254780490

254780490

site-specific tyrosine recombinase XerC

GeneID in NCBI database:8209479Locus tag:CLIBASIA_01885
Protein GI in NCBI database:254780490Protein Accession:YP_003064903.1
Gene range:+(412606, 412809)Protein Length:67aa
Gene description:site-specific tyrosine recombinase XerC
COG prediction:[L] Integrase
KEGG prediction:xerC; site-specific tyrosine recombinase XerC
SEED prediction:probable integrase/recombinase protein
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60-------
MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKKN
ccccccHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHccHHHHHHHHHHHcHHHHcccccc
cccccccHHHHHHHHHHHccHcHHHHHHHHccccccccEEEccccHHHHHHHHHHHccHHHcccccc
msttahtlRHSFATHllsnggdlrSIQSIlghsrlstTQIYTNVNSKRMMEIydqthpsitqkdkkn
msttahtlrhsFATHLLSNGGDLRSIQSilghsrlstTQIYTNVNSKRMMEiydqthpsitqkdkkn
MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKKN
**TTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYD*************
MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKKN
****AHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP*********
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MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKKN
MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKKN
MSTTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDKKN

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
254780882328 site-specific tyrosine recombinase XerC [Candidatu 4e-32
255764498300 site-specific tyrosine recombinase XerD [Candidatu 1e-13
>gi|254780882|ref|YP_003065295.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62] Length = 328 Back     alignment
 Score =  127 bits (318), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 64/71 (90%), Positives = 65/71 (91%), Gaps = 4/71 (5%)

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

Query: 57  HPSITQKDKKN 67
           HPSITQKDKKN
Sbjct: 318 HPSITQKDKKN 328

>gi|255764498|ref|YP_003065000.2| site-specific tyrosine recombinase XerD [Candidatus Liberibacter asiaticus str. psy62] Length = 300 Back     alignment
 Score = 65.9 bits (159), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 46/63 (73%), Gaps = 1/63 (1%)

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

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

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

IdentityAlignment graphLength Definition Round E-value
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
254780882328 site-specific tyrosine recombinase XerC [Candidatus Lib 1 6e-28
315122698324 site-specific tyrosine recombinase XerC [Candidatus Lib 1 7e-19
307316349330 integrase family protein [Sinorhizobium meliloti AK83] 1 9e-18
15966799330 site-specific tyrosine recombinase XerC [Sinorhizobium 1 1e-17
34222987318 RecName: Full=Tyrosine recombinase xerC Length = 318 1 1e-17
27375557321 site-specific tyrosine recombinase XerC [Bradyrhizobium 1 2e-17
255264826304 site-specific tyrosine recombinase XerC [Thalassiobium 1 2e-17
92116157300 site-specific tyrosine recombinase XerC [Nitrobacter ha 1 4e-17
328545835316 Site-specific recombinase, phage integrase family prote 1 4e-17
85713711322 phage integrase [Nitrobacter sp. Nb-311A] Length = 322 1 5e-17
>gi|254780882|ref|YP_003065295.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter asiaticus str. psy62] Length = 328 Back     alignment and organism information
 Score =  127 bits (318), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 64/71 (90%), Positives = 65/71 (91%), Gaps = 4/71 (5%)

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

Query: 57  HPSITQKDKKN 67
           HPSITQKDKKN
Sbjct: 318 HPSITQKDKKN 328


Species: Candidatus Liberibacter asiaticus
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|315122698|ref|YP_004063187.1| site-specific tyrosine recombinase XerC [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 324 Back     alignment and organism information
>gi|307316349|ref|ZP_07595793.1| integrase family protein [Sinorhizobium meliloti AK83] Length = 330 Back     alignment and organism information
>gi|15966799|ref|NP_387152.1| site-specific tyrosine recombinase XerC [Sinorhizobium meliloti 1021] Length = 330 Back     alignment and organism information
>gi|34222987|sp|Q92LK1|XERC_RHIME RecName: Full=Tyrosine recombinase xerC Length = 318 Back     alignment and organism information
>gi|27375557|ref|NP_767086.1| site-specific tyrosine recombinase XerC [Bradyrhizobium japonicum USDA 110] Length = 321 Back     alignment and organism information
>gi|255264826|ref|ZP_05344168.1| site-specific tyrosine recombinase XerC [Thalassiobium sp. R2A62] Length = 304 Back     alignment and organism information
>gi|92116157|ref|YP_575886.1| site-specific tyrosine recombinase XerC [Nitrobacter hamburgensis X14] Length = 300 Back     alignment and organism information
>gi|328545835|ref|YP_004305944.1| Site-specific recombinase, phage integrase family protein [polymorphum gilvum SL003B-26A1] Length = 316 Back     alignment and organism information
>gi|85713711|ref|ZP_01044701.1| phage integrase [Nitrobacter sp. Nb-311A] Length = 322 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
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
PRK00236297 PRK00236, xerC, site-specific tyrosine recombinase XerC 2e-25
TIGR02224295 TIGR02224, recomb_XerC, tyrosine recombinase XerC 2e-23
TIGR02225291 TIGR02225, recomb_XerD, tyrosine recombinase XerD 3e-22
PRK00283299 PRK00283, xerD, site-specific tyrosine recombinase XerD 5e-21
cd00798284 cd00798, INT_XerDC, XerD and XerC integrases, DNA break 9e-18
COG4973299 COG4973, XerC, Site-specific recombinase XerC [DNA repl 1e-16
PRK01287358 PRK01287, xerC, site-specific tyrosine recombinase XerC 6e-16
TIGR02249315 TIGR02249, integrase_gron, integron integrase 4e-14
cd01193242 cd01193, INT_IntI, IntI (E2) integrases, site-specific 3e-13
pfam00589170 pfam00589, Phage_integrase, Phage integrase family 9e-12
PRK15417337 PRK15417, PRK15417, integrase/recombinase; Provisional 5e-10
cd01185299 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA 6e-10
cd00797158 cd00797, HP1_INT_C, Phage HP1 integrase, C-terminal cat 6e-09
cd01182162 cd01182, INT_REC_C, DNA breaking-rejoining enzymes, int 7e-09
cd01190260 cd01190, INT_SG5, INT_SG5, DNA breaking-rejoining enzym 2e-08
cd00397164 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-t 2e-08
cd01188188 cd01188, INT_pAE1, pAE1 and related integrases, DNA bre 6e-08
PHA02601333 PHA02601, int, integrase; Provisional 9e-08
PRK05084357 PRK05084, xerS, site-specific tyrosine recombinase XerS 2e-06
cd01183196 cd01183, INT_SG1_C, INT_SG1, DNA breaking-rejoining enz 4e-06
cd01189191 cd01189, INT_phiLC3_C, phiLC3 phage and phage-related i 2e-05
cd01192177 cd01192, INT_P22_C, P22-like integrases, site-specific 3e-05
cd01197180 cd01197, INT_FimBE_C, FimB and FimE and related protein 4e-05
cd01199205 cd01199, INT_Tn1545_C, Tn1545-related conjugative trans 1e-04
cd01196263 cd01196, INT_VanD, VanD integrase, IntD, and related in 2e-04
cd01198186 cd01198, INT_ASSRA_C, Archaeal site-specific recombinas 2e-04
cd01195195 cd01195, INT_Tn544B_C, Tn544B and related transposases, 4e-04
PRK09870200 PRK09870, PRK09870, tyrosine recombinase; Provisional 4e-04
PRK09871198 PRK09871, PRK09871, tyrosine recombinase; Provisional 5e-04
COG4974300 COG4974, XerD, Site-specific recombinase XerD [DNA repl 5e-19
>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|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed 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|179273 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed Back     alignment and domain information
>gnl|CDD|131303 TIGR02249, integrase_gron, integron integrase 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|144254 pfam00589, Phage_integrase, Phage integrase family Back     alignment and domain information
>gnl|CDD|185315 PRK15417, PRK15417, integrase/recombinase; Provisional 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|29498 cd00797, HP1_INT_C, Phage HP1 integrase, 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|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|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|164996 PHA02601, int, integrase; Provisional Back     alignment and domain information
>gnl|CDD|179927 PRK05084, xerS, site-specific tyrosine recombinase XerS; Reviewed 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|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|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|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|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|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|29516 cd01195, INT_Tn544B_C, Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain Back     alignment and domain information
>gnl|CDD|182125 PRK09870, PRK09870, tyrosine recombinase; Provisional Back     alignment and domain information
>gnl|CDD|182126 PRK09871, PRK09871, tyrosine recombinase; Provisional Back     alignment and domain information
>gnl|CDD|34580 COG4974, XerD, Site-specific recombinase XerD [DNA replication, recombination, and repair] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 67 site-specific tyrosine recombinase XerC [Candidatus Lib
TIGR02224313 recomb_XerC tyrosine recombinase XerC; InterPro: IPR011 99.97
TIGR02225305 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011 99.97
PRK01287361 xerC site-specific tyrosine recombinase XerC; Reviewed 99.93
cd01198186 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA 99.91
COG4974300 XerD Site-specific recombinase XerD [DNA replication, r 99.91
PRK09870200 tyrosine recombinase; Provisional 99.9
PRK09871198 tyrosine recombinase; Provisional 99.9
PRK00283296 xerD site-specific tyrosine recombinase XerD; Reviewed 99.88
cd01190260 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integr 99.88
PRK00236295 xerC site-specific tyrosine recombinase XerC; Reviewed 99.88
TIGR02249320 integrase_gron integron integrase; InterPro: IPR011946 99.88
cd01196263 INT_VanD VanD integrase, IntD, and related integrases, 99.87
PRK05084360 xerS site-specific tyrosine recombinase XerS; Reviewed 99.87
COG4973299 XerC Site-specific recombinase XerC [DNA replication, r 99.87
cd01185299 INT_Tn4399 Tn4399 and related integrases, DNA breaking- 99.84
cd01195195 INT_Tn544B_C Tn544B and related transposases, DNA break 99.81
cd01194186 INT_Tn554A_C Tn544A and related transposases, DNA break 99.81
PRK02436247 xerD site-specific tyrosine recombinase XerD-like prote 99.8
cd01197180 INT_FimBE_C FimB and FimE and related proteins, DNA bre 99.79
cd01188188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejo 99.79
cd01186180 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, inte 99.79
cd00798284 INT_XerDC XerD and XerC integrases, DNA breaking-rejoin 99.79
cd01199205 INT_Tn1545_C Tn1545-related conjugative transposon inte 99.77
cd00797158 HP1_INT_C Phage HP1 integrase, C-terminal catalytic dom 99.75
cd01192177 INT_P22_C P22-like integrases, site-specific recombinas 99.75
cd01187299 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integr 99.75
cd01183196 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, inte 99.72
cd01193242 INT_IntI IntI (E2) integrases, site-specific tyrosine r 99.72
cd00796206 INT_Rci Rci recombinase, C-terminal catalytic domain. R 99.71
cd01189191 INT_phiLC3_C phiLC3 phage and phage-related integrases, 99.63
cd00799287 INT_Cre Cre recombinase, C-terminal catalytic domain. C 99.63
pfam00589170 Phage_integrase Phage integrase family. Members of this 99.53
cd00397164 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal ca 99.5
cd01191196 INT_phiCTX_C phiCTX phage and phage-related integrases, 99.48
cd00801357 INT_P4 Bacteriophage P4 integrase. P4-like integrases a 99.44
cd01184181 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, inte 99.43
cd00800162 INT_Lambda_C Lambda integrase, C-terminal catalytic dom 99.14
cd01182162 INT_REC_C DNA breaking-rejoining enzymes, intergrase/re 99.13
COG0582309 XerC Integrase [DNA replication, recombination, and rep 98.51
PRK09692413 integrase; Provisional 97.88
COG4688 665 Uncharacterized protein conserved in bacteria [Function 90.68
>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
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed 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
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09870 tyrosine recombinase; Provisional Back     alignment and domain information
>PRK09871 tyrosine recombinase; Provisional Back     alignment and domain information
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed 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
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed 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
>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
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed Back     alignment and domain information
>COG4973 XerC Site-specific recombinase XerC [DNA replication, recombination, and repair] 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
>cd01195 INT_Tn544B_C Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, 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
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed 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
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal 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
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains 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
>cd00797 HP1_INT_C Phage HP1 integrase, 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
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains 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
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains Back     alignment and domain information
>cd00796 INT_Rci Rci recombinase, C-terminal catalytic domain Back     alignment and domain information
>cd01189 INT_phiLC3_C phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain Back     alignment and domain information
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain Back     alignment and domain information
>pfam00589 Phage_integrase Phage integrase family 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
>cd00801 INT_P4 Bacteriophage P4 integrase 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
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain Back     alignment and domain information
>COG0582 XerC Integrase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09692 integrase; Provisional Back     alignment and domain information
>COG4688 Uncharacterized protein conserved in bacteria [Function unknown] 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
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
1a0p_A290 Site-Specific Recombinase, Xerd Length = 290 1e-15
2a3v_A320 Structural Basis For Broad Dna-Specificity In Integ 7e-13
1aih_A170 Catalytic Domain Of Bacteriophage Hp1 Integrase Len 5e-12
>gi|157829635|pdb|1A0P|A Chain A, Site-Specific Recombinase, Xerd Length = 290 Back     alignment and structure
 Score = 86.2 bits (213), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/53 (54%), Positives = 42/53 (79%)

Query: 2   STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYD 54
             + H LRH+FATHLL++G DLR +Q +LGHS LSTTQIYT+V ++R+ +++ 
Sbjct: 238 KLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQ 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
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
1a0p_A290 Site-specific recombinase XERD; DNA binding, DNA recomb 4e-14
2a3v_A320 Site-specific recombinase INTI4; protein-DNA complex, r 1e-13
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 1e-11
3nkh_A244 Integrase; alpha-fold, MRSA protein, structural genomic 4e-11
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 4e-09
1z19_A283 Integrase; protein-DNA complex, DNA binding protein/DNA 2e-08
1ae9_A179 Lambda integrase; DNA recombination, site-specific reco 5e-06
1aih_A170 HP1 integrase; DNA integration, recombination; 2.50A {B 1e-04
>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 = 71.4 bits (173), Expect = 4e-14
 Identities = 29/50 (58%), Positives = 42/50 (84%)

Query: 4   TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY 53
           + H LRH+FATHLL++G DLR +Q +LGHS LSTTQIYT+V ++R+ +++
Sbjct: 240 SPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLH 289


>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
>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
>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
>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
>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
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
2a3v_A320 Site-specific recombinase INTI4; protein-DNA complex, r 99.73
1a0p_A290 Site-specific recombinase XERD; DNA binding, DNA recomb 99.63
1xo0_A324 Recombinase CRE; CRE recombinase, holliday junction, re 99.59
1aih_A170 HP1 integrase; DNA integration, recombination; 2.50A {H 99.58
3nkh_A244 Integrase; alpha-fold, MRSA protein, structural genomic 99.53
1z1b_A356 Integrase; protein-DNA complex, DNA binding protein/DNA 99.01
1z19_A283 Integrase; protein-DNA complex, DNA binding protein/DNA 98.82
1ae9_A179 Lambda integrase; DNA recombination, site-specific reco 98.53
2v6e_A558 Protelemorase; hairpin telomere, hydrolase, resolvase, 91.2
>2a3v_A Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Back     alignment and structure
Probab=99.73  E-value=2.5e-19  Score=119.19  Aligned_cols=55  Identities=49%  Similarity=0.748  Sum_probs=51.0

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999995
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQT   56 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~   56 (67)
                      ++|||+|||||||.|+++|+|+..||++|||+|++||++|+|+.++.++++++.+
T Consensus       263 ~~s~H~lRHtfaT~ll~~g~~l~~vq~~lGHss~~tT~~Y~hl~~~~~~~~~~~l  317 (320)
T 2a3v_A          263 TVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPL  317 (320)
T ss_dssp             CCCHHHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHGGGCC------CCCCCHH
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9888777899999999878999999988389988999999827997899997176



>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
>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
>1aih_A HP1 integrase; DNA integration, recombination; 2.50A {Haemophilus phage HP1} SCOP: d.163.1.1 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
>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
>1ae9_A Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Enterobacteria phage lambda} SCOP: d.163.1.1 Back     alignment and structure
>2v6e_A Protelemorase; hairpin telomere, hydrolase, resolvase, protelomerase, DNA distortion; 3.20A {Klebsiella phage PHIKO2} 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 67 site-specific tyrosine recombinase XerC [Candidatus Lib
d1a0pa2182 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia col 4e-11
d1f44a2214 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 4e-07
d1aiha_170 d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 106 9e-06
d1ae9a_179 d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [T 2e-05
>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 = 60.5 bits (145), Expect = 4e-11
 Identities = 29/50 (58%), Positives = 42/50 (84%)

Query: 4   TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIY 53
           + H LRH+FATHLL++G DLR +Q +LGHS LSTTQIYT+V ++R+ +++
Sbjct: 132 SPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLH 181


>d1f44a2 d.163.1.1 (A:130-343) Cre recombinase {Bacteriophage P1 [TaxId: 10678]} Length = 214 Back     information, alignment and structure
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]} Length = 170 Back     information, alignment and structure
>d1ae9a_ d.163.1.1 (A:) Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} Length = 179 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
d1aiha_170 Integrase {Bacteriophage HP1 [TaxId: 10690]} 99.56
d1a0pa2182 Recombinase XerD {Escherichia coli [TaxId: 562]} 99.55
d1f44a2214 Cre recombinase {Bacteriophage P1 [TaxId: 10678]} 99.45
d1ae9a_179 Integrase (Int) {Bacteriophage lambda [TaxId: 10710]} 98.78
>d1aiha_ d.163.1.1 (A:) Integrase {Bacteriophage HP1 [TaxId: 10690]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: DNA breaking-rejoining enzymes
superfamily: DNA breaking-rejoining enzymes
family: Lambda integrase-like, catalytic core
domain: Integrase
species: Bacteriophage HP1 [TaxId: 10690]
Probab=99.56  E-value=3.6e-16  Score=101.69  Aligned_cols=60  Identities=30%  Similarity=0.577  Sum_probs=55.9

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHHH
Q ss_conf             2160363899999999808999999998488888999999863999999999995821133
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQ   62 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~~   62 (67)
                      .++||+|||||||.++++|+|+..|+++|||+++.+|++|++++.+++++++ +++|+.+.
T Consensus       109 ~~~~H~lRht~at~l~~~g~~~~~i~~~lGH~~~~~t~~Y~~~~~~~~~~a~-~~~p~~~~  168 (170)
T d1aiha_         109 GQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAV-KFNPLSNP  168 (170)
T ss_dssp             TCTTTHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHGGGGGGSCCCTTHHH-HHSTTTSC
T ss_pred             CCEEEECHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-HHCCCCCC
T ss_conf             6101110465514552169899999998089998999988767999999999-86857687



>d1a0pa2 d.163.1.1 (A:111-292) Recombinase XerD {Escherichia coli [TaxId: 562]} 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

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 67 site-specific tyrosine recombinase XerC [Candidatu
2a3v_A_95-144_243-320128 (A:95-144,A:243-320) Site-specific recombinase INT 1e-11
1aih_A_1-49_87-170133 (A:1-49,A:87-170) HP1 integrase; DNA integration, 3e-11
1a0p_A_101-290190 (A:101-290) Site-specific recombinase XERD; DNA bi 7e-10
1z1b_A_167-356190 (A:167-356) Integrase; protein-DNA complex, DNA bi 2e-08
1ae9_A_179 (A:) Lambda integrase; DNA recombination, site-spe 2e-08
1xo0_A_115-310196 (A:115-310) Recombinase CRE; CRE recombinase, holl 2e-05
1z19_A_94-283190 (A:94-283) Integrase; protein-DNA complex, DNA bin 7e-05
>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
 Score = 63.3 bits (154), Expect = 1e-11
 Identities = 27/55 (49%), Positives = 35/55 (63%)

Query: 4   TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP 58
           T HTLRHSFATHLL  G D+R++Q  LGH+ + TTQIYT+V  +    +      
Sbjct: 73  TCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLSPLSR 127


>1aih_A (A:1-49,A:87-170) HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1}Length = 133 Back     alignment and structure
>1a0p_A (A:101-290) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli}Length = 190 Back     alignment and structure
>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
>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
>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

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target67 site-specific tyrosine recombinase XerC [Candidatus Lib
1aih_A_1-49_87-170133 HP1 integrase; DNA integration, recombination; 2.5 99.67
2a3v_A_95-144_243-320128 Site-specific recombinase INTI4; protein-DNA compl 99.66
1a0p_A_101-290190 Site-specific recombinase XERD; DNA binding, DNA r 99.49
1xo0_A_115-310196 Recombinase CRE; CRE recombinase, holliday junctio 99.41
1z1b_A_167-356190 Integrase; protein-DNA complex, DNA binding protei 99.06
1z19_A_94-283190 Integrase; protein-DNA complex, DNA binding protei 99.05
1ae9_A_179 Lambda integrase; DNA recombination, site-specific 99.03
>1aih_A (A:1-49,A:87-170) HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1} Back     alignment and structure
Probab=99.67  E-value=1.5e-17  Score=110.79  Aligned_cols=61  Identities=30%  Similarity=0.557  Sum_probs=56.0

Q ss_pred             CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHCHHHHHH
Q ss_conf             21603638999999998089999999984888889999998639999999999958211333
Q gi|254780490|r    2 STTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQK   63 (67)
Q Consensus         2 ~~tpH~lRHt~at~l~~~G~~~~~vq~lLGH~~i~tT~~Y~~~~~~~~~~~~~~~~p~~~~k   63 (67)
                      ++|||+|||||||+++++|+|+..||++|||+|++||++|++++.++++++++. .|+.+.+
T Consensus        72 ~it~H~lRHT~At~l~~~G~d~~~Iq~~lGH~s~~tT~~Y~~~~~~~~~~~~e~-~~~~~~k  132 (133)
T 1aih_A           72 GQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVKF-NPLSNPA  132 (133)
T ss_dssp             TCTTTHHHHHHHHHHHHTTCCHHHHHHHHTCSSHHHHGGGGGGSCCCTTHHHHH-STTTSCC
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH-CCCCCCC
T ss_conf             620024688773787744730989999808998899987766799999999985-9565879



>2a3v_A (A:95-144,A:243-320) Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Back     alignment and structure
>1a0p_A (A:101-290) Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} Back     alignment and structure
>1xo0_A (A:115-310) Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1} Back     alignment and structure
>1z1b_A (A:167-356) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} Back     alignment and structure
>1z19_A (A:94-283) Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* Back     alignment and structure
>1ae9_A (A:) Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda} Back     alignment and structure