255764498

255764498

site-specific tyrosine recombinase XerD

GeneID in NCBI database:8209584Locus tag:CLIBASIA_02370
Protein GI in NCBI database:255764498Protein Accession:YP_003065000.2
Gene range:-(696058, 696960)Protein Length:300aa
Gene description:site-specific tyrosine recombinase XerD
COG prediction:[L] Site-specific recombinase XerD
KEGG prediction:xerD; site-specific tyrosine recombinase XerD; K04763 integrase/recombinase XerD
SEED prediction:Tyrosine recombinase XerD
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
MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHYN
ccHHHHcccHHHHHHHHHHHHHHHHHHHHccccHHHccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHcccccccccccccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccHHHHHcccHHHHcccccEEEEEcccccEEEEEccHHHHHHHHHHHHHccHHcccccccEEEEEccccccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHccHHHHHHHHHHHcHHHHHcccccc
ccHHHccccHHHHHHHHHHHHHHHHHHHHccccHHHccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccccccccEEcccccccccccccccHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccEHHHEEccccccEccccEEEEEcccccEEEEcccHHHHHHHHHHHHHcHHHHHccccccEEEcccccccccHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcccccccccccc
mmsserassINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYeglrkdnpsdtlelpkknhilpktlHKDTIANLLEQAKieaenpapgqwKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIqgkgnkerlvILSPSALHALQMYKKTCSsmkmtgndlwlfpsstktghlsRQVFARDLKALAARAGiqkknisphIIRHAFASHLLEGGADLRTIQILLGhtdisttqIYTHLLPDKLQKLVQDYHPLAKKEKKHYN
mmsserassintLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRkdnpsdtlelpkknhilpktlHKDTIANLLEQAKIeaenpapgqwkRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTmiiqgkgnkERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGiqkknispHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHYN
MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHYN
MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQ******SQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQD*************
**********NTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLA********
MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPL*********
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MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHYN
MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHYN
MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKHYN

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target300 site-specific tyrosine recombinase XerD [Candidatus Lib
254780882328 site-specific tyrosine recombinase XerC [Candidatu 9e-26
25478049067 site-specific tyrosine recombinase XerC [Candidatu 8e-13
>gi|254780882|ref|YP_003065295.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62] Length = 328 Back     alignment
 Score =  108 bits (271), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 88/305 (28%), Positives = 156/305 (51%), Gaps = 15/305 (4%)

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

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

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

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

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

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

>gi|254780490|ref|YP_003064903.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62] Length = 67 Back     alignment
 Score = 65.9 bits (159), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 46/63 (73%), Gaps = 1/63 (1%)

Query: 236 SPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHP-LAKK 294
           + H +RH+FA+HLL  G DLR+IQ +LGH+ +STTQIYT++   ++ ++    HP + +K
Sbjct: 4   TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQK 63

Query: 295 EKK 297
           +KK
Sbjct: 64  DKK 66

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

IdentityAlignment graphLength Definition Round E-value
Target300 site-specific tyrosine recombinase XerD [Candidatus Lib
315121780318 site-specific tyrosine recombinase XerD [Candidatus Lib 1 1e-139
86283512383 tyrosine site-specific integrase/recombinase protein [R 1 5e-90
162329627317 site-specific tyrosine recombinase XerD [Rhizobium etli 1 6e-90
150397765313 site-specific tyrosine recombinase XerD [Sinorhizobium 1 6e-88
15966434311 site-specific tyrosine recombinase XerD [Sinorhizobium 1 3e-87
116254087317 site-specific tyrosine recombinase XerD [Rhizobium legu 1 5e-87
307300528311 tyrosine recombinase XerD [Sinorhizobium meliloti BL225 1 2e-86
241206577317 site-specific tyrosine recombinase XerD [Rhizobium legu 1 1e-85
209551174317 site-specific tyrosine recombinase XerD [Rhizobium legu 1 4e-85
332716418331 tyrosine recombinase xerD [Agrobacterium sp. H13-3] Len 1 6e-85
>gi|315121780|ref|YP_004062269.1| site-specific tyrosine recombinase XerD [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 318 Back     alignment and organism information
 Score =  497 bits (1279), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 239/298 (80%), Positives = 272/298 (91%)

Query: 1   MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60
           MMSSERA+S+NTL++YK DL+E+Q FL++ ++ LS AS+++LI+YLNHLSQRKL  SSQR
Sbjct: 21  MMSSERAASVNTLTSYKSDLEEVQLFLDDDDLLLSKASSDNLIAYLNHLSQRKLKASSQR 80

Query: 61  RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120
           RKIS IRQFYNFLC EGLRKDNPS+TL+ PKKNH LPKTLHK+ IA+LL+QAKIE+E+P+
Sbjct: 81  RKISAIRQFYNFLCCEGLRKDNPSETLQFPKKNHTLPKTLHKNAIADLLKQAKIESEDPS 140

Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180
           PGQWKR+R+FLLIELLY+TGMRVSELVTLS+HTLNL ER MII+GKGN+ER VI SPS+L
Sbjct: 141 PGQWKRIRMFLLIELLYSTGMRVSELVTLSSHTLNLEERIMIIKGKGNRERFVIFSPSSL 200

Query: 181 HALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240
            ALQMYKK CS+M+MT N  WLFPSSTKTGHLSRQVFARDLK LA+RA IQ KNISPHII
Sbjct: 201 CALQMYKKMCSTMEMTKNSPWLFPSSTKTGHLSRQVFARDLKELASRASIQTKNISPHII 260

Query: 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEKKH 298
           RHAFASHLLEGGADLRTIQILLGH DISTTQIYTHLLPDKLQKLVQDYHPLAKK KK+
Sbjct: 261 RHAFASHLLEGGADLRTIQILLGHIDISTTQIYTHLLPDKLQKLVQDYHPLAKKLKKY 318


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|86283512|gb|ABC92575.1| tyrosine site-specific integrase/recombinase protein [Rhizobium etli CFN 42] Length = 383 Back     alignment and organism information
>gi|162329627|ref|YP_471302.2| site-specific tyrosine recombinase XerD [Rhizobium etli CFN 42] Length = 317 Back     alignment and organism information
>gi|150397765|ref|YP_001328232.1| site-specific tyrosine recombinase XerD [Sinorhizobium medicae WSM419] Length = 313 Back     alignment and organism information
>gi|15966434|ref|NP_386787.1| site-specific tyrosine recombinase XerD [Sinorhizobium meliloti 1021] Length = 311 Back     alignment and organism information
>gi|116254087|ref|YP_769925.1| site-specific tyrosine recombinase XerD [Rhizobium leguminosarum bv. viciae 3841] Length = 317 Back     alignment and organism information
>gi|307300528|ref|ZP_07580308.1| tyrosine recombinase XerD [Sinorhizobium meliloti BL225C] Length = 311 Back     alignment and organism information
>gi|241206577|ref|YP_002977673.1| site-specific tyrosine recombinase XerD [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 317 Back     alignment and organism information
>gi|209551174|ref|YP_002283091.1| site-specific tyrosine recombinase XerD [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 317 Back     alignment and organism information
>gi|332716418|ref|YP_004443884.1| tyrosine recombinase xerD [Agrobacterium sp. H13-3] Length = 331 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
Target300 site-specific tyrosine recombinase XerD [Candidatus Lib
PRK00283299 PRK00283, xerD, site-specific tyrosine recombinase XerD 1e-88
TIGR02225291 TIGR02225, recomb_XerD, tyrosine recombinase XerD 5e-82
PRK00236297 PRK00236, xerC, site-specific tyrosine recombinase XerC 5e-65
TIGR02224295 TIGR02224, recomb_XerC, tyrosine recombinase XerC 1e-63
cd00798284 cd00798, INT_XerDC, XerD and XerC integrases, DNA break 3e-61
COG4973299 COG4973, XerC, Site-specific recombinase XerC [DNA repl 4e-47
TIGR02249315 TIGR02249, integrase_gron, integron integrase 7e-31
cd01185299 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA 2e-19
PRK05084357 PRK05084, xerS, site-specific tyrosine recombinase XerS 9e-17
cd00799287 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic 4e-10
cd01196263 cd01196, INT_VanD, VanD integrase, IntD, and related in 5e-10
PRK02436245 PRK02436, xerD, site-specific tyrosine recombinase XerD 7e-05
COG4974300 COG4974, XerD, Site-specific recombinase XerD [DNA repl 2e-74
cd01193242 cd01193, INT_IntI, IntI (E2) integrases, site-specific 4e-38
PRK01287358 PRK01287, xerC, site-specific tyrosine recombinase XerC 8e-28
PRK15417337 PRK15417, PRK15417, integrase/recombinase; Provisional 2e-20
cd01190260 cd01190, INT_SG5, INT_SG5, DNA breaking-rejoining enzym 4e-20
cd01187299 cd01187, INT_SG4, INT_SG4, DNA breaking-rejoining enzym 2e-17
cd00801357 cd00801, INT_P4, Bacteriophage P4 integrase 6e-13
cd00796206 cd00796, INT_Rci, Rci recombinase, C-terminal catalytic 4e-08
COG0582309 COG0582, XerC, Integrase [DNA replication, recombinatio 1e-05
pfam00589170 pfam00589, Phage_integrase, Phage integrase family 3e-31
cd00397164 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-t 3e-25
cd01182162 cd01182, INT_REC_C, DNA breaking-rejoining enzymes, int 2e-24
cd01183196 cd01183, INT_SG1_C, INT_SG1, DNA breaking-rejoining enz 7e-17
cd01189191 cd01189, INT_phiLC3_C, phiLC3 phage and phage-related i 5e-16
cd00797158 cd00797, HP1_INT_C, Phage HP1 integrase, C-terminal cat 2e-14
cd01197180 cd01197, INT_FimBE_C, FimB and FimE and related protein 6e-13
cd01192177 cd01192, INT_P22_C, P22-like integrases, site-specific 2e-12
cd01199205 cd01199, INT_Tn1545_C, Tn1545-related conjugative trans 1e-10
PRK09871198 PRK09871, PRK09871, tyrosine recombinase; Provisional 2e-10
cd01186180 cd01186, INT_SG3_C, INT_SG3, DNA breaking-rejoining enz 5e-09
cd01191196 cd01191, INT_phiCTX_C, phiCTX phage and phage-related i 1e-07
cd01198186 cd01198, INT_ASSRA_C, Archaeal site-specific recombinas 2e-07
PRK09870200 PRK09870, PRK09870, tyrosine recombinase; Provisional 3e-07
cd01194186 cd01194, INT_Tn554A_C, Tn544A and related transposases, 7e-07
cd01195195 cd01195, INT_Tn544B_C, Tn544B and related transposases, 2e-06
cd00800162 cd00800, INT_Lambda_C, Lambda integrase, C-terminal cat 1e-05
cd01184181 cd01184, INT_SG2_C, INT_SG2, DNA breaking-rejoining enz 0.004
PHA02601333 PHA02601, int, integrase; Provisional 1e-13
cd01188188 cd01188, INT_pAE1, pAE1 and related integrases, DNA bre 2e-13
pfam0289983 pfam02899, Phage_integr_N, Phage integrase, N-terminal 3e-11
>gnl|CDD|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed Back     alignment and domain information
>gnl|CDD|162772 TIGR02225, recomb_XerD, tyrosine recombinase XerD Back     alignment and domain information
>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|29499 cd00798, INT_XerDC, XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains 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|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|179424 PRK02436, xerD, site-specific tyrosine recombinase XerD-like protein; Reviewed 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|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|179273 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed Back     alignment and domain information
>gnl|CDD|185315 PRK15417, PRK15417, integrase/recombinase; Provisional 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|29497 cd00796, INT_Rci, Rci recombinase, C-terminal catalytic domain 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|29495 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal catalytic domain 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|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|29498 cd00797, HP1_INT_C, Phage HP1 integrase, 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|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|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|182126 PRK09871, PRK09871, tyrosine recombinase; Provisional 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|29512 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
>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|182125 PRK09870, PRK09870, tyrosine recombinase; Provisional 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|29516 cd01195, INT_Tn544B_C, Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain 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|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|164996 PHA02601, int, integrase; Provisional 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|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 300 site-specific tyrosine recombinase XerD [Candidatus Lib
TIGR02225305 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011 100.0
TIGR02224313 recomb_XerC tyrosine recombinase XerC; 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
PRK00283296 xerD site-specific tyrosine recombinase XerD; Reviewed 100.0
PRK00236295 xerC site-specific tyrosine recombinase XerC; Reviewed 100.0
cd00798284 INT_XerDC XerD and XerC integrases, DNA breaking-rejoin 100.0
COG4973299 XerC Site-specific recombinase XerC [DNA replication, r 100.0
PRK05084360 xerS site-specific tyrosine recombinase XerS; Reviewed 100.0
cd01196263 INT_VanD VanD integrase, IntD, and related integrases, 100.0
cd01185299 INT_Tn4399 Tn4399 and related integrases, DNA breaking- 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
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 99.98
PHA00730322 int integrase 98.44
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 99.86
COG4342291 Uncharacterized protein conserved in archaea [Function 98.31
PRK09870200 tyrosine recombinase; Provisional 100.0
PRK09871198 tyrosine recombinase; Provisional 100.0
cd01188188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejo 100.0
cd01198186 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA 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
cd01199205 INT_Tn1545_C Tn1545-related conjugative transposon inte 100.0
cd01183196 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, inte 100.0
cd01192177 INT_P22_C P22-like integrases, site-specific recombinas 100.0
cd01195195 INT_Tn544B_C Tn544B and related transposases, DNA break 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
cd00397164 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal ca 100.0
cd00797158 HP1_INT_C Phage HP1 integrase, C-terminal catalytic dom 99.98
cd01184181 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, inte 99.98
cd00800162 INT_Lambda_C Lambda integrase, C-terminal catalytic dom 99.98
cd01191196 INT_phiCTX_C phiCTX phage and phage-related integrases, 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 97.45
cd00659218 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic do 97.02
pfam0289983 Phage_integr_N Phage integrase, N-terminal SAM-like dom 99.61
pfam11917 414 DUF3435 Protein of unknown function (DUF3435). This fam 98.36
PRK00283296 xerD site-specific tyrosine recombinase XerD; Reviewed 95.52
PRK01287361 xerC site-specific tyrosine recombinase XerC; Reviewed 95.48
PRK05084360 xerS site-specific tyrosine recombinase XerS; Reviewed 95.37
PRK00236295 xerC site-specific tyrosine recombinase XerC; Reviewed 94.59
cd00798284 INT_XerDC XerD and XerC integrases, DNA breaking-rejoin 92.37
cd01185299 INT_Tn4399 Tn4399 and related integrases, DNA breaking- 90.51
pfam0289983 Phage_integr_N Phage integrase, N-terminal SAM-like dom 90.5
cd01193242 INT_IntI IntI (E2) integrases, site-specific tyrosine r 92.49
cd01190260 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integr 90.79
>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
>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
>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
>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
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains Back     alignment and domain information
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair] 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
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, 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
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, 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
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal 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
>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
>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
>cd01183 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, 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
>cd01195 INT_Tn544B_C Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, 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
>cd00397 DNA_BRE_C 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
>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
>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
>PRK00283 xerD site-specific tyrosine recombinase XerD; 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
>PRK00236 xerC site-specific tyrosine recombinase XerC; 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
>pfam02899 Phage_integr_N Phage integrase, N-terminal SAM-like domain 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
>cd01190 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains 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
Target300 site-specific tyrosine recombinase XerD [Candidatus Lib
1a0p_A290 Site-Specific Recombinase, Xerd Length = 290 2e-42
2a3v_A320 Structural Basis For Broad Dna-Specificity In Integ 5e-21
1aih_A170 Catalytic Domain Of Bacteriophage Hp1 Integrase Len 1e-14
>gi|157829635|pdb|1A0P|A Chain A, Site-Specific Recombinase, Xerd Length = 290 Back     alignment and structure
 Score =  177 bits (447), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 107/285 (37%), Positives = 171/285 (60%), Gaps = 7/285 (2%)

Query: 2   MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRR 61
           +  E+  + NTL+AY+RDL  M  +L+++ ++L+ A ++ L + L    +     +S  R
Sbjct: 13  LWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSAR 72

Query: 62  KISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAP 121
            +S +R+ + +L  E  R+D+PS  L  PK    LPK L +  +  LL+   I+      
Sbjct: 73  LLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQVERLLQAPLID------ 126

Query: 122 GQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALH 181
            Q   +R   ++E+LYATG+RVSELV L+   ++L +  + + GKGNKERLV L   A++
Sbjct: 127 -QPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAVY 185

Query: 182 ALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIR 241
            L+ Y +      + G  + +   S +   ++RQ F   +K  A  AGI  + +SPH++R
Sbjct: 186 WLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLR 245

Query: 242 HAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286
           HAFA+HLL  GADLR +Q+LLGH+D+STTQIYTH+  ++L++L Q
Sbjct: 246 HAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQ 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

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target300 site-specific tyrosine recombinase XerD [Candidatus Lib
1a0p_A290 Site-specific recombinase XERD; DNA binding, DNA recomb 5e-37
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 2e-33
2a3v_A320 Site-specific recombinase INTI4; protein-DNA complex, r 1e-29
1z19_A283 Integrase; protein-DNA complex, DNA binding protein/DNA 2e-19
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 4e-17
3nkh_A244 Integrase; alpha-fold, MRSA protein, structural genomic 6e-24
3nrw_A117 Phage integrase/site-specific recombinase; alpha-helica 6e-13
2kd1_A118 DNA integration/recombination/invertion protein; protei 2e-06
2oxo_A103 Integrase; DNA-binding protein, four-helix bundle, DNA 5e-06
2kkp_A117 Phage integrase; SAM-like domain, alpha-helical bundle, 7e-05
2kiw_A111 INT protein; alpha, structural genomics, PSI-2, protein 8e-05
2key_A112 Putative phage integrase; protein structure, PSI, NESG, 1e-04
1ae9_A179 Lambda integrase; DNA recombination, site-specific reco 9e-13
1aih_A170 HP1 integrase; DNA integration, recombination; 2.50A {B 1e-12
>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 =  149 bits (377), Expect = 5e-37
 Identities = 105/286 (36%), Positives = 169/286 (59%), Gaps = 7/286 (2%)

Query: 1   MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60
            +  E+  + NTL+AY+RDL  M  +L+++ ++L+ A ++ L + L    +     +S  
Sbjct: 12  ALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSA 71

Query: 61  RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120
           R +S +R+ + +L  E  R+D+PS  L  PK    LPK L +  +       +   + P 
Sbjct: 72  RLLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQV-------ERLLQAPL 124

Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180
             Q   +R   ++E+LYATG+RVSELV L+   ++L +  + + GKGNKERLV L   A+
Sbjct: 125 IDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAV 184

Query: 181 HALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240
           + L+ Y +      + G  + +   S +   ++RQ F   +K  A  AGI  + +SPH++
Sbjct: 185 YWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVL 244

Query: 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286
           RHAFA+HLL  GADLR +Q+LLGH+D+STTQIYTH+  ++L++L Q
Sbjct: 245 RHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQ 290


>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
>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
>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
>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
>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
>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
>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
>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
>2key_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
>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

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target300 site-specific tyrosine recombinase XerD [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
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 100.0
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 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 99.97
1ae9_A179 Lambda integrase; DNA recombination, site-specific reco 99.88
3nrw_A117 Phage integrase/site-specific recombinase; alpha-helica 99.63
2oxo_A103 Integrase; DNA-binding protein, four-helix bundle, DNA 99.31
2key_A112 Putative phage integrase; protein structure, PSI, NESG, 99.31
2kd1_A118 DNA integration/recombination/invertion protein; protei 99.22
2kiw_A111 INT protein; alpha, structural genomics, PSI-2, protein 99.18
2kkp_A117 Phage integrase; SAM-like domain, alpha-helical bundle, 99.18
3lys_A112 Prophage PI2 protein 01, integrase; helical N-terminal 99.16
2khq_A110 Integrase; all-alpha, structural genomics, PSI-2, prote 99.14
2kob_A108 Uncharacterized protein; alpha beta, structural genomic 99.1
2kj9_A118 Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structur 98.46
2kkv_A121 Integrase; protein structure, PSI, nesgc, structural ge 98.44
2kj8_A118 Putative prophage CPS-53 integrase; INTS, INTC, YFDB, D 98.37
2kj5_A116 Phage integrase; GFT NMR, PSI-2, NESG, structural genom 98.23
2khv_A106 Phage integrase; solution structure, GFT, NESG, structu 97.52
3m4a_A346 Putative type I topoisomerase; type IB, topib, protein- 97.81
2v6e_A558 Protelemorase; hairpin telomere, hydrolase, resolvase, 97.42
2h7g_X314 DNA topoisomerase 1; type IB topoisomerase, DNA binding 97.07
2b9s_A432 Topoisomerase I-like protein; vanadate complex, isomera 96.16
1a31_A591 Protein (topoisomerase I); topoisomerase I/DNA, DNA, is 93.82
1a0p_A290 Site-specific recombinase XERD; DNA binding, DNA recomb 90.73
>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=325.35  Aligned_cols=276  Identities=39%  Similarity=0.594  Sum_probs=223.0

Q ss_pred             CHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             64664138999999999999999997544998688999999999999997799843532210112334321000122222
Q gi|255764498|r    2 MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKD   81 (300)
Q Consensus         2 l~~~R~~S~~T~~~Y~~~l~~f~~~~~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~T~~~~~~~l~~~~~~~~~~~~~~~   81 (300)
                      |..|||+|++|+++|+.+|+.|..||+.+++++.+++..++.+|+.++.+++.+++|++++++.|++||+|+.+.+++..
T Consensus        13 l~~er~ls~~T~~~Y~~~l~~f~~~l~~~~~~~~~i~~~~i~~~~~~l~~~~~s~~t~~~~l~~l~~~~~~~~~~~~~~~   92 (290)
T 1a0p_A           13 LWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSARLLSAVRRLFQYLYREKFRED   92 (290)
T ss_dssp             HHHTTCSCHHHHHHHHHHHHHHHHHHHHTSCCTTTCCHHHHHHHHHSCC-------CHHHHHHHHHHHHHHHHHTTSSSS
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99986908999999999999999999885999376999999999999987799889999999999999999998243346


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCC
Q ss_conf             21222212122211122332024699998643200125610277654311000122100134333432000001111000
Q gi|255764498|r   82 NPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTM  161 (300)
Q Consensus        82 np~~~i~~~k~~~~~~~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i  161 (300)
                      +|+..+..++..+.........+....+...       ........++++++.+++.||||++|+++|+|+|||++++.+
T Consensus        93 ~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~l~~~tG~R~~Ei~~L~~~did~~~~~i  165 (290)
T 1a0p_A           93 DPSAHLASPKLPQRLPKDLSEAQVERLLQAP-------LIDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVV  165 (290)
T ss_dssp             CTTSCC----------CCCCHHHHHHHHHCS-------CTTSHHHHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEE
T ss_pred             CHHHHHCCCCCCCCCCCCCCHHHHHHHHHHH-------HCCCCHHHHHHHHHHHHHHHCCCHHHHHHCCHHHCCCCCCEE
T ss_conf             8176503777666676510089999987521-------001341189999999999958778999809499957579989


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHH
Q ss_conf             111222111110000124788753232100124-6777520012333222221111111012344201466764259885
Q gi|255764498|r  162 IIQGKGNKERLVILSPSALHALQMYKKTCSSMK-MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII  240 (300)
Q Consensus       162 ~v~~K~~k~R~ipi~~~~~~~l~~y~~~~~~~~-~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~l  240 (300)
                      .+.+|++++|.+|+.+.....+..+........ ......++++. .++.......+...++.+...+|+..++++||+|
T Consensus       166 ~~~~K~~k~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~H~l  244 (290)
T 1a0p_A          166 RVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPS-QRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVL  244 (290)
T ss_dssp             EEECSSSCEEEEECCHHHHHHHHHHHHHTHHHHHTTCCCCBSSBC-TTSSBCCHHHHHHHHHHHHHHTTCCGGGCCHHHH
T ss_pred             EECCCCCCEEEECCHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             866889940141132777778999998500111013445554533-3566542378999999999994578999874517


Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             889999999858888899998558998998999645999999999
Q gi|255764498|r  241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLV  285 (300)
Q Consensus       241 Rht~at~l~~~G~~~~~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~  285 (300)
                      ||||||.++++|+|+..||++|||+|++||++|+|++.+.+++++
T Consensus       245 Rht~at~l~~~G~~~~~i~~~lGH~s~~tT~~Y~~~~~~~lr~~~  289 (290)
T 1a0p_A          245 RHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLH  289 (290)
T ss_dssp             HHHHHHHHHHHCSSCGGGSSCC--CCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             799999999878999999988189988999999878999999862



>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
>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
>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
>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
>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
>2kiw_A INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435} 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
>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
>2kob_A Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753} 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
>2kkv_A Integrase; protein structure, PSI, nesgc, structural genomics, protein structure initiative, northeast structural genomics consortium; NMR {Salmonella enterica subsp} 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
>2kj5_A Phage integrase; GFT NMR, PSI-2, NESG, structural genomics, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196} 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
>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
>2v6e_A Protelemorase; hairpin telomere, hydrolase, resolvase, protelomerase, DNA distortion; 3.20A {Klebsiella phage PHIKO2} 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
>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
>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

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 300 site-specific tyrosine recombinase XerD [Candidatus Lib
d1a0pa2182 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia col 9e-29
d1aiha_170 d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 106 3e-13
d1f44a2214 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 4e-13
d1ae9a_179 d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [T 1e-11
d1a0pa198 a.60.9.1 (A:3-100) Recombinase XerD {Escherichia coli [ 4e-12
d1f44a1110 a.60.9.1 (A:20-129) Cre recombinase {Bacteriophage P1 [ 7e-07
>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 =  120 bits (302), Expect = 9e-29
 Identities = 77/189 (40%), Positives = 117/189 (61%), Gaps = 7/189 (3%)

Query: 98  KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLT 157
           K L +  +  LL+   I+       Q   +R   ++E+LYATG+RVSELV L+   ++L 
Sbjct: 1   KDLSEAQVERLLQAPLID-------QPLELRDKAMLEVLYATGLRVSELVGLTMSDISLR 53

Query: 158 ERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVF 217
           +  + + GKGNKERLV L   A++ L+ Y +      + G  + +   S +   ++RQ F
Sbjct: 54  QGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTF 113

Query: 218 ARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLL 277
              +K  A  AGI  + +SPH++RHAFA+HLL  GADLR +Q+LLGH+D+STTQIYTH+ 
Sbjct: 114 WHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVA 173

Query: 278 PDKLQKLVQ 286
            ++L++L Q
Sbjct: 174 TERLRQLHQ 182


>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]} Length = 170 Back     information, alignment and structure
>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
>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
Target300 site-specific tyrosine recombinase XerD [Candidatus Lib
d1a0pa2182 Recombinase XerD {Escherichia coli [TaxId: 562]} 100.0
d1aiha_170 Integrase {Bacteriophage HP1 [TaxId: 10690]} 99.97
d1f44a2214 Cre recombinase {Bacteriophage P1 [TaxId: 10678]} 99.95
d1ae9a_179 Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} 99.89
d1a0pa198 Recombinase XerD {Escherichia coli [TaxId: 562]} 99.71
d1f44a1110 Cre recombinase {Bacteriophage P1 [TaxId: 10678]} 99.45
d1a41a_230 Eukaryotic DNA topoisomerase I, catalytic core {Vaccini 97.17
d1k4ta2263 Eukaryotic DNA topoisomerase I, catalytic core {Human ( 96.61
d1p4ea2287 Flp recombinase {Baker's yeast (Saccharomyces cerevisia 91.7
d1a0pa198 Recombinase XerD {Escherichia coli [TaxId: 562]} 94.46
>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=100.00  E-value=1.1e-35  Score=224.22  Aligned_cols=180  Identities=43%  Similarity=0.642  Sum_probs=147.2

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf             23320246999986432001256102776543110001221001343334320000011110001112221111100001
Q gi|255764498|r   98 KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSP  177 (300)
Q Consensus        98 ~~ls~~e~~~ll~~~~~~~~~~~~~~~~~~R~~~il~ll~~tGlR~~Ei~~L~~~di~~~~~~i~v~~K~~k~R~ipi~~  177 (300)
                      +.||+||+++|+++...       .....+||+++|.++++||||++|+++|+|+||+++++.+.+.+|++|.|.++.+.
T Consensus         1 k~Lt~eei~~ll~~~~~-------~~~~~lRd~~l~~l~~~tG~R~~ei~~L~~~~i~~~~~~i~~~~~~~k~r~~~~~~   73 (182)
T d1a0pa2           1 KDLSEAQVERLLQAPLI-------DQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGE   73 (182)
T ss_dssp             CCCCHHHHHHHHHCSCT-------TSHHHHHHHHHHHHHHHHCCCHHHHTTCBGGGEETTTTEEEEECSSSCEEEEECCH
T ss_pred             CCCCHHHHHHHHHCCCC-------CCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCEEEEEECCCCEEEEEEECC
T ss_conf             98999999999827463-------88187999999999999677647742021414114432899836898012575200


Q ss_pred             HHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHH
Q ss_conf             24788753232100124-67775200123332222211111110123442014667642598858899999998588888
Q gi|255764498|r  178 SALHALQMYKKTCSSMK-MTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLR  256 (300)
Q Consensus       178 ~~~~~l~~y~~~~~~~~-~~~~~~~lf~~~~~~~~~s~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~~~G~~~~  256 (300)
                      .....+..++....... ......++++ ..++.+++.++++..++++++.+|++.++++||+|||||||.|+++|+|+.
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~t~H~~Rht~at~l~~~G~~~~  152 (182)
T d1a0pa2          74 EAVYWLETYLEHGRPWLLNGVSIDVLFP-SQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLR  152 (182)
T ss_dssp             HHHHHHHHHHHHTHHHHHTTCCCCBSSB-CTTSSBCCHHHHHHHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHCSSCG
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCHH
T ss_conf             1335566655311230012345654210-235773668999999999999849985783614146589996556499999


Q ss_pred             HHHHHHCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf             99998558998998999645999999999
Q gi|255764498|r  257 TIQILLGHTDISTTQIYTHLLPDKLQKLV  285 (300)
Q Consensus       257 ~v~~~lGH~s~~tT~~Y~~~~~~~~~~~~  285 (300)
                      .|+++|||+|++||++|++++.+++++++
T Consensus       153 ~I~~~lGH~s~~tt~~Y~~~~~e~~re~~  181 (182)
T d1a0pa2         153 VVQMLLGHSDLSTTQIYTHVATERLRQLH  181 (182)
T ss_dssp             GGSSCC--CCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             99999589988999987687999999860



>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
>d1p4ea2 d.163.1.1 (A:136-422) Flp recombinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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 300 site-specific tyrosine recombinase XerD [Candidatu
1a0p_A_101-290190 (A:101-290) Site-specific recombinase XERD; DNA bi 5e-30
1ae9_A_179 (A:) Lambda integrase; DNA recombination, site-spe 1e-21
1z1b_A_167-356190 (A:167-356) Integrase; protein-DNA complex, DNA bi 3e-21
1z19_A_94-283190 (A:94-283) Integrase; protein-DNA complex, DNA bin 4e-21
1xo0_A_115-310196 (A:115-310) Recombinase CRE; CRE recombinase, holl 2e-13
1aih_A_1-49_87-170133 (A:1-49,A:87-170) HP1 integrase; DNA integration, 1e-18
2a3v_A_95-144_243-320128 (A:95-144,A:243-320) Site-specific recombinase INT 2e-15
1xo0_A_1-114114 (A:1-114) Recombinase CRE; CRE recombinase, hollid 7e-17
1a0p_A_1-100100 (A:1-100) Site-specific recombinase XERD; DNA bind 5e-16
2kkp_A_27-11791 (A:27-117) Phage integrase; SAM-like domain, alpha 4e-13
2kd1_A_118 (A:) DNA integration/recombination/invertion prote 8e-13
2a3v_A_1-9494 (A:1-94) Site-specific recombinase INTI4; protein- 7e-12
2kiw_A_111 (A:) INT protein; alpha, structural genomics, PSI- 2e-11
2kob_A_108 (A:) Uncharacterized protein; alpha beta, structur 5e-11
2oxo_A_103 (A:) Integrase; DNA-binding protein, four-helix bu 8e-11
2key_A_112 (A:) Putative phage integrase; protein structure, 1e-10
2khq_A_110 (A:) Integrase; all-alpha, structural genomics, PS 2e-10
1z1b_A_75-16692 (A:75-166) Integrase; protein-DNA complex, DNA bin 7e-10
1z19_A_1-9393 (A:1-93) Integrase; protein-DNA complex, DNA bindi 3e-09
2kj5_A_116 (A:) Phage integrase; GFT NMR, PSI-2, NESG, struct 1e-08
2kkv_A_121 (A:) Integrase; protein structure, PSI, nesgc, str 4e-08
2kj9_A_118 (A:) Integrase; DNA_BRE_C superfamily, INTB, PSI-2 5e-08
2kj8_A_118 (A:) Putative prophage CPS-53 integrase; INTS, INT 4e-07
2khv_A_106 (A:) Phage integrase; solution structure, GFT, NES 1e-04
2a3v_A_95-144_243-320128 (A:95-144,A:243-320) Site-specific recombinase INT 5e-06
>1a0p_A (A:101-290) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli}Length = 190 Back     alignment and structure
 Score =  125 bits (315), Expect = 5e-30
 Identities = 81/197 (41%), Positives = 121/197 (61%), Gaps = 7/197 (3%)

Query: 90  PKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTL 149
           PK    LPK L +  +  LL+   I+       Q   +R   ++E+LYATG+RVSELV L
Sbjct: 1   PKLPQRLPKDLSEAQVERLLQAPLID-------QPLELRDKAMLEVLYATGLRVSELVGL 53

Query: 150 SAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKT 209
           +   ++L +  + + GKGNKERLV L   A++ L+ Y +      + G  + +   S + 
Sbjct: 54  TMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRA 113

Query: 210 GHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDIST 269
             ++RQ F   +K  A  AGI  + +SPH++RHAFA+HLL  GADLR +Q+LLGH+D+ST
Sbjct: 114 QQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLST 173

Query: 270 TQIYTHLLPDKLQKLVQ 286
           TQIYTH+  ++L++L Q
Sbjct: 174 TQIYTHVATERLRQLHQ 190


>1ae9_A (A:) Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda}Length = 179 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
>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
>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
>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
>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
>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
>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
>2oxo_A (A:) Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage}Length = 103 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
>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
>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
>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
>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
>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
>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
>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
>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
Target300 site-specific tyrosine recombinase XerD [Candidatus Lib
1a0p_A_101-290190 Site-specific recombinase XERD; DNA binding, DNA r 99.97
1xo0_A_115-310196 Recombinase CRE; CRE recombinase, holliday junctio 99.95
2a3v_A_95-144_243-320128 Site-specific recombinase INTI4; protein-DNA compl 99.94
1z1b_A_167-356190 Integrase; protein-DNA complex, DNA binding protei 99.92
1z19_A_94-283190 Integrase; protein-DNA complex, DNA binding protei 99.91
1ae9_A_179 Lambda integrase; DNA recombination, site-specific 99.9
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 99.71
1a0p_A_1-100100 Site-specific recombinase XERD; DNA binding, DNA r 99.64
2kd1_A_118 DNA integration/recombination/invertion protein; p 99.58
2kiw_A_111 INT protein; alpha, structural genomics, PSI-2, pr 99.5
2a3v_A_1-9494 Site-specific recombinase INTI4; protein-DNA compl 99.48
2key_A_112 Putative phage integrase; protein structure, PSI, 99.42
2oxo_A_103 Integrase; DNA-binding protein, four-helix bundle, 99.4
2khq_A_110 Integrase; all-alpha, structural genomics, PSI-2, 99.38
2kkp_A_27-11791 Phage integrase; SAM-like domain, alpha-helical bu 99.32
2kob_A_108 Uncharacterized protein; alpha beta, structural ge 99.29
2kkv_A_121 Integrase; protein structure, PSI, nesgc, structur 99.25
1z19_A_1-9393 Integrase; protein-DNA complex, DNA binding protei 99.17
2kj9_A_118 Integrase; DNA_BRE_C superfamily, INTB, PSI-2, str 99.14
1z1b_A_75-16692 Integrase; protein-DNA complex, DNA binding protei 99.14