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Conserved domains on  [gi|1232827679|gb|OZA44549.1|]
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hypothetical protein B7X84_00260 [Alphaproteobacteria bacterium 17-39-52]

Protein Classification

site-specific integrase( domain architecture ID 10092408)

tyrosine based site-specific recombinase (integrase) is involved in cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct

CATH:  1.10.443.10
Gene Ontology:  GO:0015074|GO:0003677|GO:0006310
PubMed:  10047575|9278480|10577069
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 36-199 1.71e-46

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


:

Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 151.33  E-value: 1.71e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  36 RERFLNADEIERLLTILKREEKEGFYPwalhAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGK-KIIYLSSTA 114
Cdd:cd00796     1 RDRFLTEDEEARLLAALEESTNPHLRL----IVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKpRTVPLSDEA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 115 IELLQAIP-KIPENLHVICGGKEGAHLVNIHKAWGRIRKKAHLEDVRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQT 193
Cdd:cd00796    77 IAILKELKrKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKM 156


                  ....*.
gi 1232827679 194 TARYAH 199
Cdd:cd00796   157 TMRYAH 162
 
Name Accession Description Interval E-value
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 36-199 1.71e-46

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 151.33  E-value: 1.71e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  36 RERFLNADEIERLLTILKREEKEGFYPwalhAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGK-KIIYLSSTA 114
Cdd:cd00796     1 RDRFLTEDEEARLLAALEESTNPHLRL----IVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKpRTVPLSDEA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 115 IELLQAIP-KIPENLHVICGGKEGAHLVNIHKAWGRIRKKAHLEDVRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQT 193
Cdd:cd00796    77 IAILKELKrKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKM 156


                  ....*.
gi 1232827679 194 TARYAH 199
Cdd:cd00796   157 TMRYAH 162
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
21-212 3.85e-44

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 149.37  E-value: 3.85e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  21 HSNPCLHVKKYPENKRE-RFLNADEIERLLTILKREEKEGFYPWALhaIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLL 99
Cdd:COG4974    93 EDNPAAKVKLPKKPRKLpRVLTEEEIEALLEALDTETPEGLRDRAL--LLLLYATGLRVSELLGLKWSDIDLDRGTIRVR 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 100 DSKTGKK-IIYLSSTAIELLQAIPKI--PENLHVICGGKEGAHL--VNIHKAWGRIRKKAHLE-DVRLHDLRHTFASVAV 173
Cdd:COG4974   171 RGKGGKErTVPLSPEALEALREYLEErrPRDSDYLFPTRRGRPLsrRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLL 250

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1232827679 174 SQGLSLPVIGALLGHKHTQTTARYAHLMHQPLFEASEKI 212
Cdd:COG4974   251 EAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 39-200 6.36e-24

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 93.54  E-value: 6.36e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  39 FLNADEIERLLTILkreEKEGFYPWALHAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGKKI-IYLSSTAIEL 117
Cdd:pfam00589   1 RLTEDEVERLLDAA---ETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERtVPLSDAALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 118 LQ-----AIPKIPENLHVICGgKEGAHLV--NIHKAWGRIRKKAHLED-VRLHDLRHTFASVAVSQGLSLPVIGALLGHK 189
Cdd:pfam00589  78 LKewlskRLLEAPKSDYLFAS-KRGKPLSrqTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|.
gi 1232827679 190 HTQTTARYAHL 200
Cdd:pfam00589 157 SISTTQIYTHV 167
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 16-200 8.56e-14

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 68.76  E-value: 8.56e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  16 GYRPDhsNPCLHVKKyPenKRERF----LNADEIERLLTILKREEKEGFypwALHAIRLLLY-TGCRLSEILTLTWEEVD 90
Cdd:TIGR02225  82 GIRED--DPSALIEP-P--KVARKlpkvLTVEEVEALLAAPDVDTPLGL---RDRAMLELLYaTGLRVSELVGLRLEDVN 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  91 LDNQCLRLLDSKTGKKIIYLSSTAIELLQAIPKIPENLHVICGGKEGAHL-VNIHK-------AWGRIR---KKAHLE-D 158
Cdd:TIGR02225 154 LDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKESDALfLNRRGgplsrqgVWKILKeyaKRAGIEkP 233

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1232827679 159 VRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYAHL 200
Cdd:TIGR02225 234 ISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHV 275
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 38-200 3.99e-12

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 64.02  E-value: 3.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  38 RFLNADEIERLLTILKREEKEgfypwAL--HAIRLLLY-TGCRLSEILTLTWEEVDLDNQCLRLldskTGK----KIIYL 110
Cdd:PRK00236  114 KPLDVDQAKRLLDAIDEDDPL-----ALrdRAILELLYgSGLRLSELVGLDIDDLDLASGTLRV----LGKgnkeRTVPL 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 111 SSTAIELLQA----IPKIPENLHVICGGKEGAHLV--NIHKAWGRIRKKAHL-EDVRLHDLRHTFASVAVSQGLSLPVIG 183
Cdd:PRK00236  185 GRAAREALEAylalRPLFLPDDDALFLGARGGRLSprVVQRRVKKLGKKAGLpSHITPHKLRHSFATHLLESGGDLRAVQ 264

                         170
                  ....*....|....*..
gi 1232827679 184 ALLGHKHTQTTARYAHL 200
Cdd:PRK00236  265 ELLGHASLSTTQIYTHV 281
 
Name Accession Description Interval E-value
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 36-199 1.71e-46

Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain; Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271177 [Multi-domain]  Cd Length: 162  Bit Score: 151.33  E-value: 1.71e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  36 RERFLNADEIERLLTILKREEKEGFYPwalhAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGK-KIIYLSSTA 114
Cdd:cd00796     1 RDRFLTEDEEARLLAALEESTNPHLRL----IVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKpRTVPLSDEA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 115 IELLQAIP-KIPENLHVICGGKEGAHLVNIHKAWGRIRKKAHLEDVRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQT 193
Cdd:cd00796    77 IAILKELKrKRGKDGFFVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKM 156


                  ....*.
gi 1232827679 194 TARYAH 199
Cdd:cd00796   157 TMRYAH 162
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
21-212 3.85e-44

Site-specific recombinase XerD [Replication, recombination and repair];


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 149.37  E-value: 3.85e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  21 HSNPCLHVKKYPENKRE-RFLNADEIERLLTILKREEKEGFYPWALhaIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLL 99
Cdd:COG4974    93 EDNPAAKVKLPKKPRKLpRVLTEEEIEALLEALDTETPEGLRDRAL--LLLLYATGLRVSELLGLKWSDIDLDRGTIRVR 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 100 DSKTGKK-IIYLSSTAIELLQAIPKI--PENLHVICGGKEGAHL--VNIHKAWGRIRKKAHLE-DVRLHDLRHTFASVAV 173
Cdd:COG4974   171 RGKGGKErTVPLSPEALEALREYLEErrPRDSDYLFPTRRGRPLsrRAIRKILKRLAKRAGIPkRVTPHSLRHTFATHLL 250

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1232827679 174 SQGLSLPVIGALLGHKHTQTTARYAHLMHQPLFEASEKI 212
Cdd:COG4974   251 EAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
21-205 2.78e-32

Site-specific recombinase XerC [Replication, recombination and repair];


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 118.14  E-value: 2.78e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  21 HSNPCLHVK--KYPEnKRERFLNADEIERLLTILKREEKEGFYPWAlhaIRLLLYTGCRLSEILTLTWEEVDLDNQCLRL 98
Cdd:COG4973    92 EANPAAGVKapKAPR-KLPRALTVDELAQLLDALADDPLAVRDRAI---VELLYSTGLRLGELVGLDWEDVDLDAGEVRV 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  99 LdSKTGKK-IIYLSSTAIELLQA------IPKIPENLHVICGgKEGAHLV--NIHKAWGRIRKKAHLED-VRLHDLRHTF 168
Cdd:COG4973   168 R-GKTGKSrTVPLGPKALAALREwlavrpELAAPDEGALFPS-RRGTRLSprNVQKRLRRLAKKAGLPKhVHPHDLRHSF 245

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1232827679 169 ASVAVSQGLSLPVIGALLGHKHTQTTARYAHLMHQPL 205
Cdd:COG4973   246 ATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHL 282
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 15-199 7.53e-31

Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 116.68  E-value: 7.53e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  15 WGYRPdhSNPCLHVK---KYPENKRERFLNADEIERLLTILkreEKEGFYPWALHAIRLLLYTGCRLSEILTLTWEEVDL 91
Cdd:COG0582   180 RGLIE--RNPAADLKgalPKPKVKHHPALTPEELPELLRAL---DAYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDL 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  92 DNQCLRLL--DSKTGKK-IIYLSSTAIELLQAIPKI-PENLHVICGGKEGAHLVNiHKAWGRIRKKAHLEDVRLHDLRHT 167
Cdd:COG0582   255 EAALWTIPaeRMKTRRPhIVPLSRQALEILKELKPLtGDSEYVFPSRRGPKKPMS-ENTLNKALRRMGYGRFTPHGFRHT 333

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1232827679 168 FASVAVSQGLSLPVIGALLGHKHTQTT-ARYAH 199
Cdd:COG0582   334 ASTLLNEAGFPPDVIERQLAHKDGNKVrAAYNR 366
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 42-199 1.34e-26

C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271189 [Multi-domain]  Cd Length: 147  Bit Score: 99.56  E-value: 1.34e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  42 ADEIERLLTILKREEkegfYPWALhAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRL---LDSKTGKK------------ 106
Cdd:cd01189     1 PEELKKLLEALKKRG----DRYYL-LFLLALLTGLRRGELLALTWSDIDFENGTIRInrtLVRKKKGGyvikppktkssi 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 107 -IIYLSSTAIELLQAipkipenlhvicggkegahlvniHKAWGRIRKKAHLEDVRLHDLRHTFASVAVSQGLSLPVIGAL 185
Cdd:cd01189    76 rTIPLPDELIELLKE-----------------------LKAFKKLLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAER 132

                         170
                  ....*....|....*
gi 1232827679 186 LGHKHTQTTAR-YAH 199
Cdd:cd01189   133 LGHSDISTTLDvYAH 147
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 44-198 3.50e-24

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271175 [Multi-domain]  Cd Length: 167  Bit Score: 94.08  E-value: 3.50e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  44 EIERLLTILKREEKEGFYPWALhaIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGKK---IIYLSSTAIELLQA 120
Cdd:cd00397     1 ELEKLLDAIDEDKKIDLRDRAI--LLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGkerTVPLPKELAEELKE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 121 IPKI----------PENLHVICGGKEGAHLVN--IHKAWGRIRKKAHlEDVRLHDLRHTFASVAVSQGLSLPVIGALLGH 188
Cdd:cd00397    79 YLKErrdkrgpllkSLYLNKLFGTKLGERLSRrtLRRIFKKAGIEAG-RKITPHSLRHTFATNLLENGVDIKVVQKLLGH 157

                         170
                  ....*....|
gi 1232827679 189 KHTQTTARYA 198
Cdd:cd00397   158 SSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 39-200 6.36e-24

Phage integrase family; Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324.


Pssm-ID: 395471 [Multi-domain]  Cd Length: 169  Bit Score: 93.54  E-value: 6.36e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  39 FLNADEIERLLTILkreEKEGFYPWALHAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGKKI-IYLSSTAIEL 117
Cdd:pfam00589   1 RLTEDEVERLLDAA---ETGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERtVPLSDAALEL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 118 LQ-----AIPKIPENLHVICGgKEGAHLV--NIHKAWGRIRKKAHLED-VRLHDLRHTFASVAVSQGLSLPVIGALLGHK 189
Cdd:pfam00589  78 LKewlskRLLEAPKSDYLFAS-KRGKPLSrqTVRKIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|.
gi 1232827679 190 HTQTTARYAHL 200
Cdd:pfam00589 157 SISTTQIYTHV 167
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 44-199 5.32e-20

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 83.47  E-value: 5.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  44 EIERLLTILKREEKEGFYPWALHAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGKK---IIYLSSTAIELLQA 120
Cdd:cd00801     1 SPDELPELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKrphRVPLSDQALEILEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 121 IPKIPENLHVICGGKEGAHL----VNIHKAWGRIRKKAHLedVRLHDLRHTFASVAVSQGLSLPVIGALLGHK-HTQTTA 195
Cdd:cd00801    81 LKEFTGDSGYLFPSRRKKKKpiseNTINKALKRLGYKGKE--FTPHDLRRTFSTLLNELGIDPEVIERLLNHVlGGVVRA 158


                  ....
gi 1232827679 196 RYAH 199
Cdd:cd00801   159 AYNR 162
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 42-200 5.48e-15

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 69.85  E-value: 5.48e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  42 ADEIERLLTILKREEKEGFypwALHAIRLLLY-TGCRLSEILTLTWEEVDLDNQCLRLldskTGK----KIIYLSSTAIE 116
Cdd:cd00798     1 VDEVERLLDAPDTDTPLGL---RDRAILELLYaSGLRVSELVGLDLSDVDLDEGLVRV----TGKgnkeRLVPFGSYAVE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 117 LLQA----------IPKIPENLHVicgGKEGAHL--VNIHKAWGRIRKKAHL-EDVRLHDLRHTFASVAVSQGLSLPVIG 183
Cdd:cd00798    74 ALEEyleerrplllKKKPPDALFL---NKRGKRLsrRGVWRILKKYAERAGLpKHVSPHTLRHSFATHLLEGGADLRVVQ 150

                         170
                  ....*....|....*..
gi 1232827679 184 ALLGHKHTQTTARYAHL 200
Cdd:cd00798   151 ELLGHASLSTTQIYTHV 167
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 42-198 3.18e-14

C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271188 [Multi-domain]  Cd Length: 179  Bit Score: 68.04  E-value: 3.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  42 ADEIERLLTILKREEkegfyPWAL--HAIRLLLYT-GCRLSEILTLTWEEVDLDNQCLRLLDSKTGKKIIY-LSST---A 114
Cdd:cd01188     2 PDEVRRLLAAIDRLT-----PVGLrdYAILLLLARlGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELpLTEPvgeA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 115 IE--LLQAIPKIPENLHVICGGKEGAHLVN---IHKAWGRIRKKAHLEDVRL--HDLRHTFASVAVSQGLSLPVIGALLG 187
Cdd:cd01188    77 LAdyLRDGRPRTDSREVFLRARAPYRPLSStsqISSIVRRYLRKAGIEPSHRgtHSLRHSLATRMLRAGTSLKVIADLLG 156

                         170
                  ....*....|.
gi 1232827679 188 HKHTQTTARYA 198
Cdd:cd01188   157 HRSIETTAIYA 167
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 62-197 5.78e-14

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 66.98  E-value: 5.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  62 PWALHAIRLLLYTGCRLSEILTLTWEevDLDNQCLRLLDSKTGKKI-IYLSSTAIELLQAIPKIPEN--LHVICGGKEGA 138
Cdd:cd00800    12 PLLRLAMELALLTGQRQGDLLRLKWS--DITDGGLLVEQSKTGKKLlIPWTPSLRALVDRIRALPRKrsEYLINSRKGGP 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1232827679 139 HLVN-IHKAWGRIRKKAHL----EDVRLHDLRHTFASVAVSQGLSlPVIGALLGHKHTQTTARY 197
Cdd:cd00800    90 LSYDtLKSAWRRARKAAGLkgetEGFTFHDLRAKAATDYAEQGGS-TDAQALLGHKSDAMTERY 152
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 40-211 8.33e-14

C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271178 [Multi-domain]  Cd Length: 198  Bit Score: 67.33  E-value: 8.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  40 LNADEIERLLTILKREEKEGFY-PWALH-AIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKTGK-KIIYLSSTAIE 116
Cdd:cd00797     1 YTDAEIRRLLAAADQLPPESPLrPLTYAtLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKsRLVPLHPSTVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 117 LL--------QAIPKIPENLHVICGGKEGAHLVNIHKAWGRIRKKAHLEDV------RLHDLRHTFASVAVSQ----GLS 178
Cdd:cd00797    81 ALrdylarrdRLLPSPSSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRGAgdgrgpRLHDLRHTFAVNRLTRwyreGAD 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1232827679 179 ----LPVIGALLGHKHTQTTARYAHLMHQPLFEASEK 211
Cdd:cd00797   161 verkLPVLSTYLGHVNVTDTYWYLTATPELMELASLR 197
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 16-200 8.56e-14

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 68.76  E-value: 8.56e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  16 GYRPDhsNPCLHVKKyPenKRERF----LNADEIERLLTILKREEKEGFypwALHAIRLLLY-TGCRLSEILTLTWEEVD 90
Cdd:TIGR02225  82 GIRED--DPSALIEP-P--KVARKlpkvLTVEEVEALLAAPDVDTPLGL---RDRAMLELLYaTGLRVSELVGLRLEDVN 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  91 LDNQCLRLLDSKTGKKIIYLSSTAIELLQAIPKIPENLHVICGGKEGAHL-VNIHK-------AWGRIR---KKAHLE-D 158
Cdd:TIGR02225 154 LDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKESDALfLNRRGgplsrqgVWKILKeyaKRAGIEkP 233

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1232827679 159 VRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYAHL 200
Cdd:TIGR02225 234 ISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHV 275
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 43-199 8.93e-13

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 64.25  E-value: 8.93e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  43 DEIERLLTILKREEKEGFYPWALHAIRLLLYTGCRLSEILTLTWEEVDLDNQ--CLRLLD--------SKTGKKIIYLSS 112
Cdd:cd01184     4 EELAKIFSSPLYTGCKKKDPALYWLPLIGLYTGARLNEICQLRVDDIKEEDGiwCIDINDdaegrrlkTKASRRLVPIHP 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 113 TAIEL--------LQAIPKIPENLHVICGGKEGAHlvNIHKAWGRIRKKA---HLEDVRLHDLRHTFASVAVSQGLSLPV 181
Cdd:cd01184    84 RLIELgfldyveaLRADGKLFLFPEKRDKDGKYSK--AASKWFNRLLRKLgikDDERKSFHSFRHTFITALKRAGVPEEL 161

                         170
                  ....*....|....*....
gi 1232827679 182 IGALLGHKH-TQTTARYAH 199
Cdd:cd01184   162 IAQIVGHSRgGVTHDTYGK 180
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 73-200 1.76e-12

Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain; IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271185 [Multi-domain]  Cd Length: 161  Bit Score: 63.05  E-value: 1.76e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  73 YTGCRLSEILTLTWEEVDLDNQCLRLLD--SKTGKK-IIYLSSTAIELLQAIP--KIPENL-HVICGGKEGAHLVNIHKA 146
Cdd:cd01185    29 YTGLRFSDLKNLTWKNIVEASGRTWIRYrrKKTGKPvTVPLLPVAREILEKYKddRSEGKLfPVLSNQKINRYLKEIAKI 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1232827679 147 WGrIRKKAHLedvrlHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYAHL 200
Cdd:cd01185   109 AG-IDKHLTF-----HVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKI 156
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 39-200 3.51e-12

Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.


Pssm-ID: 271193 [Multi-domain]  Cd Length: 176  Bit Score: 62.29  E-value: 3.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  39 FLNADEIERLLTILKREEKegfypwalHAIRLLLY-TGCRLSEILTLTWEEVDLDNQCLRLLDSKTGK-KIIYLSSTAIE 116
Cdd:cd01193     5 VLSPDEVRRILGALTELRH--------RLILSLLYgAGLRISELLRLRVKDIDFERGVIRVRQGKGGKdRVVPLPEKLLE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 117 LLQAIPKIPENLHVICGGKEGAHLVN---------------IHKAWGRIRKKAHLE-DVRLHDLRHTFASVAVSQGLSLP 180
Cdd:cd01193    77 PLRRYLKSARPKEELDPAEGRAGVLDprtgverrhhisettVQRALKKAVEQAGITkRVTPHTLRHSFATHLLEAGTDIR 156

                         170       180
                  ....*....|....*....|
gi 1232827679 181 VIGALLGHKHTQTTARYAHL 200
Cdd:cd01193   157 TIQELLGHSDLSTTMIYTHV 176
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 38-200 3.99e-12

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 64.02  E-value: 3.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  38 RFLNADEIERLLTILKREEKEgfypwAL--HAIRLLLY-TGCRLSEILTLTWEEVDLDNQCLRLldskTGK----KIIYL 110
Cdd:PRK00236  114 KPLDVDQAKRLLDAIDEDDPL-----ALrdRAILELLYgSGLRLSELVGLDIDDLDLASGTLRV----LGKgnkeRTVPL 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 111 SSTAIELLQA----IPKIPENLHVICGGKEGAHLV--NIHKAWGRIRKKAHL-EDVRLHDLRHTFASVAVSQGLSLPVIG 183
Cdd:PRK00236  185 GRAAREALEAylalRPLFLPDDDALFLGARGGRLSprVVQRRVKKLGKKAGLpSHITPHKLRHSFATHLLESGGDLRAVQ 264

                         170
                  ....*....|....*..
gi 1232827679 184 ALLGHKHTQTTARYAHL 200
Cdd:PRK00236  265 ELLGHASLSTTQIYTHV 281
int PHA02601
integrase; Provisional
 23-200 2.31e-10

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 58.97  E-value: 2.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  23 NPCLHVKKYPENKRE-RFLNADEIERLLTILKREEKEGFYPWAlhaiRLLLYTGCRLSEILTLTWEEVDldNQCLRLLDS 101
Cdd:PHA02601  155 NPLDGIRPFKEAEPElAFLTKEEIERLLDACDGSRSPDLGLIA----KICLATGARWSEAETLKRSQIS--PYKITFVKT 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 102 KTGKKiiylsstaiellQAIPkIPENLHVICGGKEGAHLVNIHKAWGRIRKKAHLE---DVRLHDLRHTFASVAVSQGLS 178
Cdd:PHA02601  229 KGKKN------------RTVP-ISEELYKMLPKRRGRLFKDAYESFERAVKRAGIDlpeGQATHVLRHTFASHFMMNGGN 295

                         170       180
                  ....*....|....*....|..
gi 1232827679 179 LPVIGALLGHKHTQTTARYAHL 200
Cdd:PHA02601  296 ILVLQRILGHATIEMTMAYAHF 317
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 66-198 1.89e-08

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 52.28  E-value: 1.89e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  66 HAIRLLLY-TGCRLSEILTLTWEEVDLDNQCLRLLDSKTGK-KIIYLSSTAIELLQAIPK------IPENLHVICGGKEG 137
Cdd:cd01182    24 HALLLLLYdTGARVQELADLTIRDLRLDDPATVRLHGKGRKeRTVPLWKETVAALKAYLQefhltpDPKQLFPLFPNRRG 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1232827679 138 --------AHLVNIHKAWGRIRKKAHLEDVRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYA 198
Cdd:cd01182   104 qpltrdgvAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYA 172
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 71-200 3.12e-07

Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 48.95  E-value: 3.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  71 LLY-TGCRLSEILTLTWEEVDLDNQCLRLLD----------SKTGKKIIYLSSTAIELLQAIPKIPENLHVIC------- 132
Cdd:cd01186    25 LLYeTGLRIGEALGLRIEDIDMADNQIELVPredntnearaKSMRERRIPVSQDLIDLYADYLTYIYCEEAEFsitvfvn 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1232827679 133 --GGKEGAHL--VNIHKAWGRIRKKAHLeDVRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTAR-YAHL 200
Cdd:cd01186   105 vkGGNQGKAMnySDVYDLVRRLKKRTGI-DFTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTLNtYGHL 176
xerD PRK00283
tyrosine recombinase;
16-200 3.49e-07

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 49.42  E-value: 3.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  16 GYRPDhsNPCLHVK--KYPeNKRERFLNADEIERLLTILKREEKEGFypwALHAIRLLLY-TGCRLSEILTLTWEEVDLD 92
Cdd:PRK00283   91 GLRED--DPSALLDspKLP-RRLPKTLSEAQVEALLDAPDIDTPLGL---RDRAMLELLYaTGLRVSELVGLTLDDVSLR 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  93 NQCLRLldskTGK----KIIYLSSTAIELLQA--IPKIPENLHvicGGKEGAHLVNIH-------KAWGRIRKKAHL--- 156
Cdd:PRK00283  165 QGVVRV----TGKgnkeRLVPLGEEAVYAIERylERGRPALLN---GRSSDALFPSARggqltrqTFWHRIKHYAKRagi 237

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1232827679 157 --EDVRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYAHL 200
Cdd:PRK00283  238 dpKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHV 283
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 68-200 3.86e-07

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 49.53  E-value: 3.86e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  68 IRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLdSKTGKK-IIYLSSTAIELLQAIPKIpENLHVICGGKEGAHLVNIHKA 146
Cdd:PRK05084  201 IALILGSGLRVSELVNLDLSDLNLKQMTIDVT-RKGGKRdSVNIAPFALPYLEEYLKI-RASRYKAEKQEKALFLTKYRG 278

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1232827679 147 WG-RIRKKAhLE----------DVRL--HDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYAHL 200
Cdd:PRK05084  279 KPnRISARA-IEkmvakyseafGVRLtpHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHI 344
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 28-203 9.85e-07

integron integrase; Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 131303 [Multi-domain]  Cd Length: 315  Bit Score: 48.16  E-value: 9.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  28 VKKYPENKRERFLNADEIERLLTILKREEK----EGFYPWALHAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKT 103
Cdd:TIGR02249  78 ILKTPLSLMERFVRAKRPRKLPVVLTREEVrrllEHLEGKYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKG 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 104 GK-KIIYLSSTAIELLQAIPKIPENLHVIcGGKEGAHLV-----------NIHKAW-----------------GRIRK-- 152
Cdd:TIGR02249 158 GKdRTVTLPKELIPPLREQIELARAYHEA-DLAEGYGGVylphalarkypNAPKEWgwqylfpshrlsrdpesGVIRRhh 236

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1232827679 153 ---------------KAHLED-VRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYAHLMHQ 203
Cdd:TIGR02249 237 inettiqravrraveRAGIEKpVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLNR 303
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 62-199 3.41e-06

Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 45.11  E-value: 3.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  62 PWALHAIRLLLYTGCRLSEILTLtweevdlDNQCLRLLDSKTGKKIIYLSSTAIELLQAIPKIPENLHVICGgKEGAHLV 141
Cdd:cd01187    13 PQPIPVVQAAVFTGARASELATL-------KFGCLHAQTSDDGTFLYWLKWENKGGKQLDIPISKKVAELIK-TINWTLN 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1232827679 142 NIHKAWGRIRKKAHLEDVRLHDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARYAH 199
Cdd:cd01187    85 ELSELKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 35-197 7.66e-06

FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily.


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 44.81  E-value: 7.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  35 KRERFLNADEIERLLtilkREEKEGFYPWALHAIRLLLYT-GCRLSEILTLTWEEVDLDNQCLRLLDSKTGKKIIY-LSS 112
Cdd:cd01197     2 KQRKYLTGKEVQALL----QAACRGRTPARDYCLLLLAFRhGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHpLRF 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 113 TAIELLQAIPKIPENL-----HVICGGKEGAHLVNiHKAWGRIRKKAHLEDVRL----HDLRHTFASVAVSQGLSLPVIG 183
Cdd:cd01197    78 DEREALEAWLKERANWkgadtDWIFLSRRGGPLSR-QQAYRIIRDLGKEAGTVTqthpHMLRHACGYALADRGADTRLIQ 156

                         170
                  ....*....|....
gi 1232827679 184 ALLGHKHTQTTARY 197
Cdd:cd01197   157 DYLGHRNIRHTVIY 170
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 74-197 1.67e-05

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 43.82  E-value: 1.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  74 TGCRLSEILTLTWEEVDLDNQcLRLLDSKTGK-KIIYLSSTAIELLQAI-----PKIPENLHVICGGKEGAHLvNIHKAW 147
Cdd:cd01192    36 TGLRISDLLSLKVEDVTNKDK-LSIKEQKTGKqKTFPLNPTLVKALKEYiddldLKRNDYLFKSLKQGPEKPI-SRKQAY 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1232827679 148 gRIRKKAHlEDVRL------HDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARY 197
Cdd:cd01192   114 -KILKKAA-DDLGLnynigtHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 40-199 6.99e-05

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 41.98  E-value: 6.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  40 LNADEIERLLTILKREEK-EGFYPWALhaIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLL------DSKTGkkIIYLSS 112
Cdd:cd01194     1 LTLEQARQLLASLPIDDSiIGLRDRAI--ISLMVTEGLRTVEIVRADVGDLRQEGEGTILYvqgkgkTSKDD--FVYLRP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 113 TAIELLQAIPKIPENLH-------VICGGKEGAHLVNIHKAWgRIR---KKAHLEDVRL--HDLRHTFASVAVSQGLSLP 180
Cdd:cd01194    77 DVLKALQAYLKARGKLDfeeplftSLSNNSKGQRLTTRSIRR-IIKkylRKAGLDDDRLtaHSLRHTAGTLALKAGKSLR 155

                         170
                  ....*....|....*....
gi 1232827679 181 VIGALLGHKHTQTTARYAH 199
Cdd:cd01194   156 EVQQLLRHSDPNTTMIYAH 174
xerD PRK02436
site-specific tyrosine recombinase XerD;
70-121 5.64e-04

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 39.97  E-value: 5.64e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1232827679  70 LLLYTGCRLSEILTLTWEEVDLDNQCLRlLDSKTGKKIIYLSSTAIELLQAI 121
Cdd:PRK02436  120 LILELGLTPSEIAGLKVADIDLDFQVLT-IEKAGGKRVLTLPEALLPFLEAI 170
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 43-199 6.98e-04

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 38.99  E-value: 6.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679  43 DEIERLLTILKREEKEGFYPWALhaIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLL-DSKTGKKIIYLSSTAIELLQAI 121
Cdd:cd01195     3 EEARQRLDAADRHTAKGKRDEAL--VRLLLDNALRRSEAVALDVEDLEKEHRRLRILgKGKKQREVVTLPPTTREALAAW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1232827679 122 PKIPenlhvicGGKEGAHLVNIHKA-----------WGRIRKKAHL----EDVRLHDLRHTFASVAVSQGLSLP-VIGAL 185
Cdd:cd01195    81 LAAR-------GEAEGPLFVSLDRAsrgrrlspqavYRIVRRLAERiglgKRLSPHGLRHSAITLALDAGAGLIrKVQDF 153

                         170
                  ....*....|....
gi 1232827679 186 LGHKHTQTTARYAH 199
Cdd:cd01195   154 SRHADLRTLQVYDD 167
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 162-197 1.23e-03

C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.


Pssm-ID: 271180  Cd Length: 188  Bit Score: 38.43  E-value: 1.23e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1232827679 162 HDLRHTFASVAVSQGLSLPVIGALLGHKHTQTTARY 197
Cdd:cd00799   138 HSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRY 173
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 58-123 2.40e-03

Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA.


Pssm-ID: 271190  Cd Length: 150  Bit Score: 37.33  E-value: 2.40e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1232827679  58 EGFYPWALHAIRLLLYTGCRLSEILTLTWEEVDLDNQCLRLLDSKtGKKIIYLSSTAIELLQAIPK 123
Cdd:cd01190    13 QGDFLKGQLIALLILELGLTPSEIANLKWADFDLDFQVLTIEKGG-IKRVLPLPKKLLPFLEQHIK 77
COG4342 COG4342
Phage integrase/recombinase [Mobilome: prophages, transposons];
27-84 2.95e-03

Phage integrase/recombinase [Mobilome: prophages, transposons];


Pssm-ID: 443483 [Multi-domain]  Cd Length: 278  Bit Score: 37.77  E-value: 2.95e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1232827679  27 HVKKYPENKRERFLNADEIERLLTILKREEKEgfypwALHAIRLLLYTGCRLSEILTL 84
Cdd:COG4342    98 VLKVKRSGVDLYVPTDEEIREALKYLKEKDEE-----VYLLYKLLLFSGLRLSEALRL 150
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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