-terminal catalytic dom 99.95
cd01194186 INT_Tn554A_C Tn544A and related transposases, DNA break 99.95
cd01198186 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA 99.95
cd01189191 INT_phiLC3_C phiLC3 phage and phage-related integrases, 99.95
pfam00589170 Phage_integrase Phage integrase family. Members of this 99.95
cd01191196 INT_phiCTX_C phiCTX phage and phage-related integrases, 99.95
cd01199205 INT_Tn1545_C Tn1545-related conjugative transposon inte 99.94
cd01195195 INT_Tn544B_C Tn544B and related transposases, DNA break 99.94
cd01184181 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, inte 99.93
cd01183196 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, inte 99.93
cd00397164 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal ca 99.92
cd01182162 INT_REC_C DNA breaking-rejoining enzymes, intergrase/re 99.85
pfam0289983 Phage_integr_N Phage integrase, N-terminal SAM-like dom 98.29
pfam11917 414 DUF3435 Protein of unknown function (DUF3435). This fam 98.28
pfam0900381 Phage_integ_N Bacteriophage lambda integrase, N-termina 95.88
pfam01028244 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic co 95.54
cd00659218 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic do 95.19
>TIGR02225 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011932 Proteins in this entry are part of the wider so-called "phage" integrase fmaily which describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA Back     alignment and domain information
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed Back     alignment and domain information
>TIGR02224 recomb_XerC tyrosine recombinase XerC; InterPro: IPR011931 The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA Back     alignment and domain information
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed Back     alignment and domain information
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed Back     alignment and domain information
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains Back     alignment and domain information
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains Back     alignment and domain information
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed Back     alignment and domain information
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed Back     alignment and domain information
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains Back     alignment and domain information
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains Back     alignment and domain information
>cd01196 INT_VanD VanD integrase, IntD, and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains Back     alignment and domain information
>cd01190 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains Back     alignment and domain information
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946 Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA Back     alignment and domain information
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair] Back     alignment and domain information
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain Back     alignment and domain information
>cd00801 INT_P4 Bacteriophage P4 integrase Back     alignment and domain information
>PRK09692 integrase; Provisional Back     alignment and domain information
>cd00796 INT_Rci Rci recombinase, C-terminal catalytic domain Back     alignment and domain information
>COG0582 XerC Integrase [DNA replication, recombination, and repair] Back     alignment and domain information
>COG4342 Uncharacterized protein conserved in archaea [Function unknown] Back     alignment and domain information
>PHA00730 int integrase Back     alignment and domain information
>PRK09870 tyrosine recombinase; Provisional Back     alignment and domain information
>cd01197 INT_FimBE_C FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain Back     alignment and domain information
>PRK09871 tyrosine recombinase; Provisional Back     alignment and domain information
>cd01192 INT_P22_C P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain Back     alignment and domain information
>cd00800 INT_Lambda_C Lambda integrase, C-terminal catalytic domain Back     alignment and domain information
>cd01186 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain Back     alignment and domain information
>cd00797 HP1_INT_C Phage HP1 integrase, C-terminal catalytic domain Back     alignment and domain information
>cd01194 INT_Tn554A_C Tn544A and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain Back     alignment and domain information
>cd01198 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA), DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain Back     alignment and domain information
>cd01189 INT_phiLC3_C phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>pfam00589 Phage_integrase Phage integrase family Back     alignment and domain information
>cd01191 INT_phiCTX_C phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>cd01195 INT_Tn544B_C Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain Back     alignment and domain information
>cd01184 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain Back     alignment and domain information
>cd01183 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain Back     alignment and domain information
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain Back     alignment and domain information
>pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain Back     alignment and domain information
>pfam11917 DUF3435 Protein of unknown function (DUF3435) Back     alignment and domain information
>pfam09003 Phage_integ_N Bacteriophage lambda integrase, N-terminal domain Back     alignment and domain information
>pfam01028 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic core Back     alignment and domain information
>cd00659 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic domain 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
Target348 phage-related integrase/recombinase [Candidatus Liberib
1a0p_A290 Site-Specific Recombinase, Xerd Length = 290 1e-31
1p7d_A283 Crystal Structure Of The Lambda Integrase (Residues 2e-15
1z19_A283 Crystal Structure Of A Lambda Integrase(75-356) Dim 4e-14
1z1b_A356 Crystal Structure Of A Lambda Integrase Dimer Bound 2e-20
1z1g_A356 Crystal Structure Of A Lambda Integrase Tetramer Bo 8e-20
2a3v_A320 Structural Basis For Broad Dna-Specificity In Integ 1e-16
>gi|157829635|pdb|1A0P|A Chain A, Site-Specific Recombinase, Xerd Length = 290 Back     alignment and structure
 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 42/279 (15%), Positives = 94/279 (33%), Gaps = 24/279 (8%)

Query: 75  ISEYRKSAHW-GSLAVNSRISFESYFDQIIRKSGDFDYRKITTKH-----IRSGVESRKH 128
           I ++  +     +LA N+  ++      ++           T +      + +      +
Sbjct: 6   IEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGY 65

Query: 129 TPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSE 188
             +S+ + L+++R LF++  R+++   +P   +  PK      +  ++  +++       
Sbjct: 66  KATSSARLLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQVERLLQAPLI 125

Query: 189 G----SQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKT-GTIITVELPDGFMK 243
                 + +   E L  +GLR S+     +  +      ++          V L +  + 
Sbjct: 126 DQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAVY 185

Query: 244 LLAMTPIGKETF----------FINNDKQKMNATQFSIWFKAKATKAGVN---KSAHGVR 290
            L         +          F +   Q+M    F    K  A  AG++    S H +R
Sbjct: 186 WLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLR 245

Query: 291 KFSATISADAGATAHELMATYGWKTVDQAETYTKGADRI 329
              AT   + GA    +    G   +   + YT  A   
Sbjct: 246 HAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATER 284


>gi|34810656|pdb|1P7D|A Chain A, Crystal Structure Of The Lambda Integrase (Residues 75-356) Bound To Dna Length = 283 Back     alignment and structure
>gi|71042119|pdb|1Z19|A Chain A, Crystal Structure Of A Lambda Integrase(75-356) Dimer Bound To A Coc' Core Site Length = 283 Back     alignment and structure
>gi|71042126|pdb|1Z1B|A Chain A, Crystal Structure Of A Lambda Integrase Dimer Bound To A Coc' Core Site Length = 356 Back     alignment and structure
>gi|71042133|pdb|1Z1G|A Chain A, Crystal Structure Of A Lambda Integrase Tetramer Bound To A Holliday Junction Length = 356 Back     alignment and structure
>gi|99031762|pdb|2A3V|A Chain A, Structural Basis For Broad Dna-Specificity In Integron Recombination Length = 320 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target348 phage-related integrase/recombinase [Candidatus Liberib
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 3e-12
1z19_A283 Integrase; protein-DNA complex, DNA binding protein/DNA 5e-10
2kiw_A111 INT protein; alpha, structural genomics, PSI-2, protein 8e-07
2kd1_A118 DNA integration/recombination/invertion protein; protei 2e-06
2kob_A108 Uncharacterized protein; alpha beta, structural genomic 6e-06
2oxo_A103 Integrase; DNA-binding protein, four-helix bundle, DNA 2e-05
2kkp_A117 Phage integrase; SAM-like domain, alpha-helical bundle, 2e-05
2khq_A110 Integrase; all-alpha, structural genomics, PSI-2, prote 2e-04
3lys_A112 Prophage PI2 protein 01, integrase; helical N-terminal 0.001
3nrw_A117 Phage integrase/site-specific recombinase; alpha-helica 5e-04
>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} SCOP: d.10.1.4 d.163.1.1 PDB: 1z1g_A 1kjk_A 2wcc_3* Length = 356 Back     alignment and structure
 Score = 68.0 bits (164), Expect = 3e-12
 Identities = 65/349 (18%), Positives = 120/349 (34%), Gaps = 25/349 (7%)

Query: 7   LPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTF---IPAYMSALTGSTPKREYINS 63
           LPP +     R+     Y     G+   L           I A +   +G   K      
Sbjct: 12  LPPNLYI---RNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARI 68

Query: 64  PRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGV 123
                 TL   +  Y K      +   + I++ S    I R   D     ITTK I + +
Sbjct: 69  NSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAML 128

Query: 124 ESR--KHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQ 181
                +   +SA    +++   F+ A+ + ++  N   +    K K    R    E ++ 
Sbjct: 129 NGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKI 188

Query: 182 FKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGF 241
           +++  S     RLA E  + +G R  D C      + +    ++  KTG  I +      
Sbjct: 189 YQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHI 248

Query: 242 MKLLA---------MTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNK-----SAH 287
             L              +G ET   +  ++ +++   S +F      +G++      + H
Sbjct: 249 DALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFH 308

Query: 288 GVRKFSATISADAGATAHELMATYGWKTVDQAETYTK--GADRIRLGIK 334
            +R  SA +  +   +        G K+   A  Y    G +  ++ IK
Sbjct: 309 ELRSLSARL-YEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK 356


>1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* Length = 283 Back     alignment and structure
>2kiw_A INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435} Length = 111 Back     alignment and structure
>2kd1_A DNA integration/recombination/invertion protein; protein structure initiative, structural genomics, unknown function, PSI-2; HET: DNA; NMR {Bacillus cereus atcc 14579} Length = 118 Back     alignment and structure
>2kob_A Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753} Length = 108 Back     alignment and structure
>2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage} Length = 103 Back     alignment and structure
>2kkp_A Phage integrase; SAM-like domain, alpha-helical bundle, structural genomics, PSI-2, protein structure initiative; NMR {Moorella thermoacetica atcc 39073} Length = 117 Back     alignment and structure
>2khq_A Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp} Length = 110 Back     alignment and structure
>3lys_A Prophage PI2 protein 01, integrase; helical N-terminal domain, structural genomics, PSI-2, protein structure initiative; 2.80A {Lactococcus lactis} Length = 112 Back     alignment and structure
>3nrw_A Phage integrase/site-specific recombinase; alpha-helical domain, structural genomics, PSI-2, protein ST initiative; 1.70A {Haloarcula marismortui} Length = 117 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target348 phage-related integrase/recombinase [Candidatus Liberib
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 100.0
1z19_A283 Integrase; protein-DNA complex, DNA binding protein/DNA 100.0
1a0p_A290 Site-specific recombinase XERD; DNA binding, DNA recomb 100.0
2a3v_A320 Site-specific recombinase INTI4; protein-DNA complex, r 100.0
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 99.95
3nkh_A244 Integrase; alpha-fold, MRSA protein, structural genomic 99.92
1aih_A170 HP1 integrase; DNA integration, recombination; 2.50A {H 99.9
1ae9_A179 Lambda integrase; DNA recombination, site-specific reco 99.84
2kob_A108 Uncharacterized protein; alpha beta, structural genomic 99.63
2oxo_A103 Integrase; DNA-binding protein, four-helix bundle, DNA 99.58
2kiw_A111 INT protein; alpha, structural genomics, PSI-2, protein 99.55
2khq_A110 Integrase; all-alpha, structural genomics, PSI-2, prote 99.54
3lys_A112 Prophage PI2 protein 01, integrase; helical N-terminal 99.5
2kd1_A118 DNA integration/recombination/invertion protein; protei 99.45
2kkp_A117 Phage integrase; SAM-like domain, alpha-helical bundle, 99.44
2kj9_A118 Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structur 99.37
3nrw_A117 Phage integrase/site-specific recombinase; alpha-helica 99.36
2kj8_A118 Putative prophage CPS-53 integrase; INTS, INTC, YFDB, D 99.33
2kkv_A121 Integrase; protein structure, PSI, nesgc, structural ge 99.31
2kj5_A116 Phage integrase; GFT NMR, PSI-2, NESG, structural genom 99.29
2key_A112 Putative phage integrase; protein structure, PSI, NESG, 99.23
2khv_A106 Phage integrase; solution structure, GFT, NESG, structu 99.15
2v6e_A558 Protelemorase; hairpin telomere, hydrolase, resolvase, 97.3
3m4a_A346 Putative type I topoisomerase; type IB, topib, protein- 96.06
2h7g_X314 DNA topoisomerase 1; type IB topoisomerase, DNA binding 91.53
>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} SCOP: d.10.1.4 d.163.1.1 PDB: 1z1g_A 1kjk_A 2wcc_3* Back     alignment and structure
Probab=100.00  E-value=0  Score=315.49  Aligned_cols=316  Identities=18%  Similarity=0.239  Sum_probs=245.6

Q ss_pred             CCCCCCCCEEEECCCCCEEEEEE-ECCCCEEECCCCCCHHHHHHHH---HHHHCCCCCHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             88887981896228993899997-0895657558899988999999---9985343101231023234487899999999
Q gi|254780134|r    4 SLRLPPFVTKERTRHGKIIYYFR-KGHGRRIRLPYPHESTFIPAYM---SALTGSTPKREYINSPRKKPTTLKWLISEYR   79 (348)
Q Consensus         4 ~~~~p~~v~~~~~r~G~~~~~~r-~~~~~~~~~~~~~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~Tl~~l~~~y~   79 (348)
                      ++.+||++++..  +|  +|+|+ ...|+.+.++.........+..   .....................||.++++.|+
T Consensus         9 ~~~~P~~~y~r~--~g--~~~~r~~~~gk~~~lg~~~~~a~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~   84 (356)
T 1z1b_A            9 RRDLPPNLYIRN--NG--YYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYE   84 (356)
T ss_dssp             CCCCCTTEEEET--TT--EEEEECTTTCCEEEEESCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHSCBHHHHHHHHH
T ss_pred             CCCCCCCEEEEC--CE--EEEEEECCCCEEEECCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             889999889739--98--99999789997986899999999999999999986744035566532455752999999999


Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             835543569788999999999999995699958969999999887515--997899999999999996445520010566
Q gi|254780134|r   80 KSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRK--HTPSSAIQFLTSMRVLFKWAVRQEYVAINP  157 (348)
Q Consensus        80 ~~~~~~~l~~~T~~~~~~~~~~~~~~~g~~~l~~it~~~i~~~~~~~~--~~~~t~n~~~~~l~~~~~~a~~~~~i~~NP  157 (348)
                      .......++++|+.+|...+++|.+.||+.++.+|+..+|.+|++.+.  .++.|+|++++.|+++|+||++.+++..||
T Consensus        85 ~~~~~~~~~~~T~~~y~~~~~~l~~~~g~~~l~~it~~~i~~~~~~~~~~~~~~t~~~~~~~l~~~~~~a~~~~~~~~np  164 (356)
T 1z1b_A           85 KILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNH  164 (356)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHHHHHHHSCSCBGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTTSCSSCT
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99886599999999999999999999769996878999999999999984999999999999999999999851212481


Q ss_pred             HHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC-CHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHHC
Q ss_conf             51034643244442116523445666640378-08999989898618873100256640144302332113310243311
Q gi|254780134|r  158 CLSVERPKRKTEGIRPWTKEDMQQFKSFWSEG-SQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVE  236 (348)
Q Consensus       158 ~~~v~~~~~~~~~~~~~t~~ei~~~~~~~~~~-~~~~~~~~l~~~TG~R~~Ei~~L~~~did~~~i~~~~~Kt~~~~~vp  236 (348)
                      +..++.++.+... ..++.+|+..|++.+... ...++++.|+++||||.+|+++|+|+|||++.+.+..+|++....+|
T Consensus       165 ~~~~~~~~~~~~~-~~lt~~E~~~l~~~~~~~~~~~~~~~~l~~~tG~R~~Ei~~L~~~di~~~~~~i~~~K~~~~~~~p  243 (356)
T 1z1b_A          165 VAATRAAKSKVRR-SRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIP  243 (356)
T ss_dssp             TTTSCCCCCCCCB-CCCCHHHHHHHHHHTTSSCHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTEEEEECTTTCCEEEEE
T ss_pred             HHHHHCCCCCCCC-CCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHCCCHHHHCCCCEEEEECCCCCEEEEC
T ss_conf             5432012235778-768989987875201247657899999999968785457509299922464599988888424602


Q ss_pred             CH-------HHHHHHHHHHC--CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC-----CCCCHHHHHHHHHHHHCCC
Q ss_conf             21-------68999996420--1332211222457758778999999999983889-----9814026999999998489
Q gi|254780134|r  237 LP-------DGFMKLLAMTP--IGKETFFINNDKQKMNATQFSIWFKAKATKAGVN-----KSAHGVRKFSATISADAGA  302 (348)
Q Consensus       237 l~-------~~l~~~l~~~~--~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~agi~-----~~~H~lRht~at~l~~~G~  302 (348)
                      +.       ..+.+.+....  ..+..+|++..|+|++.++++..|+++|+.+|++     .++|+|||+ ||.+.++|+
T Consensus       244 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~~t~H~lRh~-a~~l~~~g~  322 (356)
T 1z1b_A          244 TALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSL-SARLYEKQI  322 (356)
T ss_dssp             TTCEETTTTEEHHHHHHHHHHHTCSSBSSCCTTSCCCCHHHHHHHHHHHHHHHTCCCSSBCCCTTHHHHH-HHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH-HHHHHHCCC
T ss_conf             7187899999999999864401577650011346667778999999999998599988899975868999-999998699


Q ss_pred             CHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             98899999649998999999999
Q gi|254780134|r  303 TAHELMATYGWKTVDQAETYTKG  325 (348)
Q Consensus       303 ~~~~i~~~lGHss~~~t~~Y~~~  325 (348)
                      ++.+|+++|||+|..||++|.+.
T Consensus       323 ~~~~i~~~lGH~~~~~t~~Y~~~  345 (356)
T 1z1b_A          323 SDKFAQHLLGHKSDTMASQYRDD  345 (356)
T ss_dssp             CHHHHHHHHTCSSHHHHHHHTCC
T ss_pred             CHHHHHHHHCCCCHHHHHHHCCC
T ss_conf             99999988189998999988047



>1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* Back     alignment and structure
>1a0p_A Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} SCOP: a.60.9.1 d.163.1.1 Back     alignment and structure
>2a3v_A Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Back     alignment and structure
>1xo0_A Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1} SCOP: a.60.9.1 d.163.1.1 PDB: 3crx_A* 1kbu_A 1ma7_A 1q3u_A* 1q3v_A* 3mgv_A* 1ouq_A* 1nzb_A* 2crx_A* 1xns_A 5crx_A* 1f44_A* 2hof_A 2hoi_A 4crx_A* 1drg_A 3c29_A* 3c28_A 1crx_A* 1pvr_A ... Back     alignment and structure
>3nkh_A Integrase; alpha-fold, MRSA protein, structural genomics, PSI-2, protei structure initiative; 2.50A {Staphylococcus aureus subsp} Back     alignment and structure
>1aih_A HP1 integrase; DNA integration, recombination; 2.50A {Haemophilus phage HP1} SCOP: d.163.1.1 Back     alignment and structure
>1ae9_A Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Enterobacteria phage lambda} SCOP: d.163.1.1 Back     alignment and structure
>2kob_A Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753} Back     alignment and structure
>2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage} Back     alignment and structure
>2kiw_A INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435} Back     alignment and structure
>2khq_A Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp} Back     alignment and structure
>3lys_A Prophage PI2 protein 01, integrase; helical N-terminal domain, structural genomics, PSI-2, protein structure initiative; 2.80A {Lactococcus lactis} Back     alignment and structure
>2kd1_A DNA integration/recombination/invertion protein; protein structure initiative, structural genomics, unknown function, PSI-2; HET: DNA; NMR {Bacillus cereus atcc 14579} Back     alignment and structure
>2kkp_A Phage integrase; SAM-like domain, alpha-helical bundle, structural genomics, PSI-2, protein structure initiative; NMR {Moorella thermoacetica atcc 39073} Back     alignment and structure
>2kj9_A Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} Back     alignment and structure
>3nrw_A Phage integrase/site-specific recombinase; alpha-helical domain, structural genomics, PSI-2, protein ST initiative; 1.70A {Haloarcula marismortui} Back     alignment and structure
>2kj8_A Putative prophage CPS-53 integrase; INTS, INTC, YFDB, DNA integration, DNA recombination, structural genomics, protein structure initiative; NMR {Escherichia coli k-12} Back     alignment and structure
>2kkv_A Integrase; protein structure, PSI, nesgc, structural genomics, protein structure initiative, northeast structural genomics consortium; NMR {Salmonella enterica subsp} Back     alignment and structure
>2kj5_A Phage integrase; GFT NMR, PSI-2, NESG, structural genomics, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196} Back     alignment and structure
>2key_A Putative phage integrase; protein structure, PSI, NESG, structural genomics, unknown function, protein structure initiative; NMR {Bacteroides fragilis nctc 9343} Back     alignment and structure
>2khv_A Phage integrase; solution structure, GFT, NESG, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196} Back     alignment and structure
>2v6e_A Protelemorase; hairpin telomere, hydrolase, resolvase, protelomerase, DNA distortion; 3.20A {Klebsiella phage PHIKO2} Back     alignment and structure
>3m4a_A Putative type I topoisomerase; type IB, topib, protein-DNA complex, isomerase-DNA complex; HET: DNA; 1.65A {Deinococcus radiodurans} PDB: 2f4q_A* Back     alignment and structure
>2h7g_X DNA topoisomerase 1; type IB topoisomerase, DNA binding, protein-DNA complex, isomerase/DNA complex; HET: DNA; 1.90A {Variola virus} PDB: 2h7f_X* 3igc_A* 1a41_A 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 348 phage-related integrase/recombinase [Candidatus Liberib
d1a0pa2182 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia col 2e-04
>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]} Length = 182 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: DNA breaking-rejoining enzymes
superfamily: DNA breaking-rejoining enzymes
family: Lambda integrase-like, catalytic core
domain: Recombinase XerD
species: Escherichia coli [TaxId: 562]
 Score = 40.4 bits (93), Expect = 2e-04
 Identities = 26/146 (17%), Positives = 48/146 (32%), Gaps = 14/146 (9%)

Query: 193 RLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGT-----------IITVELPDGF 241
           +   E L  +GLR S+     +  +      ++    G            +  +E     
Sbjct: 26  KAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEH 85

Query: 242 MKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNK---SAHGVRKFSATISA 298
            +   +  +  +  F +   Q+M    F    K  A  AG++    S H +R   AT   
Sbjct: 86  GRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLL 145

Query: 299 DAGATAHELMATYGWKTVDQAETYTK 324
           + GA    +    G   +   + YT 
Sbjct: 146 NHGADLRVVQMLLGHSDLSTTQIYTH 171


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

IdentityAlignment graphLength Definition Probability
Target348 phage-related integrase/recombinase [Candidatus Liberib
d1aiha_170 Integrase {Bacteriophage HP1 [TaxId: 10690]} 99.91
d1a0pa2182 Recombinase XerD {Escherichia coli [TaxId: 562]} 99.88
d1ae9a_179 Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} 99.85
d1f44a2214 Cre recombinase {Bacteriophage P1 [TaxId: 10678]} 99.83
d1a41a_230 Eukaryotic DNA topoisomerase I, catalytic core {Vaccini 92.54
d1a0pa198 Recombinase XerD {Escherichia coli [TaxId: 562]} 98.88
d1f44a1110 Cre recombinase {Bacteriophage P1 [TaxId: 10678]} 97.31
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: DNA breaking-rejoining enzymes
superfamily: DNA breaking-rejoining enzymes
family: Lambda integrase-like, catalytic core
domain: Integrase
species: Bacteriophage HP1 [TaxId: 10690]
Probab=99.91  E-value=6e-25  Score=177.74  Aligned_cols=149  Identities=15%  Similarity=0.134  Sum_probs=115.6

Q ss_pred             CCCCCCHHHHHHHHHHHCC--CCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHHCCHHHHHHHHHH
Q ss_conf             4211652344566664037--80899998989861887310025664014430233211331024331121689999964
Q gi|254780134|r  170 GIRPWTKEDMQQFKSFWSE--GSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAM  247 (348)
Q Consensus       170 ~~~~~t~~ei~~~~~~~~~--~~~~~~~~~l~~~TG~R~~Ei~~L~~~did~~~i~~~~~Kt~~~~~vpl~~~l~~~l~~  247 (348)
                      +...++++|+.+|++.+..  ....++++.|+++||||++|+++|+|+||+++.+.+...|+++.+.|||++.+.++|..
T Consensus         3 ~~~~Lt~eEi~~l~~~~~~~~~~~~~~~i~l~~~tG~R~~E~~~L~~~dI~~~~~~~~~~K~~~~r~ipl~~~~~~~l~~   82 (170)
T d1aiha_           3 ELAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTKSKKNRTVPISDELFDMLPK   82 (170)
T ss_dssp             CCCCCCHHHHHHHHHHHTTSSSTTHHHHHHHHHHHCCCHHHHHTCBTTTEETTEEEEESSSSSCEEEEECCHHHHHHSCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             46689999999999986365896699999999997776112444331024421102114444300577669999999875


Q ss_pred             HCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             20133221122245775877899999999998388998140269999999984899889999964999899999999998
Q gi|254780134|r  248 TPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTKGAD  327 (348)
Q Consensus       248 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~agi~~~~H~lRht~at~l~~~G~~~~~i~~~lGHss~~~t~~Y~~~~~  327 (348)
                      .   ....|      +.....+...+.+.....+...++|+|||||+|.|.++|+++.+|+.+|||++..||++|++..+
T Consensus        83 ~---~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~~g~~~~~i~~~lGH~~~~~t~~Y~~~~~  153 (170)
T d1aiha_          83 K---RGRLF------NDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAP  153 (170)
T ss_dssp             C---SSBSS------CCCHHHHHHHHHHTTCCCCTTCTTTHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHGGGGGGSC
T ss_pred             H---HCCCC------CCCHHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHCCCH
T ss_conf             1---00110------11112443345666502577610111046551455216989999999808999899998876799



>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} Back     information, alignment and structure
>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]} Back     information, alignment and structure
>d1a41a_ d.163.1.2 (A:) Eukaryotic DNA topoisomerase I, catalytic core {Vaccinia virus [TaxId: 10245]} Back     information, alignment and structure
>d1a0pa1 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1f44a1 a.60.9.1 (A:20-129) Cre recombinase {Bacteriophage P1 [TaxId: 10678]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 348 phage-related integrase/recombinase [Candidatus Li
2kob_A_108 (A:) Uncharacterized protein; alpha beta, structur 1e-10
2kiw_A_111 (A:) INT protein; alpha, structural genomics, PSI- 2e-10
2oxo_A_103 (A:) Integrase; DNA-binding protein, four-helix bu 4e-10
2kd1_A_118 (A:) DNA integration/recombination/invertion prote 4e-10
2khq_A_110 (A:) Integrase; all-alpha, structural genomics, PS 7e-10
2key_A_112 (A:) Putative phage integrase; protein structure, 2e-09
2kkv_A_121 (A:) Integrase; protein structure, PSI, nesgc, str 6e-09
1z19_A_1-9393 (A:1-93) Integrase; protein-DNA complex, DNA bindi 6e-09
2kj8_A_118 (A:) Putative prophage CPS-53 integrase; INTS, INT 1e-08
1z1b_A_75-16692 (A:75-166) Integrase; protein-DNA complex, DNA bin 2e-08
2khv_A_106 (A:) Phage integrase; solution structure, GFT, NES 2e-08
2kj5_A_116 (A:) Phage integrase; GFT NMR, PSI-2, NESG, struct 5e-08
2kkp_A_27-11791 (A:27-117) Phage integrase; SAM-like domain, alpha 1e-07
2kj9_A_118 (A:) Integrase; DNA_BRE_C superfamily, INTB, PSI-2 2e-07
1a0p_A_1-100100 (A:1-100) Site-specific recombinase XERD; DNA bind 1e-04
2a3v_A_1-9494 (A:1-94) Site-specific recombinase INTI4; protein- 9e-04
1xo0_A_1-114114 (A:1-114) Recombinase CRE; CRE recombinase, hollid 0.001
1a0p_A_101-290190 (A:101-290) Site-specific recombinase XERD; DNA bi 4e-06
1ae9_A_179 (A:) Lambda integrase; DNA recombination, site-spe 5e-06
1z19_A_94-283190 (A:94-283) Integrase; protein-DNA complex, DNA bin 1e-05
1z1b_A_167-356190 (A:167-356) Integrase; protein-DNA complex, DNA bi 3e-04
>2kob_A (A:) Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753}Length = 108 Back     alignment and structure
 Score = 61.9 bits (150), Expect = 1e-10
 Identities = 16/99 (16%), Positives = 36/99 (36%)

Query: 69  TTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKH 128
            +      ++ KS     ++V+   S+++Y    +         +I    I+S +   K 
Sbjct: 2   DSFGDWAEKFLKSKEADGVSVSQLNSYKNYCRNHLSPLYMKSLSEILPADIQSIINETKL 61

Query: 129 TPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRK 167
             ++      +   +F+ A+    +  NP   V  PK  
Sbjct: 62  AKNTLKAIRNTASQIFRLAIENRAIDFNPADYVRIPKIA 100


>2kiw_A (A:) INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435}Length = 111 Back     alignment and structure
>2oxo_A (A:) Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage}Length = 103 Back     alignment and structure
>2kd1_A (A:) DNA integration/recombination/invertion protein; protein structure initiative, structural genomics, unknown function, PSI-2; HET: DNA; NMR {Bacillus cereus atcc 14579}Length = 118 Back     alignment and structure
>2khq_A (A:) Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp}Length = 110 Back     alignment and structure
>2key_A (A:) Putative phage integrase; protein structure, PSI, NESG, structural genomics, unknown function, protein structure initiative; NMR {Bacteroides fragilis nctc 9343}Length = 112 Back     alignment and structure
>2kkv_A (A:) Integrase; protein structure, PSI, nesgc, structural genomics, protein structure initiative, northeast structural genomics consortium; NMR {Salmonella enterica subsp}Length = 121 Back     alignment and structure
>1z19_A (A:1-93) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A*Length = 93 Back     alignment and structure
>2kj8_A (A:) Putative prophage CPS-53 integrase; INTS, INTC, YFDB, DNA integration, DNA recombination, structural genomics, protein structure initiative; NMR {Escherichia coli k-12}Length = 118 Back     alignment and structure
>1z1b_A (A:75-166) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda}Length = 92 Back     alignment and structure
>2khv_A (A:) Phage integrase; solution structure, GFT, NESG, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196}Length = 106 Back     alignment and structure
>2kj5_A (A:) Phage integrase; GFT NMR, PSI-2, NESG, structural genomics, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196}Length = 116 Back     alignment and structure
>2kkp_A (A:27-117) Phage integrase; SAM-like domain, alpha-helical bundle, structural genomics, PSI-2, protein structure initiative; NMR {Moorella thermoacetica atcc 39073}Length = 91 Back     alignment and structure
>2kj9_A (A:) Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum}Length = 118 Back     alignment and structure
>1a0p_A (A:1-100) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli}Length = 100 Back     alignment and structure
>2a3v_A (A:1-94) Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str}Length = 94 Back     alignment and structure
>1xo0_A (A:1-114) Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1}Length = 114 Back     alignment and structure
>1a0p_A (A:101-290) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli}Length = 190 Back     alignment and structure
>1ae9_A (A:) Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda}Length = 179 Back     alignment and structure
>1z19_A (A:94-283) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A*Length = 190 Back     alignment and structure
>1z1b_A (A:167-356) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda}Length = 190 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target348 phage-related integrase/recombinase [Candidatus Liberib
1z1b_A_167-356190 Integrase; protein-DNA complex, DNA binding protei 99.87
1a0p_A_101-290190 Site-specific recombinase XERD; DNA binding, DNA r 99.85
1xo0_A_115-310196 Recombinase CRE; CRE recombinase, holliday junctio 99.84
1z19_A_94-283190 Integrase; protein-DNA complex, DNA binding protei 99.83
2a3v_A_95-144_243-320128 Site-specific recombinase INTI4; protein-DNA compl 99.81
1ae9_A_179 Lambda integrase; DNA recombination, site-specific 99.78
1aih_A_1-49_87-170133 HP1 integrase; DNA integration, recombination; 2.5 99.71
2kiw_A_111 INT protein; alpha, structural genomics, PSI-2, pr 99.62
2kob_A_108 Uncharacterized protein; alpha beta, structural ge 99.62
2oxo_A_103 Integrase; DNA-binding protein, four-helix bundle, 99.57
2khq_A_110 Integrase; all-alpha, structural genomics, PSI-2, 99.57
2kd1_A_118 DNA integration/recombination/invertion protein; p 99.54
2khv_A_106 Phage integrase; solution structure, GFT, NESG, st 99.53
2key_A_112 Putative phage integrase; protein structure, PSI, 99.51
2kkv_A_121 Integrase; protein structure, PSI, nesgc, structur 99.48
2kj9_A_118 Integrase; DNA_BRE_C superfamily, INTB, PSI-2, str 99.48
2kj8_A_118 Putative prophage CPS-53 integrase; INTS, INTC, YF 99.46
1z19_A_1-9393 Integrase; protein-DNA complex, DNA binding protei 99.46
1z1b_A_75-16692 Integrase; protein-DNA complex, DNA binding protei 99.45
2kj5_A_116 Phage integrase; GFT NMR, PSI-2, NESG, structural 99.42
2a3v_A_1-9494 Site-specific recombinase INTI4; protein-DNA compl 99.2
1a0p_A_1-100100 Site-specific recombinase XERD; DNA binding, DNA r 99.15
1xo0_A_1-114114 Recombinase CRE; CRE recombinase, holliday junctio 99.13
2kkp_A_27-11791 Phage integrase; SAM-like domain, alpha-helical bu 99.08
3ju0_A_108 Phage integrase; four stranded beta-sheet, DNA bin 91.08
>1z1b_A (A:167-356) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} Back     alignment and structure
Probab=99.87  E-value=3.6e-21  Score=155.73  Aligned_cols=163  Identities=13%  Similarity=0.131  Sum_probs=121.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCC-CCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEC--CCCCCCCCHHHHH--HCC
Q ss_conf             64324444211652344566664037-808999989898618873100256640144302--3321133102433--112
Q gi|254780134|r  163 RPKRKTEGIRPWTKEDMQQFKSFWSE-GSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNI--FSIKTQKTGTIIT--VEL  237 (348)
Q Consensus       163 ~~~~~~~~~~~~t~~ei~~~~~~~~~-~~~~~~~~~l~~~TG~R~~Ei~~L~~~did~~~--i~~~~~Kt~~~~~--vpl  237 (348)
                      +++.......+++++|+.+|++++.. +...++++.|+++||||.||+++|+|+|||...  +.+...+++....  .+.
T Consensus         3 k~k~~~~~~~~lt~eei~~l~~~~~~~~~~~~~~~~l~~~tGlR~~E~~~l~~~di~~~~~~~~~~~~~~~~~~~~~~~~   82 (190)
T 1z1b_A            3 RAAKSKVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHI   82 (190)
T ss_dssp             CCCCCCCCBCCCCHHHHHHHHHHTTSSCHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTEEEEECTTTCCEEEEETTCEE
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCH
T ss_conf             22233443322203667664201224550245788999874124466433332212232222223444330212554210


Q ss_pred             H----HHHHHHH-HHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC----CCCCHHHHHHHHHHHHCCCCHHHHH
Q ss_conf             1----6899999-64201332211222457758778999999999983889----9814026999999998489988999
Q gi|254780134|r  238 P----DGFMKLL-AMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVN----KSAHGVRKFSATISADAGATAHELM  308 (348)
Q Consensus       238 ~----~~l~~~l-~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~agi~----~~~H~lRht~at~l~~~G~~~~~i~  308 (348)
                      .    ..+.... .........+|.+..+...........+..+...++..    ...|.+||||||.|.++|+++..|+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~t~at~l~~~g~~~~~i~  162 (190)
T 1z1b_A           83 DALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQ  162 (190)
T ss_dssp             TTTTEEHHHHHHHHHHHTCSSBSSCCTTSCCCCHHHHHHHHHHHHHHHTCCCSSBCCCTTHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHH
T ss_conf             25677654433310345777314115567757888999999999998599978899974828999999998699999999


Q ss_pred             HHHCCCCHHHHHHHHHH
Q ss_conf             99649998999999999
Q gi|254780134|r  309 ATYGWKTVDQAETYTKG  325 (348)
Q Consensus       309 ~~lGHss~~~t~~Y~~~  325 (348)
                      ++|||+|..||++|...
T Consensus       163 ~~lGH~~~~~T~~yy~~  179 (190)
T 1z1b_A          163 HLLGHKSDTMASQXRDD  179 (190)
T ss_dssp             HHHTCSSHHHHHHHTCC
T ss_pred             HHHCCCCHHHHHHHHCC
T ss_conf             98389988999988327



>1a0p_A (A:101-290) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} Back     alignment and structure
>1xo0_A (A:115-310) Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1} Back     alignment and structure
>1z19_A (A:94-283) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* Back     alignment and structure
>2a3v_A (A:95-144,A:243-320) Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Back     alignment and structure
>1ae9_A (A:) Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda} Back     alignment and structure
>1aih_A (A:1-49,A:87-170) HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1} Back     alignment and structure
>2kiw_A (A:) INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435} Back     alignment and structure
>2kob_A (A:) Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753} Back     alignment and structure
>2oxo_A (A:) Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage} Back     alignment and structure
>2khq_A (A:) Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp} Back     alignment and structure
>2kd1_A (A:) DNA integration/recombination/invertion protein; protein structure initiative, structural genomics, unknown function, PSI-2; HET: DNA; NMR {Bacillus cereus atcc 14579} Back     alignment and structure
>2khv_A (A:) Phage integrase; solution structure, GFT, NESG, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196} Back     alignment and structure
>2key_A (A:) Putative phage integrase; protein structure, PSI, NESG, structural genomics, unknown function, protein structure initiative; NMR {Bacteroides fragilis nctc 9343} Back     alignment and structure
>2kkv_A (A:) Integrase; protein structure, PSI, nesgc, structural genomics, protein structure initiative, northeast structural genomics consortium; NMR {Salmonella enterica subsp} Back     alignment and structure
>2kj9_A (A:) Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} Back     alignment and structure
>2kj8_A (A:) Putative prophage CPS-53 integrase; INTS, INTC, YFDB, DNA integration, DNA recombination, structural genomics, protein structure initiative; NMR {Escherichia coli k-12} Back     alignment and structure
>1z19_A (A:1-93) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* Back     alignment and structure
>1z1b_A (A:75-166) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} Back     alignment and structure
>2kj5_A (A:) Phage integrase; GFT NMR, PSI-2, NESG, structural genomics, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196} Back     alignment and structure
>2a3v_A (A:1-94) Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Back     alignment and structure
>1a0p_A (A:1-100) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} Back     alignment and structure
>1xo0_A (A:1-114) Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1} Back     alignment and structure
>2kkp_A (A:27-117) Phage integrase; SAM-like domain, alpha-helical bundle, structural genomics, PSI-2, protein structure initiative; NMR {Moorella thermoacetica atcc 39073} Back     alignment and structure
>3ju0_A (A:) Phage integrase; four stranded beta-sheet, DNA binding protein; 1.60A {Pectobacterium atrosepticum} Back     alignment and structure