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Conserved domains on  [gi|2727058495|ref|WP_343032199|]
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tyrosine-type recombinase/integrase [Allochromatium palmeri]

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 ...
 43-206 2.12e-44

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: 146.70  E-value: 2.12e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  43 RIRWLTREEAQRLINECP----EHLADMVRFSLATGLREANVTGLRWDQVDLERRvaWIHDDEAKARRGIGVPLNRDAVL 118
Cdd:cd00796     1 RDRFLTEDEEARLLAALEestnPHLRLIVLLALYTGARRGEILSLRWDDIDLEVG--LIVLPETKNGKPRTVPLSDEAIA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 119 VLRRWQGRHSTRVFcyplKRKGVSVWTPIEKAGAAWKKALKRAGIENFRWHDLRHTWASWHVQSGTPLHVLQELGGWQSV 198
Cdd:cd00796    79 ILKELKRKRGKDGF----FVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSI 154


                  ....*...
gi 2727058495 199 EMVRRYAH 206
Cdd:cd00796   155 KMTMRYAH 162
SGNH_hydrolase super family cl01053
SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary ...
 1-25 7.51e-04

SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.


The actual alignment was detected with superfamily member cd01822:

Pssm-ID: 470049 [Multi-domain]  Cd Length: 177  Bit Score: 39.03  E-value: 7.51e-04
                          10        20
                  ....*....|....*....|....*
gi 2727058495   1 MLLLEGGNDILRNLDPEQAQANLAA 25
Cdd:cd01822    68 VILELGGNDGLRGIPPDQTRANLRQ 92
 
Name Accession Description Interval E-value
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 43-206 2.12e-44

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: 146.70  E-value: 2.12e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  43 RIRWLTREEAQRLINECP----EHLADMVRFSLATGLREANVTGLRWDQVDLERRvaWIHDDEAKARRGIGVPLNRDAVL 118
Cdd:cd00796     1 RDRFLTEDEEARLLAALEestnPHLRLIVLLALYTGARRGEILSLRWDDIDLEVG--LIVLPETKNGKPRTVPLSDEAIA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 119 VLRRWQGRHSTRVFcyplKRKGVSVWTPIEKAGAAWKKALKRAGIENFRWHDLRHTWASWHVQSGTPLHVLQELGGWQSV 198
Cdd:cd00796    79 ILKELKRKRGKDGF----FVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSI 154


                  ....*...
gi 2727058495 199 EMVRRYAH 206
Cdd:cd00796   155 KMTMRYAH 162
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
26-220 4.14e-41

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 142.06  E-value: 4.14e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  26 GWIDKSPA--LRLLPEPKRRIRWLTREEAQRLINECPEHLAD------MVRFSLATGLREANVTGLRWDQVDLERRVAWI 97
Cdd:COG4974    90 GLLEDNPAakVKLPKKPRKLPRVLTEEEIEALLEALDTETPEglrdraLLLLLYATGLRVSELLGLKWSDIDLDRGTIRV 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  98 HDdeAKARRGIGVPLNRDAVLVLRRW----QGRHSTRVFC----YPLKRKGVSvwtpiekagAAWKKALKRAGIE-NFRW 168
Cdd:COG4974   170 RR--GKGGKERTVPLSPEALEALREYleerRPRDSDYLFPtrrgRPLSRRAIR---------KILKRLAKRAGIPkRVTP 238

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2727058495 169 HDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRYAHLAPEHLSEHASRIE 220
Cdd:COG4974   239 HSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 46-209 5.23e-36

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: 125.12  E-value: 5.23e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  46 WLTREEAQRLINEC-----PEHLADMVRFSLATGLREANVTGLRWDQVDLERRVAWIHddEAKARRGIGVPLNRDAVLVL 120
Cdd:pfam00589   1 RLTEDEVERLLDAAetgplSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 121 RRWQGRHSTR------VFC----YPLKRKGVSvwtpiekagAAWKKALKRAGIEN-FRWHDLRHTWASWHVQSGTPLHVL 189
Cdd:pfam00589  79 KEWLSKRLLEapksdyLFAskrgKPLSRQTVR---------KIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVV 149

                         170       180
                  ....*....|....*....|
gi 2727058495 190 QELGGWQSVEMVRRYAHLAP 209
Cdd:pfam00589 150 QKLLGHSSISTTQIYTHVAD 169
int PHA02601
integrase; Provisional
 34-212 1.73e-16

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 77.08  E-value: 1.73e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  34 LRLLPEPKRRIRWLTREEAQRLINECP----EHLADMVRFSLATGLREANVTGLRWDQVdLERRVAWIhddEAKARRGIG 109
Cdd:PHA02601  160 IRPFKEAEPELAFLTKEEIERLLDACDgsrsPDLGLIAKICLATGARWSEAETLKRSQI-SPYKITFV---KTKGKKNRT 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 110 VPLNRDAVLVLRRWQGRhstrVF--CYPlkrkgvsvwtpiekagaAWKKALKRAGIE---NFRWHDLRHTWASWHVQSGT 184
Cdd:PHA02601  236 VPISEELYKMLPKRRGR----LFkdAYE-----------------SFERAVKRAGIDlpeGQATHVLRHTFASHFMMNGG 294

                         170       180
                  ....*....|....*....|....*...
gi 2727058495 185 PLHVLQELGGWQSVEMVRRYAHLAPEHL 212
Cdd:PHA02601  295 NILVLQRILGHATIEMTMAYAHFAPDHL 322
Lysophospholipase_L1_like cd01822
Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this ...
 1-25 7.51e-04

Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.


Pssm-ID: 238860 [Multi-domain]  Cd Length: 177  Bit Score: 39.03  E-value: 7.51e-04
                          10        20
                  ....*....|....*....|....*
gi 2727058495   1 MLLLEGGNDILRNLDPEQAQANLAA 25
Cdd:cd01822    68 VILELGGNDGLRGIPPDQTRANLRQ 92
 
Name Accession Description Interval E-value
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 43-206 2.12e-44

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: 146.70  E-value: 2.12e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  43 RIRWLTREEAQRLINECP----EHLADMVRFSLATGLREANVTGLRWDQVDLERRvaWIHDDEAKARRGIGVPLNRDAVL 118
Cdd:cd00796     1 RDRFLTEDEEARLLAALEestnPHLRLIVLLALYTGARRGEILSLRWDDIDLEVG--LIVLPETKNGKPRTVPLSDEAIA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 119 VLRRWQGRHSTRVFcyplKRKGVSVWTPIEKAGAAWKKALKRAGIENFRWHDLRHTWASWHVQSGTPLHVLQELGGWQSV 198
Cdd:cd00796    79 ILKELKRKRGKDGF----FVDGRFFGIPIASLRRAFKKARKRAGLEDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSI 154


                  ....*...
gi 2727058495 199 EMVRRYAH 206
Cdd:cd00796   155 KMTMRYAH 162
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
26-220 4.14e-41

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 142.06  E-value: 4.14e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  26 GWIDKSPA--LRLLPEPKRRIRWLTREEAQRLINECPEHLAD------MVRFSLATGLREANVTGLRWDQVDLERRVAWI 97
Cdd:COG4974    90 GLLEDNPAakVKLPKKPRKLPRVLTEEEIEALLEALDTETPEglrdraLLLLLYATGLRVSELLGLKWSDIDLDRGTIRV 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  98 HDdeAKARRGIGVPLNRDAVLVLRRW----QGRHSTRVFC----YPLKRKGVSvwtpiekagAAWKKALKRAGIE-NFRW 168
Cdd:COG4974   170 RR--GKGGKERTVPLSPEALEALREYleerRPRDSDYLFPtrrgRPLSRRAIR---------KILKRLAKRAGIPkRVTP 238

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2727058495 169 HDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRYAHLAPEHLSEHASRIE 220
Cdd:COG4974   239 HSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 46-209 5.23e-36

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: 125.12  E-value: 5.23e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  46 WLTREEAQRLINEC-----PEHLADMVRFSLATGLREANVTGLRWDQVDLERRVAWIHddEAKARRGIGVPLNRDAVLVL 120
Cdd:pfam00589   1 RLTEDEVERLLDAAetgplSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVH--RGKGNKERTVPLSDAALELL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 121 RRWQGRHSTR------VFC----YPLKRKGVSvwtpiekagAAWKKALKRAGIEN-FRWHDLRHTWASWHVQSGTPLHVL 189
Cdd:pfam00589  79 KEWLSKRLLEapksdyLFAskrgKPLSRQTVR---------KIFKRAGKEAGLELpLHPHMLRHSFATHLLEAGVDLRVV 149

                         170       180
                  ....*....|....*....|
gi 2727058495 190 QELGGWQSVEMVRRYAHLAP 209
Cdd:pfam00589 150 QKLLGHSSISTTQIYTHVAD 169
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 24-206 1.10e-30

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: 1.10e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  24 AAGWIDKSPALRL---LPEPK-RRIRWLTREEAQRLINECPE-----HLADMVRFSLATGLREANVTGLRWDQVDLERRV 94
Cdd:COG0582   179 ARGLIERNPAADLkgaLPKPKvKHHPALTPEELPELLRALDAyrgspVTRLALRLLLLTGVRPGELRGARWSEIDLEAAL 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  95 AWIHDDEAKARRGIGVPLNRDAVLVLRRWQG--RHSTRVFCYPLKRKGvsvwtPIEKAgaAWKKALKRAGIENFRWHDLR 172
Cdd:COG0582   259 WTIPAERMKTRRPHIVPLSRQALEILKELKPltGDSEYVFPSRRGPKK-----PMSEN--TLNKALRRMGYGRFTPHGFR 331

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2727058495 173 HTWASWHVQSGTPLHVLQELGGWQSVEMVRR-YAH 206
Cdd:COG0582   332 HTASTLLNEAGFPPDVIERQLAHKDGNKVRAaYNR 366
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
26-214 1.37e-30

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 114.29  E-value: 1.37e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  26 GWIDKSPA--LRLLPEPKRRIRWLTREEAQRLINECPE-----HLADMVRFSLATGLREANVTGLRWDQVDLERRVAWIH 98
Cdd:COG4973    89 GLLEANPAagVKAPKAPRKLPRALTVDELAQLLDALADdplavRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVR 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  99 ddeAKARRGIGVPLNRDAVLVLRRWQGR-------HSTRVFCyplKRKGvsvwTPIEKAG--AAWKKALKRAGIE-NFRW 168
Cdd:COG4973   169 ---GKTGKSRTVPLGPKALAALREWLAVrpelaapDEGALFP---SRRG----TRLSPRNvqKRLRRLAKKAGLPkHVHP 238

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 2727058495 169 HDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRYAHLAPEHLSE 214
Cdd:COG4973   239 HDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAE 284
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 49-206 1.54e-23

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: 92.24  E-value: 1.54e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  49 REEAQRLINECPE---HLADMVRFSLATGLREANVTGLRWDQVDLERRVAWIHD------------DEAKARRGIG-VPL 112
Cdd:cd01189     1 PEELKKLLEALKKrgdRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlvrkkkggyviKPPKTKSSIRtIPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 113 NRDAVLVLRRWQgrhstrvfcyplkrkgvsvwtpiekagaAWKKALKRAGIENFRWHDLRHTWASWHVQSGTPLHVLQEL 192
Cdd:cd01189    81 PDELIELLKELK----------------------------AFKKLLKKAGLPRITPHDLRHTFASLLLEAGVPLKVIAER 132

                         170
                  ....*....|....*
gi 2727058495 193 GGWQSVEMVRR-YAH 206
Cdd:cd01189   133 LGHSDISTTLDvYAH 147
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 51-205 3.30e-19

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: 81.37  E-value: 3.30e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  51 EAQRLINECPEHLAD------MVRFSLATGLREANVTGLRWDQVDLERRVAWIHDDEAKARRGIGVPLNRDAVLVLRRW- 123
Cdd:cd00397     1 ELEKLLDAIDEDKKIdlrdraILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKEYl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 124 ---QGRHSTRVFCYPLKRKGVSVWTPiEKAGAAWKKALKRAGIE---NFRWHDLRHTWASWHVQSGTPLHVLQELGGWQS 197
Cdd:cd00397    81 kerRDKRGPLLKSLYLNKLFGTKLGE-RLSRRTLRRIFKKAGIEagrKITPHSLRHTFATNLLENGVDIKVVQKLLGHSS 159


                  ....*...
gi 2727058495 198 VEMVRRYA 205
Cdd:cd00397   160 ISTTQRYL 167
int PHA02601
integrase; Provisional
 34-212 1.73e-16

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 77.08  E-value: 1.73e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  34 LRLLPEPKRRIRWLTREEAQRLINECP----EHLADMVRFSLATGLREANVTGLRWDQVdLERRVAWIhddEAKARRGIG 109
Cdd:PHA02601  160 IRPFKEAEPELAFLTKEEIERLLDACDgsrsPDLGLIAKICLATGARWSEAETLKRSQI-SPYKITFV---KTKGKKNRT 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 110 VPLNRDAVLVLRRWQGRhstrVF--CYPlkrkgvsvwtpiekagaAWKKALKRAGIE---NFRWHDLRHTWASWHVQSGT 184
Cdd:PHA02601  236 VPISEELYKMLPKRRGR----LFkdAYE-----------------SFERAVKRAGIDlpeGQATHVLRHTFASHFMMNGG 294

                         170       180
                  ....*....|....*....|....*...
gi 2727058495 185 PLHVLQELGGWQSVEMVRRYAHLAPEHL 212
Cdd:PHA02601  295 NILVLQRILGHATIEMTMAYAHFAPDHL 322
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 48-216 1.64e-11

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: 61.10  E-value: 1.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  48 TREEAQRLINEC----PEHLAD--MVRFSLATGLREANVTGLRWDQVDLERRVAWIHddEAKARRGIGVPLN---RDAVL 118
Cdd:cd01188     1 SPDEVRRLLAAIdrltPVGLRDyaILLLLARLGLRAGDVAGLRLDDIDWRSGTITVR--QKKTGRPVELPLTepvGEALA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 119 V-LRRWQGR-HSTRVFcyplkrkgVSVWTPIEKA------GAAWKKALKRAGIENFRW--HDLRHTWASWHVQSGTPLHV 188
Cdd:cd01188    79 DyLRDGRPRtDSREVF--------LRARAPYRPLsstsqiSSIVRRYLRKAGIEPSHRgtHSLRHSLATRMLRAGTSLKV 150

                         170       180
                  ....*....|....*....|....*...
gi 2727058495 189 LQELGGWQSVEMVRRYAHLAPEHLSEHA 216
Cdd:cd01188   151 IADLLGHRSIETTAIYAKIDVDDLREVA 178
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 50-210 5.59e-11

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: 59.20  E-value: 5.59e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  50 EEAQRLIN-ECP-----EHLADMVRFSLATGLREANVTGLRWDQVDLERRVAWIHDDEAKARRGIGVPLNRDAVLVLRRW 123
Cdd:cd01185     1 EELKRLMAlELSdtsrlELVRDMFLFSCYTGLRFSDLKNLTWKNIVEASGRTWIRYRRKKTGKPVTVPLLPVAREILEKY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 124 Q-GRHSTRVFcyplkrKGVSVWTPIEkagaAWKKALKRAGIE-NFRWHDLRHTWASWHVQSGTPLHVLQELGGWQSVEMV 201
Cdd:cd01185    81 KdDRSEGKLF------PVLSNQKINR----YLKEIAKIAGIDkHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTT 150


                  ....*....
gi 2727058495 202 RRYAHLAPE 210
Cdd:cd01185   151 QIYAKIVDS 159
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 54-188 1.39e-10

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: 58.44  E-value: 1.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  54 RLINECPEHL--ADMVRFSLATGLREANVTGLRWDQVDLERRVAWIHDDEAKARRGIGVPLNRDAVLVLRRWQGRHSTRV 131
Cdd:cd00801    10 RALDTANLSPptKLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVPLSDQALEILEELKEFTGDSG 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2727058495 132 FCYPlKRKGVSVWTPIEKAGAAWKKALKRAGIenFRWHDLRHTWASWHVQSGTPLHV 188
Cdd:cd00801    90 YLFP-SRRKKKKPISENTINKALKRLGYKGKE--FTPHDLRRTFSTLLNELGIDPEV 143
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 49-212 5.47e-10

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: 56.75  E-value: 5.47e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  49 REEAQRLINEC----PEHLADMVRFSL--ATGLREANVTGLRWDQVDLERRVAWIHDDEAKARRgigVPLNRDAV----- 117
Cdd:cd00798     1 VDEVERLLDAPdtdtPLGLRDRAILELlyASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERL---VPFGSYAVealee 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 118 -LVLRRWQGRHSTRVFCYPLKRKG-----VSVWTPIekagaawKKALKRAGIEN-FRWHDLRHTWASWHVQSGTPLHVLQ 190
Cdd:cd00798    78 yLEERRPLLLKKKPPDALFLNKRGkrlsrRGVWRIL-------KKYAERAGLPKhVSPHTLRHSFATHLLEGGADLRVVQ 150

                         170       180
                  ....*....|....*....|..
gi 2727058495 191 ELGGWQSVEMVRRYAHLAPEHL 212
Cdd:cd00798   151 ELLGHASLSTTQIYTHVSFERL 172
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 47-207 2.29e-09

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: 54.97  E-value: 2.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  47 LTREEAQRLINECPEhLADMVRFSL--ATGLREANVTGLRWDQVDLERrvAWIHDDEAKARRGIGVPLNRDAVLVLRRW- 123
Cdd:cd01193     6 LSPDEVRRILGALTE-LRHRLILSLlyGAGLRISELLRLRVKDIDFER--GVIRVRQGKGGKDRVVPLPEKLLEPLRRYl 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 124 -QGRHSTRVFcypLKRKGVSVWTPIEKAGA-----------AWKKALKRAGIEN-FRWHDLRHTWASWHVQSGTPLHVLQ 190
Cdd:cd01193    83 kSARPKEELD---PAEGRAGVLDPRTGVERrhhisettvqrALKKAVEQAGITKrVTPHTLRHSFATHLLEAGTDIRTIQ 159

                         170
                  ....*....|....*..
gi 2727058495 191 ELGGWQSVEMVRRYAHL 207
Cdd:cd01193   160 ELLGHSDLSTTMIYTHV 176
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 26-214 1.20e-08

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 54.39  E-value: 1.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  26 GWIDKSPALRL-LPEPKRRI-RWLTREEAQRLINEC----PEHLAD--MVRFSLATGLREANVTGLRWDQVDLERRVAWI 97
Cdd:PRK00236   93 GLLKANPAAGLrAPKIPKRLpKPLDVDQAKRLLDAIdeddPLALRDraILELLYGSGLRLSELVGLDIDDLDLASGTLRV 172

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  98 HDDEAKARRgigVPLNRDAVLVLRRW--QGRHSTR----VFcypLKRKGvsvwTPIEKAGA--AWKKALKRAGI-ENFRW 168
Cdd:PRK00236  173 LGKGNKERT---VPLGRAAREALEAYlaLRPLFLPdddaLF---LGARG----GRLSPRVVqrRVKKLGKKAGLpSHITP 242

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2727058495 169 HDLRHTWASwHV-QSGTPLHVLQELGGWQSVEMVRRYAHLAPEHLSE 214
Cdd:PRK00236  243 HKLRHSFAT-HLlESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAE 288
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 58-204 2.35e-08

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: 51.96  E-value: 2.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  58 ECPEHLADMVRFSLATGLREANVTGLRWDQVDLERrvawIHDDEAKARRGIGVPLN---RDAVLVLRRWQGRHSTRVFCY 134
Cdd:cd00800     9 EAPPLLRLAMELALLTGQRQGDLLRLKWSDITDGG----LLVEQSKTGKKLLIPWTpslRALVDRIRALPRKRSEYLINS 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2727058495 135 PLKRKgVSvWTPIEKagaAWKKALKRAGI----ENFRWHDLRHTWASWHVQSGTpLHVLQELGGWQSVEMVRRY 204
Cdd:cd00800    85 RKGGP-LS-YDTLKS---AWRRARKAAGLkgetEGFTFHDLRAKAATDYAEQGG-STDAQALLGHKSDAMTERY 152
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 47-218 7.96e-08

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: 50.77  E-value: 7.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  47 LTREEAQRLINECPEH----------LADMVRFSLATGLREANVTGLRWDQVDLERRVAWIHDdeAKARRGIGVPLNRDA 116
Cdd:cd00797     1 YTDAEIRRLLAAADQLppesplrpltYATLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQ--TKFGKSRLVPLHPST 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 117 VLVLRRWQGR-------HSTRVFCYPLKRKGVSVWTpiekAGAAWKKALKRAGIENF------RWHDLRHTWA-----SW 178
Cdd:cd00797    79 VGALRDYLARrdrllpsPSSSYFFVSQQGGRLTGGG----VYRVFRRLLRRIGLRGAgdgrgpRLHDLRHTFAvnrltRW 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2727058495 179 HVQSGTPLHVLQELG---GWQSVEMVRRYAHLAPEhLSEHASR 218
Cdd:cd00797   155 YREGADVERKLPVLStylGHVNVTDTYWYLTATPE-LMELASL 196
xerD PRK00283
tyrosine recombinase;
23-214 4.83e-07

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 49.42  E-value: 4.83e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  23 LAAGWIDKSPALRL-LPEPKRRI-RWLTREEAQRLINEC----PEHLAD--MVRFSLATGLREANVTGLRWDQVDLERRV 94
Cdd:PRK00283   88 LREGLREDDPSALLdSPKLPRRLpKTLSEAQVEALLDAPdidtPLGLRDraMLELLYATGLRVSELVGLTLDDVSLRQGV 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  95 AWIhddeakarRGIG-----VPLNRDAVLVLRRWqGRHSTRVFcypLKRKGVSVWTPIEKAG-----AAW---KKALKRA 161
Cdd:PRK00283  168 VRV--------TGKGnkerlVPLGEEAVYAIERY-LERGRPAL---LNGRSSDALFPSARGGqltrqTFWhriKHYAKRA 235

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2727058495 162 GI--ENFRWHDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRYAHLAPEHLSE 214
Cdd:PRK00283  236 GIdpKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKE 290
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 53-204 3.48e-06

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: 46.14  E-value: 3.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  53 QRLINECPE-HLAD-----MVRFSLATGLREANVTGLRWDqvDLER--------RVAWIHDDEAKARRGIGVP--LNRDA 116
Cdd:cd00799     2 KAMLATLDDtTLRGlrdraLLLLGFAGALRRSELVALRVE--DLTRfvdgglliRLRRSKTDQDGEGEIKALPygPETCP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 117 VLVLRRW---QGRHSTRVFCyPLKRKGVSVWTPIEKAGAA--WKKALKRAGIENFRW--HDLRHTWASWHVQSGTPLHVL 189
Cdd:cd00799    80 VRALRAWleaAGIPSGPLFR-RIRRGGSVGTTRLSDRSVAriVKRRAALAGLDPGDFsgHSLRRGFATEAARAGASLPEI 158

                         170
                  ....*....|....*
gi 2727058495 190 QELGGWQSVEMVRRY 204
Cdd:cd00799   159 MAQGGHKSVATVMRY 173
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 47-214 1.25e-05

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: 44.33  E-value: 1.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  47 LTREEAQRLINECpEHLADMVRFSL--ATGLREANVTGLRWDQVDLERRVAWIHDDE-------AKARRGIGVPLNRDav 117
Cdd:cd01186     2 LTPREVQELINAC-NNLRDKFLLALlyETGLRIGEALGLRIEDIDMADNQIELVPREdntnearAKSMRERRIPVSQD-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 118 lVLRRW----------QGRHSTRVFcypLKRKGVSVWTPIeKAGAAWK--KALKRAGIENFRWHDLRHTWASWHVQSGTP 185
Cdd:cd01186    79 -LIDLYadyltyiyceEAEFSITVF---VNVKGGNQGKAM-NYSDVYDlvRRLKKRTGIDFTPHMFRHTHATALIRAGWS 153

                         170       180       190
                  ....*....|....*....|....*....|
gi 2727058495 186 LHVLQELGGWQSVE-MVRRYAHLAPEHLSE 214
Cdd:cd01186   154 IEVVARRLGHAHVQtTLNTYGHLSEEDIRR 183
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 159-206 5.27e-05

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: 42.03  E-value: 5.27e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2727058495 159 KRAGIENFRWHDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRYAH 206
Cdd:cd01187    95 DHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 31-217 1.19e-04

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 42.43  E-value: 1.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  31 SPALRL-LP-EPKRRIRW-LTREEAQRLINEC----PEHLADMVRFSL--ATGLREANVTGLRWDQVDLERRVAWIhdde 101
Cdd:PRK01287  118 NPAEDLeLPkEEKRLPRQiLSEAETEQVLASPdlttLQGLRDRALLELlwSTGIRRGELARLDLYDVDASRGVVTV---- 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 102 akaRRGIG-----VPLNRDAVLVLRRWQG--------RHSTRVFCYPLKRKGVSVWTPIEKAGAAWKK-ALKRAGienfR 167
Cdd:PRK01287  194 ---RQGKGnkdrvVPVGERALAWLQRYLQdvrpqlavRPDSGALFVAMDGDGLARNTLTNMVGRYIRAaGIEKAG----A 266

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2727058495 168 WHDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRYAHLAPEHLSE-HAS 217
Cdd:PRK01287  267 CHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAvHAS 317
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 47-205 1.69e-04

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: 41.11  E-value: 1.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  47 LTREEAQRLINECPEHLAD------MVRFSLATGLREANVTGLRWDQVDLER-RVAWIHDDEAKARRgigVPLNRDAVLV 119
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLgrrdhaLLLLLYDTGARVQELADLTIRDLRLDDpATVRLHGKGRKERT---VPLWKETVAA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 120 LRRW-QGRHSTR-------VFC----YPLKRKGVSVWtpIEKAGAawkkaLKRAGIENFRW----HDLRHTWASWHVQSG 183
Cdd:cd01182    78 LKAYlQEFHLTPdpkqlfpLFPnrrgQPLTRDGVAYI--LNKYVA-----LASNRCPSLPKritpHTLRHTKAMHLLQAG 150

                         170       180
                  ....*....|....*....|..
gi 2727058495 184 TPLHVLQELGGWQSVEMVRRYA 205
Cdd:cd01182   151 VDLTVIRDWLGHESVETTQIYA 172
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 47-206 2.91e-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: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 40.44  E-value: 2.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  47 LTREEAQRLINECPEH-----LADMVRFSLA--TGLRE-----ANVTGLRWDqvdLERRVAWIHDDEAKARRGIgVPLNR 114
Cdd:cd01194     1 LTLEQARQLLASLPIDdsiigLRDRAIISLMvtEGLRTveivrADVGDLRQE---GEGTILYVQGKGKTSKDDF-VYLRP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495 115 DAVLVLRRWQGRHSTRVFCYPL------KRKGvsvwTPIEKAGAAW--KKALKRAGIENFRW--HDLRHTWASWHVQSGT 184
Cdd:cd01194    77 DVLKALQAYLKARGKLDFEEPLftslsnNSKG----QRLTTRSIRRiiKKYLRKAGLDDDRLtaHSLRHTAGTLALKAGK 152

                         170       180
                  ....*....|....*....|..
gi 2727058495 185 PLHVLQELGGWQSVEMVRRYAH 206
Cdd:cd01194   153 SLREVQQLLRHSDPNTTMIYAH 174
Lysophospholipase_L1_like cd01822
Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this ...
 1-25 7.51e-04

Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.


Pssm-ID: 238860 [Multi-domain]  Cd Length: 177  Bit Score: 39.03  E-value: 7.51e-04
                          10        20
                  ....*....|....*....|....*
gi 2727058495   1 MLLLEGGNDILRNLDPEQAQANLAA 25
Cdd:cd01822    68 VILELGGNDGLRGIPPDQTRANLRQ 92
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 69-204 8.16e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 39.20  E-value: 8.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  69 FSLATGLREANVTGLRWDQVDLERRVaWIHDDEAKARRGIgvPLNRDAVL-VLRRWQGRHSTRV--FCYPLKRKGVsvwT 145
Cdd:cd01192    32 VGINTGLRISDLLSLKVEDVTNKDKL-SIKEQKTGKQKTF--PLNPTLVKaLKEYIDDLDLKRNdyLFKSLKQGPE---K 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2727058495 146 PIEKAGAAwkKALKRAGI-----ENFRWHDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRY 204
Cdd:cd01192   106 PISRKQAY--KILKKAADdlglnYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
PRK15417 PRK15417
integron integrase;
64-208 4.18e-03

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 37.72  E-value: 4.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2727058495  64 ADMVRFSLATGLREanvtglrwdqvDLERRVAWIHDDEAKARRGIGVP--LNRDAVLVLRRW-------QGRHSTRVFCY 134
Cdd:PRK15417  177 ALMLPESLAPSLRE-----------QLSRARAWWLKDQAEGRSGVALPdaLERKYPRAGHSWpwfwvfaQHTHSTDPRSG 245

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2727058495 135 PLKRKGVSVWTpiekAGAAWKKALKRAGIEN-FRWHDLRHTWASWHVQSGTPLHVLQELGGWQSVEMVRRYAHLA 208
Cdd:PRK15417  246 VVRRHHMYDQT----FQRAFKRAVEQAGITKpATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVL 316
 
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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