254780882

254780882

site-specific tyrosine recombinase XerC

GeneID in NCBI database:8209902Locus tag:CLIBASIA_03895
Protein GI in NCBI database:254780882Protein Accession:YP_003065295.1
Gene range:-(859804, 860790)Protein Length:328aa
Gene description:site-specific tyrosine recombinase XerC
COG prediction:[L] Integrase
KEGG prediction:xerC; site-specific tyrosine recombinase XerC; K03733 integrase/recombinase XerC
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
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------33
MEGNNLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKDKKN
cccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccHHHHHcccHHHccccccEEEEEcccccEEEEEccHHHHHHHHHHHHHHHHcccccccccEEEccccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHccHHHHHHHHHHHHHHHccccccccccc
cccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccccccHccccccccccccccccHHHHHHHHHccccccccccccHcHHHHHHHHHHHHHcccEEHHEEccccccEccccEEEEEcccccEEEEcccHHHHHHHHHHHHHcHHHHccccccEEEEccccccccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHccccHHHHHHHHccccccccEEEEcccHHHHcHHHHHHHHHHccccccccccc
megnnlpeiVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMrnlkksnslpralneKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLrisealsltpqnimddqstlriqgkgdkirivpllpSVRKAILEYYdlcpfdlnlniqlplfrgirgkplnpgvFQRYIRQLRRYlglplsttahtLRHSFATHllsnggdlRSIQSILGHFRLSTTQIYTnvnsknggdWMMEIYdqthpsitqkdkkn
megnnlpeIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAfiskrrtqkigdrslkrslsgiKSFLKYLKKRkittesnilnmrnlkksnslprALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLriqgkgdkirivpllPSVRKAILEYYDLCPFDLNLNIQLPLfrgirgkplnpGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDqthpsitqkdkkn
MEGNNLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKDKKN
***********FELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFIS***************LSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQ************
MEGNNLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKDKKN
*****LPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHP*********
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MEGNNLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKDKKN
MEGNNLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKDKKN
MEGNNLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQKDKKN

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
25478049067 site-specific tyrosine recombinase XerC [Candidatu 3e-31
255764498300 site-specific tyrosine recombinase XerD [Candidatu 1e-25
>gi|254780490|ref|YP_003064903.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62] Length = 67 Back     alignment
 Score =  127 bits (318), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 64/71 (90%), Positives = 65/71 (91%), Gaps = 4/71 (5%)

Query: 258 LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQT 317
           +STTAHTLRHSFATHLLSNGGDLRSIQSILGH RLSTTQIYTNVNSK     MMEIYDQT
Sbjct: 1   MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKR----MMEIYDQT 56

Query: 318 HPSITQKDKKN 328
           HPSITQKDKKN
Sbjct: 57  HPSITQKDKKN 67

>gi|255764498|ref|YP_003065000.2| site-specific tyrosine recombinase XerD [Candidatus Liberibacter asiaticus str. psy62] Length = 300 Back     alignment
 Score =  108 bits (271), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 88/305 (28%), Positives = 156/305 (51%), Gaps = 15/305 (4%)

Query: 28  ERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRS 87
           ER  S  TL +Y+ D ++   FL     ++I++      S   + ++++    +K+   S
Sbjct: 5   ERASSINTLSAYKRDLKEMQNFL---NNKEISLSAA---STNHLISYLNHLSQRKLVTSS 58

Query: 88  LKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSH 147
            +R +S I+ F  +L    +  ++    +   KK++ LP+ L++     L++   +   +
Sbjct: 59  QRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAEN 118

Query: 148 ET--KWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPS 205
               +W   R   ++ LLY  G+R+SE ++L+   +   + T+ IQGKG+K R+V L PS
Sbjct: 119 PAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPS 178

Query: 206 VRKAILEYYDLCPFDLNLNIQLPLF-RGIRGKPLNPGVFQRYIRQLRRYLGL-PLSTTAH 263
              A+  Y   C         L LF    +   L+  VF R ++ L    G+   + + H
Sbjct: 179 ALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPH 238

Query: 264 TLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSITQ 323
            +RH+FA+HLL  G DLR+IQ +LGH  +STTQIYT++      D + ++    HP + +
Sbjct: 239 IIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHL----LPDKLQKLVQDYHP-LAK 293

Query: 324 KDKKN 328
           K+KK+
Sbjct: 294 KEKKH 298

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

IdentityAlignment graphLength Definition Round E-value
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
315122698324 site-specific tyrosine recombinase XerC [Candidatus Lib 1 1e-123
222150032322 site-specific tyrosine recombinase XerC [Agrobacterium 1 5e-80
190893726311 tyrosine site-specific integrase/recombinase [Rhizobium 1 7e-80
86359460311 site-specific tyrosine recombinase XerC [Rhizobium etli 1 9e-80
241206644311 site-specific tyrosine recombinase XerC [Rhizobium legu 1 6e-79
209551233311 site-specific tyrosine recombinase XerC [Rhizobium legu 1 8e-79
222087447311 tyrosine recombinase XerC [Agrobacterium radiobacter K8 1 8e-79
325293997311 site-specific tyrosine recombinase XerC [Agrobacterium 1 9e-78
116254158299 site-specific tyrosine recombinase XerC [Rhizobium legu 1 2e-77
150398130313 site-specific tyrosine recombinase XerC [Sinorhizobium 1 3e-75
>gi|315122698|ref|YP_004063187.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 324 Back     alignment and organism information
 Score =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 235/327 (71%), Positives = 279/327 (85%), Gaps = 7/327 (2%)

Query: 1   MEGNNLPEIVSFELLKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITI 60
           ME  NL EIV+ ELL+ERQNWL +L++E GLSKLTLQSYE D RQFL F+AFYT EKI +
Sbjct: 1   MERKNLHEIVTTELLEERQNWLNSLKVEHGLSKLTLQSYERDMRQFLTFMAFYTGEKIDL 60

Query: 61  QTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLK 120
           Q +RQL YT+IRAF+SKRR   I +RSL RSLSGI+SFLKYLKKR+IT E+NILNM+NLK
Sbjct: 61  QAMRQLLYTDIRAFVSKRRLHGIENRSLTRSLSGIRSFLKYLKKRQITGEANILNMKNLK 120

Query: 121 KSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQN 180
           KSNSLP+ L+EKQAL L+ N  ++T ++TKWI+ARNSAILYLLYGCGLRISE LSLTPQN
Sbjct: 121 KSNSLPKPLSEKQALNLI-NYDINTHNDTKWINARNSAILYLLYGCGLRISETLSLTPQN 179

Query: 181 IMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNP 240
           I+DD+S+LRI GKG+K RIVPLL SVR+ I++YY LCPFD  L+I+LPLFRG RGKPLNP
Sbjct: 180 IIDDESSLRITGKGNKTRIVPLLSSVREIIMKYYTLCPFD--LHIELPLFRGARGKPLNP 237

Query: 241 GVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTN 300
           GVFQRYIR LR+ L LP +TT HTLRHSFATH+LSNGGDLRSIQS+LGH RLS+TQ+YTN
Sbjct: 238 GVFQRYIRYLRQNLSLPTTTTPHTLRHSFATHILSNGGDLRSIQSVLGHARLSSTQVYTN 297

Query: 301 VNSKNGGDWMMEIYDQTHPSITQKDKK 327
           V+SK     ++EIYDQ+HP +T  +KK
Sbjct: 298 VDSKR----IIEIYDQSHPIVTNNNKK 320


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222150032|ref|YP_002550989.1| site-specific tyrosine recombinase XerC [Agrobacterium vitis S4] Length = 322 Back     alignment and organism information
>gi|190893726|ref|YP_001980268.1| tyrosine site-specific integrase/recombinase [Rhizobium etli CIAT 652] Length = 311 Back     alignment and organism information
>gi|86359460|ref|YP_471352.1| site-specific tyrosine recombinase XerC [Rhizobium etli CFN 42] Length = 311 Back     alignment and organism information
>gi|241206644|ref|YP_002977740.1| site-specific tyrosine recombinase XerC [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 311 Back     alignment and organism information
>gi|209551233|ref|YP_002283150.1| site-specific tyrosine recombinase XerC [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 311 Back     alignment and organism information
>gi|222087447|ref|YP_002545984.1| tyrosine recombinase XerC [Agrobacterium radiobacter K84] Length = 311 Back     alignment and organism information
>gi|325293997|ref|YP_004279861.1| site-specific tyrosine recombinase XerC [Agrobacterium sp. H13-3] Length = 311 Back     alignment and organism information
>gi|116254158|ref|YP_769996.1| site-specific tyrosine recombinase XerC [Rhizobium leguminosarum bv. viciae 3841] Length = 299 Back     alignment and organism information
>gi|150398130|ref|YP_001328597.1| site-specific tyrosine recombinase XerC [Sinorhizobium medicae WSM419] Length = 313 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
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
PRK00236297 PRK00236, xerC, site-specific tyrosine recombinase XerC 1e-86
TIGR02224295 TIGR02224, recomb_XerC, tyrosine recombinase XerC 6e-77
TIGR02225291 TIGR02225, recomb_XerD, tyrosine recombinase XerD 3e-54
COG4974300 COG4974, XerD, Site-specific recombinase XerD [DNA repl 3e-52
PRK00283299 PRK00283, xerD, site-specific tyrosine recombinase XerD 3e-51
COG4973299 COG4973, XerC, Site-specific recombinase XerC [DNA repl 3e-42
TIGR02249315 TIGR02249, integrase_gron, integron integrase 5e-25
cd01185299 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA 3e-15
PRK05084357 PRK05084, xerS, site-specific tyrosine recombinase XerS 1e-12
cd00799287 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic 2e-09
cd00798284 cd00798, INT_XerDC, XerD and XerC integrases, DNA break 3e-57
cd01193242 cd01193, INT_IntI, IntI (E2) integrases, site-specific 4e-32
cd01190260 cd01190, INT_SG5, INT_SG5, DNA breaking-rejoining enzym 3e-22
cd01187299 cd01187, INT_SG4, INT_SG4, DNA breaking-rejoining enzym 8e-13
cd00801357 cd00801, INT_P4, Bacteriophage P4 integrase 7e-06
COG0582309 COG0582, XerC, Integrase [DNA replication, recombinatio 1e-05
pfam00589170 pfam00589, Phage_integrase, Phage integrase family 1e-31
cd01182162 cd01182, INT_REC_C, DNA breaking-rejoining enzymes, int 8e-25
PRK01287358 PRK01287, xerC, site-specific tyrosine recombinase XerC 1e-22
cd00397164 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-t 7e-21
cd01188188 cd01188, INT_pAE1, pAE1 and related integrases, DNA bre 8e-16
cd01183196 cd01183, INT_SG1_C, INT_SG1, DNA breaking-rejoining enz 1e-13
cd01189191 cd01189, INT_phiLC3_C, phiLC3 phage and phage-related i 2e-13
cd01197180 cd01197, INT_FimBE_C, FimB and FimE and related protein 2e-10
cd01194186 cd01194, INT_Tn554A_C, Tn544A and related transposases, 1e-08
cd01199205 cd01199, INT_Tn1545_C, Tn1545-related conjugative trans 6e-08
cd01186180 cd01186, INT_SG3_C, INT_SG3, DNA breaking-rejoining enz 2e-07
PRK09871198 PRK09871, PRK09871, tyrosine recombinase; Provisional 1e-05
cd01192177 cd01192, INT_P22_C, P22-like integrases, site-specific 3e-05
PRK09870200 PRK09870, PRK09870, tyrosine recombinase; Provisional 6e-05
cd00800162 cd00800, INT_Lambda_C, Lambda integrase, C-terminal cat 2e-04
cd00797158 cd00797, HP1_INT_C, Phage HP1 integrase, C-terminal cat 2e-14
PRK15417337 PRK15417, PRK15417, integrase/recombinase; Provisional 2e-12
PHA02601333 PHA02601, int, integrase; Provisional 3e-12
cd01196263 cd01196, INT_VanD, VanD integrase, IntD, and related in 2e-06
cd01195195 cd01195, INT_Tn544B_C, Tn544B and related transposases, 6e-05
cd01184181 cd01184, INT_SG2_C, INT_SG2, DNA breaking-rejoining enz 2e-04
cd01198186 cd01198, INT_ASSRA_C, Archaeal site-specific recombinas 8e-04
pfam0289983 pfam02899, Phage_integr_N, Phage integrase, N-terminal 2e-08
>gnl|CDD|178942 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed 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|34580 COG4974, XerD, Site-specific recombinase XerD [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed Back     alignment and domain information
>gnl|CDD|34579 COG4973, XerC, Site-specific recombinase XerC [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|131303 TIGR02249, integrase_gron, integron integrase 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|179927 PRK05084, xerS, site-specific tyrosine recombinase XerS; Reviewed Back     alignment and domain information
>gnl|CDD|29500 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic domain 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|29514 cd01193, INT_IntI, IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains Back     alignment and domain information
>gnl|CDD|29511 cd01190, INT_SG5, INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains Back     alignment and domain information
>gnl|CDD|29508 cd01187, INT_SG4, INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains Back     alignment and domain information
>gnl|CDD|29502 cd00801, INT_P4, Bacteriophage P4 integrase Back     alignment and domain information
>gnl|CDD|30927 COG0582, XerC, Integrase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|144254 pfam00589, Phage_integrase, Phage integrase family 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|179273 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed 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|29509 cd01188, INT_pAE1, pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain Back     alignment and domain information
>gnl|CDD|29504 cd01183, INT_SG1_C, INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|29510 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
>gnl|CDD|29518 cd01197, INT_FimBE_C, FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain Back     alignment and domain information
>gnl|CDD|29515 cd01194, INT_Tn554A_C, Tn544A and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|29520 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
>gnl|CDD|29507 cd01186, INT_SG3_C, INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain Back     alignment and domain information
>gnl|CDD|182126 PRK09871, PRK09871, tyrosine recombinase; Provisional Back     alignment and domain information
>gnl|CDD|29513 cd01192, INT_P22_C, P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|182125 PRK09870, PRK09870, tyrosine recombinase; Provisional Back     alignment and domain information
>gnl|CDD|29501 cd00800, INT_Lambda_C, Lambda integrase, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|29498 cd00797, HP1_INT_C, Phage HP1 integrase, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|185315 PRK15417, PRK15417, integrase/recombinase; Provisional Back     alignment and domain information
>gnl|CDD|164996 PHA02601, int, integrase; Provisional Back     alignment and domain information
>gnl|CDD|29517 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
>gnl|CDD|29516 cd01195, INT_Tn544B_C, Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain Back     alignment and domain information
>gnl|CDD|29505 cd01184, INT_SG2_C, INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain Back     alignment and domain information
>gnl|CDD|29519 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
>gnl|CDD|145844 pfam02899, Phage_integr_N, Phage integrase, N-terminal SAM-like domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 328 site-specific tyrosine recombinase XerC [Candidatus Lib
TIGR02224313 recomb_XerC tyrosine recombinase XerC; InterPro: IPR011 100.0
TIGR02225305 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011 100.0
COG4974300 XerD Site-specific recombinase XerD [DNA replication, r 100.0
PRK01287361 xerC site-specific tyrosine recombinase XerC; Reviewed 100.0
PRK00236295 xerC site-specific tyrosine recombinase XerC; Reviewed 100.0
PRK00283296 xerD site-specific tyrosine recombinase XerD; Reviewed 100.0
COG4973299 XerC Site-specific recombinase XerC [DNA replication, r 100.0
cd00798284 INT_XerDC XerD and XerC integrases, DNA breaking-rejoin 100.0
PRK05084360 xerS site-specific tyrosine recombinase XerS; Reviewed 100.0
cd01196263 INT_VanD VanD integrase, IntD, and related integrases, 100.0
cd01187299 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integr 100.0
PRK02436247 xerD site-specific tyrosine recombinase XerD-like prote 100.0
cd01185299 INT_Tn4399 Tn4399 and related integrases, DNA breaking- 100.0
TIGR02249320 integrase_gron integron integrase; InterPro: IPR011946 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 99.97
PHA00730322 int integrase 98.62
cd01190260 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integr 100.0
cd01193242 INT_IntI IntI (E2) integrases, site-specific tyrosine r 100.0
COG0582309 XerC Integrase [DNA replication, recombination, and rep 99.9
COG4342291 Uncharacterized protein conserved in archaea [Function 98.45
PRK09870200 tyrosine recombinase; Provisional 100.0
PRK09871198 tyrosine recombinase; Provisional 100.0
cd01198186 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA 100.0
cd01188188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejo 100.0
cd01197180 INT_FimBE_C FimB and FimE and related proteins, DNA bre 100.0
cd01186180 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, inte 100.0
cd01194186 INT_Tn554A_C Tn544A and related transposases, DNA break 100.0
cd01183196 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, inte 100.0
cd01199205 INT_Tn1545_C Tn1545-related conjugative transposon inte 100.0
cd01192177 INT_P22_C P22-like integrases, site-specific recombinas 100.0
pfam00589170 Phage_integrase Phage integrase family. Members of this 100.0
cd01189191 INT_phiLC3_C phiLC3 phage and phage-related integrases, 100.0
cd01195195 INT_Tn544B_C Tn544B and related transposases, DNA break 100.0
cd00397164 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal ca 99.98
cd01191196 INT_phiCTX_C phiCTX phage and phage-related integrases, 99.97
cd00797158 HP1_INT_C Phage HP1 integrase, C-terminal catalytic dom 99.97
cd01184181 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, inte 99.97
cd00800162 INT_Lambda_C Lambda integrase, C-terminal catalytic dom 99.97
cd00796206 INT_Rci Rci recombinase, C-terminal catalytic domain. R 100.0
cd01182162 INT_REC_C DNA breaking-rejoining enzymes, intergrase/re 99.94
pfam01028244 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic co 96.88
cd00659218 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic do 96.85
pfam0289983 Phage_integr_N Phage integrase, N-terminal SAM-like dom 99.65
pfam11917 414 DUF3435 Protein of unknown function (DUF3435). This fam 97.78
COG4688 665 Uncharacterized protein conserved in bacteria [Function 92.1
cd01190260 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integr 96.18
cd01193242 INT_IntI IntI (E2) integrases, site-specific tyrosine r 95.61
cd01185299 INT_Tn4399 Tn4399 and related integrases, DNA breaking- 95.02
PRK00283296 xerD site-specific tyrosine recombinase XerD; Reviewed 93.78
PRK00236295 xerC site-specific tyrosine recombinase XerC; Reviewed 92.89
PRK01287361 xerC site-specific tyrosine recombinase XerC; Reviewed 94.92
PRK05084360 xerS site-specific tyrosine recombinase XerS; Reviewed 94.63
pfam0289983 Phage_integr_N Phage integrase, N-terminal SAM-like dom 91.28
>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
>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
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed Back     alignment and domain information
>PRK00236 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
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair] 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
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed 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
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains Back     alignment and domain information
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed 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
>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
>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
>PHA00730 int integrase 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
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains 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
>PRK09870 tyrosine recombinase; Provisional Back     alignment and domain information
>PRK09871 tyrosine recombinase; Provisional 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
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain 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
>cd01186 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, 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
>cd01183 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, 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
>cd01192 INT_P22_C P22-like 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
>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
>cd01195 INT_Tn544B_C Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain Back     alignment and domain information
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain 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
>cd00797 HP1_INT_C Phage HP1 integrase, C-terminal 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
>cd00800 INT_Lambda_C Lambda integrase, C-terminal catalytic domain Back     alignment and domain information
>cd00796 INT_Rci Rci recombinase, 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
>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
>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
>COG4688 Uncharacterized protein conserved in bacteria [Function unknown] 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
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, 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
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed Back     alignment and domain information
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed Back     alignment and domain information
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed Back     alignment and domain information
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed Back     alignment and domain information
>pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like 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
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
1a0p_A290 Site-Specific Recombinase, Xerd Length = 290 2e-40
2a3v_A320 Structural Basis For Broad Dna-Specificity In Integ 7e-24
1aih_A170 Catalytic Domain Of Bacteriophage Hp1 Integrase Len 3e-14
3nkh_A244 Crystal Structure Of Integrase From Mrsa Strain Sta 1e-12
>gi|157829635|pdb|1A0P|A Chain A, Site-Specific Recombinase, Xerd Length = 290 Back     alignment and structure
 Score =  170 bits (430), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 87/300 (29%), Positives = 146/300 (48%), Gaps = 17/300 (5%)

Query: 18  RQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISK 77
            + +L  L +E+ L++ TL +Y  D    + +L           T+      +++A +++
Sbjct: 6   IEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRG------LTLATAQSDDLQALLAE 59

Query: 78  RRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTL 137
           R        S  R LS ++   +YL + K   +    ++ + K    LP+ L+E Q   L
Sbjct: 60  RLEGGYKATSSARLLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQVERL 119

Query: 138 VDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKI 197
           +   L+        ++ R+ A+L +LY  GLR+SE + LT  +I   Q  +R+ GKG+K 
Sbjct: 120 LQAPLIDQ-----PLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKE 174

Query: 198 RIVPLLPSVRKAILEY-YDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGL 256
           R+VPL       +  Y     P+ LN      LF   R + +    F   I+      G+
Sbjct: 175 RLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGI 234

Query: 257 P-LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYD 315
                + H LRH+FATHLL++G DLR +Q +LGH  LSTTQIYT+V ++     + +++ 
Sbjct: 235 DSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATER----LRQLHQ 290


>gi|99031762|pdb|2A3V|A Chain A, Structural Basis For Broad Dna-Specificity In Integron Recombination Length = 320 Back     alignment and structure
>gi|2392139|pdb|1AIH|A Chain A, Catalytic Domain Of Bacteriophage Hp1 Integrase Length = 170 Back     alignment and structure
>gi|303325117|pdb|3NKH|A Chain A, Crystal Structure Of Integrase From Mrsa Strain Staphylococcus Aureus Length = 244 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
1a0p_A290 Site-specific recombinase XERD; DNA binding, DNA recomb 8e-29
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 7e-24
2a3v_A320 Site-specific recombinase INTI4; protein-DNA complex, r 2e-23
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 1e-16
1z19_A283 Integrase; protein-DNA complex, DNA binding protein/DNA 9e-16
3nkh_A244 Integrase; alpha-fold, MRSA protein, structural genomic 2e-20
1ae9_A179 Lambda integrase; DNA recombination, site-specific reco 3e-10
1aih_A170 HP1 integrase; DNA integration, recombination; 2.50A {B 2e-05
3nrw_A117 Phage integrase/site-specific recombinase; alpha-helica 3e-06
>1a0p_A Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} SCOP: a.60.9.1 d.163.1.1 Length = 290 Back     alignment and structure
 Score =  123 bits (307), Expect = 8e-29
 Identities = 85/302 (28%), Positives = 147/302 (48%), Gaps = 17/302 (5%)

Query: 15  LKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAF 74
           L   + +L  L +E+ L++ TL +Y  D    + +L       +T+ T       +++A 
Sbjct: 3   LARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLH---HRGLTLATA---QSDDLQAL 56

Query: 75  ISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQA 134
           +++R        S  R LS ++   +YL + K   +    ++ + K    LP+ L+E Q 
Sbjct: 57  LAERLEGGYKATSSARLLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQ- 115

Query: 135 LTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKG 194
                  LL      + ++ R+ A+L +LY  GLR+SE + LT  +I   Q  +R+ GKG
Sbjct: 116 ----VERLLQAPLIDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKG 171

Query: 195 DKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGI-RGKPLNPGVFQRYIRQLRRY 253
           +K R+VPL       +  Y +     L   + + +     R + +    F   I+     
Sbjct: 172 NKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVL 231

Query: 254 LGLPLST-TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMME 312
            G+     + H LRH+FATHLL++G DLR +Q +LGH  LSTTQIYT+V ++     + +
Sbjct: 232 AGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATER----LRQ 287

Query: 313 IY 314
           ++
Sbjct: 288 LH 289


>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* 2crx_A* 1ouq_A* 1nzb_A* 1xns_A 5crx_A* 1f44_A* 2hof_A 2hoi_A 4crx_A* 1drg_A 3c29_A* 3c28_A 1crx_A* 1pvr_A 1pvq_A ... Length = 324 Back     alignment and structure
>2a3v_A Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Length = 320 Back     alignment and structure
>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
>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
>3nkh_A Integrase; alpha-fold, MRSA protein, structural genomics, PSI-2, protei structure initiative; 2.50A {Staphylococcus aureus subsp} Length = 244 Back     alignment and structure
>1ae9_A Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda} SCOP: d.163.1.1 Length = 179 Back     alignment and structure
>1aih_A HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1} SCOP: d.163.1.1 Length = 170 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
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
1a0p_A290 Site-specific recombinase XERD; DNA binding, DNA recomb 100.0
2a3v_A320 Site-specific recombinase INTI4; protein-DNA complex, r 100.0
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 100.0
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 100.0
1z19_A283 Integrase; protein-DNA complex, DNA binding protein/DNA 100.0
3nkh_A244 Integrase; alpha-fold, MRSA protein, structural genomic 100.0
1aih_A170 HP1 integrase; DNA integration, recombination; 2.50A {H 99.96
1ae9_A179 Lambda integrase; DNA recombination, site-specific reco 99.89
3nrw_A117 Phage integrase/site-specific recombinase; alpha-helica 99.74
2oxo_A103 Integrase; DNA-binding protein, four-helix bundle, DNA 99.44
2kkp_A117 Phage integrase; SAM-like domain, alpha-helical bundle, 99.39
2kd1_A118 DNA integration/recombination/invertion protein; protei 99.38
2key_A112 Putative phage integrase; protein structure, PSI, NESG, 99.34
2kiw_A111 INT protein; alpha, structural genomics, PSI-2, protein 99.33
2kob_A108 Uncharacterized protein; alpha beta, structural genomic 99.26
3lys_A112 Prophage PI2 protein 01, integrase; helical N-terminal 99.25
2khq_A110 Integrase; all-alpha, structural genomics, PSI-2, prote 99.22
2kkv_A121 Integrase; protein structure, PSI, nesgc, structural ge 98.75
2kj5_A116 Phage integrase; GFT NMR, PSI-2, NESG, structural genom 98.64
2kj9_A118 Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structur 98.63
2kj8_A118 Putative prophage CPS-53 integrase; INTS, INTC, YFDB, D 98.61
2khv_A106 Phage integrase; solution structure, GFT, NESG, structu 97.97
2v6e_A558 Protelemorase; hairpin telomere, hydrolase, resolvase, 97.27
3m4a_A346 Putative type I topoisomerase; type IB, topib, protein- 97.12
2h7g_X314 DNA topoisomerase 1; type IB topoisomerase, DNA binding 96.2
3nrw_A117 Phage integrase/site-specific recombinase; alpha-helica 95.12
2key_A112 Putative phage integrase; protein structure, PSI, NESG, 93.6
2b9s_A432 Topoisomerase I-like protein; vanadate complex, isomera 95.08
1a31_A 591 Protein (topoisomerase I); topoisomerase I/DNA, DNA, is 93.13
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 91.25
>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
Probab=100.00  E-value=0  Score=335.89  Aligned_cols=281  Identities=30%  Similarity=0.426  Sum_probs=229.1

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999862548899999999999999999851214788789689899999999999986121013321123444
Q gi|254780882|r   16 KERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGI   95 (328)
Q Consensus        16 ~~~e~~L~~l~~~r~~s~~T~~~Y~~~l~~f~~~~~~~~~~~~~~~~~~~i~~~~i~~~l~~l~~~~~s~~T~~~~ls~l   95 (328)
                      ..||+||+++..|||+||+|+++|+.+|+.|..||....      .++.+++..+|.+|+.++...+.+++|+++++++|
T Consensus         4 ~~i~~fl~~l~~er~ls~~T~~~Y~~~l~~f~~~l~~~~------~~~~~i~~~~i~~~~~~l~~~~~s~~t~~~~l~~l   77 (290)
T 1a0p_A            4 ARIEQFLDALWLEKNLAENTLNAYRRDLSMMVEWLHHRG------LTLATAQSDDLQALLAERLEGGYKATSSARLLSAV   77 (290)
T ss_dssp             HHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHTS------CCTTTCCHHHHHHHHHSCC-------CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC------CCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             999999999999869089999999999999999998859------99376999999999999987799889999999999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             22223332101232222222222222212111111101567877653101356775775320122210011233222221
Q gi|254780882|r   96 KSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALS  175 (328)
Q Consensus        96 r~f~~~~~~~~~i~~np~~~i~~~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~  175 (328)
                      ++||+|+..++++..+|+..+..|+..+..+......+....+.     ..........|+++++.+++.||||++|+++
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~l~~~tG~R~~Ei~~  152 (290)
T 1a0p_A           78 RRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQVERLLQ-----APLIDQPLELRDKAMLEVLYATGLRVSELVG  152 (290)
T ss_dssp             HHHHHHHHHTTSSSSCTTSCC----------CCCCHHHHHHHHH-----CSCTTSHHHHHHHHHHHHHHHHCCCHHHHTT
T ss_pred             HHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCCCHHHHHHHHH-----HHHCCCCHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             99999999824334681765037776666765100899999875-----2100134118999999999995877899980


Q ss_pred             CCCCCCCCCCCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf             122222332322033237853100011221002343221110012-3446655432111122111000123567899976
Q gi|254780882|r  176 LTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFD-LNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYL  254 (328)
Q Consensus       176 L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~~~~l~~yl~~~~~~-~~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~  254 (328)
                      |+|+|||++.+.+.+.+||+|+|.+|........+..+....... ......+++|+..++.+.+...+.+.++.+++.+
T Consensus       153 L~~~did~~~~~i~~~~K~~k~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (290)
T 1a0p_A          153 LTMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLA  232 (290)
T ss_dssp             CBGGGEETTTTEEEEECSSSCEEEEECCHHHHHHHHHHHHHTHHHHHTTCCCCBSSBCTTSSBCCHHHHHHHHHHHHHHT
T ss_pred             CCHHHCCCCCCEEEECCCCCCEEEECCHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             94999575799898668899401411327777789999985001110134455545333566542378999999999994


Q ss_pred             CCC-CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHCHHHHH
Q ss_conf             869-99880541799999999848998899998378887897999961989999
Q gi|254780882|r  255 GLP-LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGG  307 (328)
Q Consensus       255 gi~-~~~spH~lRHtfAt~ll~~G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~  307 (328)
                      |+. .++|||+|||||||.|+++|+|+..||++|||+|++||++|+|++.++.+
T Consensus       233 ~~~~~~~s~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~tT~~Y~~~~~~~lr  286 (290)
T 1a0p_A          233 GIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLR  286 (290)
T ss_dssp             TCCGGGCCHHHHHHHHHHHHHHHCSSCGGGSSCC--CCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHH
T ss_conf             578999874517799999999878999999988189988999999878999999



>2a3v_A Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Back     alignment and structure
>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
>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
>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
>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
>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
>2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage} 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
>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
>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
>2kiw_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 Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753} 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
>2khq_A Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp} 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
>2kj9_A Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} 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
>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
>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
>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
>2b9s_A Topoisomerase I-like protein; vanadate complex, isomerase/DNA complex; HET: DNA; 2.27A {Leishmania donovani} Back     alignment and structure
>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* 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

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 328 site-specific tyrosine recombinase XerC [Candidatus Lib
d1a0pa2182 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia col 3e-22
d1f44a2214 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 2e-13
d1ae9a_179 d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [T 7e-08
d1aiha_170 d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 106 4e-06
d1a0pa198 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [ 2e-08
d1f44a1110 a.60.9.1 (A:20-129) Cre recombinase {Bacteriophage P1 [ 5e-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 = 99.8 bits (247), Expect = 3e-22
 Identities = 62/175 (35%), Positives = 94/175 (53%), Gaps = 6/175 (3%)

Query: 142 LLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVP 201
           LL      + ++ R+ A+L +LY  GLR+SE + LT  +I   Q  +R+ GKG+K R+VP
Sbjct: 11  LLQAPLIDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVP 70

Query: 202 LL-PSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLS- 259
           L   +V           P+ LN      LF   R + +    F   I+      G+    
Sbjct: 71  LGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEK 130

Query: 260 TTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIY 314
            + H LRH+FATHLL++G DLR +Q +LGH  LSTTQIYT+V ++     + +++
Sbjct: 131 LSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATER----LRQLH 181


>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]} Length = 214 Back     information, alignment and structure
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} Length = 179 Back     information, alignment and structure
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]} Length = 170 Back     information, alignment and structure
>d1a0pa1 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [TaxId: 562]} Length = 98 Back     information, alignment and structure
>d1f44a1 a.60.9.1 (A:20-129) Cre recombinase {Bacteriophage P1 [TaxId: 10678]} Length = 110 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
d1a0pa2182 Recombinase XerD {Escherichia coli [TaxId: 562]} 99.97
d1aiha_170 Integrase {Bacteriophage HP1 [TaxId: 10690]} 99.96
d1f44a2214 Cre recombinase {Bacteriophage P1 [TaxId: 10678]} 99.94
d1ae9a_179 Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} 99.89
d1a0pa198 Recombinase XerD {Escherichia coli [TaxId: 562]} 99.76
d1f44a1110 Cre recombinase {Bacteriophage P1 [TaxId: 10678]} 99.39
d1a41a_230 Eukaryotic DNA topoisomerase I, catalytic core {Vaccini 96.87
d1k4ta2263 Eukaryotic DNA topoisomerase I, catalytic core {Human ( 95.91
d1a0pa198 Recombinase XerD {Escherichia coli [TaxId: 562]} 92.07
>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]} 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]
Probab=99.97  E-value=1.1e-33  Score=226.77  Aligned_cols=176  Identities=36%  Similarity=0.490  Sum_probs=146.1

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCC
Q ss_conf             11111015678776531013567757753201222100112332222211222223323220332378531000112210
Q gi|254780882|r  127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSV  206 (328)
Q Consensus       127 ~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R~Vpi~~~~  206 (328)
                      +.||.+|+.++++++..     ....++||++||.++++||||++|+++|+|+||+++.+.+.+.+|+.|.|.++.....
T Consensus         1 k~Lt~eei~~ll~~~~~-----~~~~~lRd~~l~~l~~~tG~R~~ei~~L~~~~i~~~~~~i~~~~~~~k~r~~~~~~~~   75 (182)
T d1a0pa2           1 KDLSEAQVERLLQAPLI-----DQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEA   75 (182)
T ss_dssp             CCCCHHHHHHHHHCSCT-----TSHHHHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEEEEECSSSCEEEEECCHHH
T ss_pred             CCCCHHHHHHHHHCCCC-----CCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCEEEEEECCCCEEEEEEECCHH
T ss_conf             98999999999827463-----8818799999999999967764774202141411443289983689801257520013


Q ss_pred             HHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-CCCCCCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf             023432211100123-446655432111122111000123567899976869-998805417999999998489988999
Q gi|254780882|r  207 RKAILEYYDLCPFDL-NLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP-LSTTAHTLRHSFATHLLSNGGDLRSIQ  284 (328)
Q Consensus       207 ~~~l~~yl~~~~~~~-~~~~~~~lF~~~~g~~ls~~~i~~~~~~~~~~~gi~-~~~spH~lRHtfAt~ll~~G~~~~~v~  284 (328)
                      ...+..++....... ......+++++..+.+++.+++++.++++++.+|++ .+++||+|||||||.|+++|+|+.+|+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~t~H~~Rht~at~l~~~G~~~~~I~  155 (182)
T d1a0pa2          76 VYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQ  155 (182)
T ss_dssp             HHHHHHHHHHTHHHHHTTCCCCBSSBCTTSSBCCHHHHHHHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHCSSCGGGS
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHH
T ss_conf             35566655311230012345654210235773668999999999999849985783614146589996556499999999


Q ss_pred             HHHCCCCHHHHHHHHHHCHHHHH
Q ss_conf             98378887897999961989999
Q gi|254780882|r  285 SILGHFRLSTTQIYTNVNSKNGG  307 (328)
Q Consensus       285 ~~lGH~s~~tT~~Y~h~~~~~~~  307 (328)
                      ++|||+|++||++|+|++.++.+
T Consensus       156 ~~lGH~s~~tt~~Y~~~~~e~~r  178 (182)
T d1a0pa2         156 MLLGHSDLSTTQIYTHVATERLR  178 (182)
T ss_dssp             SCC--CCCCHHHHHHHHHHHHHH
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHH
T ss_conf             99589988999987687999999



>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]} Back     information, alignment and structure
>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]} Back     information, alignment and structure
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} 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
>d1a41a_ d.163.1.2 (A:) Eukaryotic DNA topoisomerase I, catalytic core {Vaccinia virus [TaxId: 10245]} Back     information, alignment and structure
>d1k4ta2 d.163.1.2 (A:431-640,A:713-765) Eukaryotic DNA topoisomerase I, catalytic core {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1a0pa1 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 328 site-specific tyrosine recombinase XerC [Candidatu
1a0p_A_101-290190 (A:101-290) Site-specific recombinase XERD; DNA bi 2e-24
1z1b_A_167-356190 (A:167-356) Integrase; protein-DNA complex, DNA bi 9e-21
1ae9_A_179 (A:) Lambda integrase; DNA recombination, site-spe 3e-19
1z19_A_94-283190 (A:94-283) Integrase; protein-DNA complex, DNA bin 1e-18
1xo0_A_115-310196 (A:115-310) Recombinase CRE; CRE recombinase, holl 1e-14
1xo0_A_1-114114 (A:1-114) Recombinase CRE; CRE recombinase, hollid 2e-13
1a0p_A_1-100100 (A:1-100) Site-specific recombinase XERD; DNA bind 8e-12
2kd1_A_118 (A:) DNA integration/recombination/invertion prote 2e-09
2a3v_A_1-9494 (A:1-94) Site-specific recombinase INTI4; protein- 7e-08
2kkp_A_27-11791 (A:27-117) Phage integrase; SAM-like domain, alpha 1e-07
2kiw_A_111 (A:) INT protein; alpha, structural genomics, PSI- 2e-07
2kob_A_108 (A:) Uncharacterized protein; alpha beta, structur 4e-06
2kkv_A_121 (A:) Integrase; protein structure, PSI, nesgc, str 7e-06
1z1b_A_75-16692 (A:75-166) Integrase; protein-DNA complex, DNA bin 1e-05
2key_A_112 (A:) Putative phage integrase; protein structure, 1e-05
2oxo_A_103 (A:) Integrase; DNA-binding protein, four-helix bu 2e-05
2kj5_A_116 (A:) Phage integrase; GFT NMR, PSI-2, NESG, struct 2e-05
2khq_A_110 (A:) Integrase; all-alpha, structural genomics, PS 3e-05
1z19_A_1-9393 (A:1-93) Integrase; protein-DNA complex, DNA bindi 7e-05
2kj9_A_118 (A:) Integrase; DNA_BRE_C superfamily, INTB, PSI-2 1e-04
2kj8_A_118 (A:) Putative prophage CPS-53 integrase; INTS, INT 4e-04
2a3v_A_95-144_243-320128 (A:95-144,A:243-320) Site-specific recombinase INT 1e-12
1aih_A_1-49_87-170133 (A:1-49,A:87-170) HP1 integrase; DNA integration, 4e-11
2a3v_A_95-144_243-320128 (A:95-144,A:243-320) Site-specific recombinase INT 7e-07
>1a0p_A (A:101-290) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli}Length = 190 Back     alignment and structure
 Score =  107 bits (268), Expect = 2e-24
 Identities = 61/187 (32%), Positives = 92/187 (49%), Gaps = 7/187 (3%)

Query: 120 KKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQ 179
           K    LP+ L+E Q   L+   L+        ++ R+ A+L +LY  GLR+SE + LT  
Sbjct: 2   KLPQRLPKDLSEAQVERLLQAPLIDQ-----PLELRDKAMLEVLYATGLRVSELVGLTMS 56

Query: 180 NIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQ--LPLFRGIRGKP 237
           +I   Q  +R+ GKG+K R+VPL       +  Y +     L   +   +        + 
Sbjct: 57  DISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQM 116

Query: 238 LNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQI 297
                + R               + H LRH+FATHLL++G DLR +Q +LGH  LSTTQI
Sbjct: 117 TRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQI 176

Query: 298 YTNVNSK 304
           YT+V ++
Sbjct: 177 YTHVATE 183


>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
>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
>1xo0_A (A:115-310) Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1}Length = 196 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:1-100) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli}Length = 100 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
>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
>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
>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
>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
>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
>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
>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
>2oxo_A (A:) Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage}Length = 103 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
>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
>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
>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
>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
>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}Length = 128 Back     alignment and structure
>1aih_A (A:1-49,A:87-170) HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1}Length = 133 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}Length = 128 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target328 site-specific tyrosine recombinase XerC [Candidatus Lib
1a0p_A_101-290190 Site-specific recombinase XERD; DNA binding, DNA r 99.96
1xo0_A_115-310196 Recombinase CRE; CRE recombinase, holliday junctio 99.96
2a3v_A_95-144_243-320128 Site-specific recombinase INTI4; protein-DNA compl 99.95
1z1b_A_167-356190 Integrase; protein-DNA complex, DNA binding protei 99.93
1z19_A_94-283190 Integrase; protein-DNA complex, DNA binding protei 99.92
1ae9_A_179 Lambda integrase; DNA recombination, site-specific 99.89
1aih_A_1-49_87-170133 HP1 integrase; DNA integration, recombination; 2.5 99.87
1xo0_A_1-114114 Recombinase CRE; CRE recombinase, holliday junctio 99.76
1a0p_A_1-100100 Site-specific recombinase XERD; DNA binding, DNA r 99.71
2kd1_A_118 DNA integration/recombination/invertion protein; p 99.65
2kiw_A_111 INT protein; alpha, structural genomics, PSI-2, pr 99.6
2a3v_A_1-9494 Site-specific recombinase INTI4; protein-DNA compl 99.56
2key_A_112 Putative phage integrase; protein structure, PSI, 99.53
2oxo_A_103 Integrase; DNA-binding protein, four-helix bundle, 99.53
2khq_A_110 Integrase; all-alpha, structural genomics, PSI-2, 99.51
2kob_A_108 Uncharacterized protein; alpha beta, structural ge 99.44
2kkv_A_121 Integrase; protein structure, PSI, nesgc, structur 99.35
1z19_A_1-9393 Integrase; protein-DNA complex, DNA binding protei 99.34
1z1b_A_75-16692 Integrase; protein-DNA complex, DNA binding protei 99.33
2kkp_A_27-11791 Phage integrase; SAM-like domain, alpha-helical bu 99.27
2kj8_A_118 Putative prophage CPS-53 integrase; INTS, INTC, YF 99.23
2kj9_A_118 Integrase; DNA_BRE_C superfamily, INTB, PSI-2, str 99.22
2kj5_A_116 Phage integrase; GFT NMR, PSI-2, NESG, structural 99.2
2khv_A_106 Phage integrase; solution structure, GFT, NESG, st 99.19
2a3v_A_1-9494 Site-specific recombinase INTI4; protein-DNA compl 95.13
2key_A_112 Putative phage integrase; protein structure, PSI, 93.74
1xo0_A_1-114114 Recombinase CRE; CRE recombinase, holliday junctio 93.26
1a0p_A_1-100100 Site-specific recombinase XERD; DNA binding, DNA r 91.28
>1a0p_A (A:101-290) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} Back     alignment and structure
Probab=99.96  E-value=3.3e-30  Score=207.57  Aligned_cols=186  Identities=35%  Similarity=0.434  Sum_probs=125.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCC
Q ss_conf             22221211111110156787765310135677577532012221001123322222112222233232203323785310
Q gi|254780882|r  119 LKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIR  198 (328)
Q Consensus       119 ~k~~~~~p~~lt~~e~~~ll~~~~~~~~~~~~~~~~Rd~~i~~ll~~TGlR~~El~~L~~~did~~~~~i~v~gKg~K~R  198 (328)
                      ||.+++.|++++.+|+.++++++..     ......||++||.+++.||||+||+++|+|+||+++.+.+.|..++.+..
T Consensus         1 PK~~~~~~~~lt~eel~~ll~~~~~-----~~~~~~r~~~i~~l~~~TGlR~~Ei~~L~~~di~~~~~~i~i~~~~~~~~   75 (190)
T 1a0p_A            1 PKLPQRLPKDLSEAQVERLLQAPLI-----DQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKER   75 (190)
T ss_dssp             --------CCCCHHHHHHHHHCSCT-----TSHHHHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEEEEECSSSCEE
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC-----HHHHHHHHHHHHHHHHHHHCCHHHHCCCCHHHCCCCCCEEEECCCCCCCC
T ss_conf             6411023222222222222222210-----11336899999998656412045540584999054232899668898201


Q ss_pred             CCCCCCCCHHHHHHHHHHHCCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHH-HHHHHCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             0011221002343221110012-3446655432111122111000123567-8999768699988054179999999984
Q gi|254780882|r  199 IVPLLPSVRKAILEYYDLCPFD-LNLNIQLPLFRGIRGKPLNPGVFQRYIR-QLRRYLGLPLSTTAHTLRHSFATHLLSN  276 (328)
Q Consensus       199 ~Vpi~~~~~~~l~~yl~~~~~~-~~~~~~~~lF~~~~g~~ls~~~i~~~~~-~~~~~~gi~~~~spH~lRHtfAt~ll~~  276 (328)
                      ..+...........+....... .......+.+......+........... ......+...++++|++||||||.++++
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~Rht~~t~~~~~  155 (190)
T 1a0p_A           76 LVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNH  155 (190)
T ss_dssp             EEECCHHHHHHHHHHHHHTHHHHHTTCCCCBSSBCTTSSBCCHHHHHHHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHH
T ss_pred             CCEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHC
T ss_conf             01001110035677776520211223456554432222321117899999999999468999877651889999999987


Q ss_pred             CCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHH
Q ss_conf             899889999837888789799996198999999
Q gi|254780882|r  277 GGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDW  309 (328)
Q Consensus       277 G~~~~~v~~~lGH~s~~tT~~Y~h~~~~~~~~~  309 (328)
                      |+|+..||++|||+|++||++|+|++++..+++
T Consensus       156 ~~~~~~i~~~lGH~s~~~T~~Y~~~~~~~~~~a  188 (190)
T 1a0p_A          156 GADLRVVQMLLGHSDLSTTQIYTHVATERLRQL  188 (190)
T ss_dssp             CSSCGGGSSCC--CCCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             899999998818998899999977899999986



>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