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Conserved domains on  [gi|486141544|ref|WP_001515717|]
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MULTISPECIES: tyrosine-type recombinase/integrase [Gammaproteobacteria]

Protein Classification

tyrosine-type recombinase/integrase( domain architecture ID 11471964)

tyrosine-type recombinase/integrase cleaves 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.

Gene Ontology:  GO:0009009|GO:0006310
PubMed:  10047575|9278480

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
42-215 6.04e-29

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


:

Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 110.47  E-value: 6.04e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYMPD-----QRHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVLSEKvrarrgrppKDEVR 116
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 117 LVPLTDaSFVRQMESWMVTTRPRRREPLW------PVTDETMRNWLKQAVKRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974  179 TVPLSP-EALEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                        170       180
                 ....*....|....*....|....*
gi 486141544 191 RQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:COG4974  253 GVDLRTVQELLGHSSISTTQIYTHV 277
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
42-215 6.04e-29

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 110.47  E-value: 6.04e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYMPD-----QRHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVLSEKvrarrgrppKDEVR 116
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 117 LVPLTDaSFVRQMESWMVTTRPRRREPLW------PVTDETMRNWLKQAVKRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974  179 TVPLSP-EALEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                        170       180
                 ....*....|....*....|....*
gi 486141544 191 RQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:COG4974  253 GVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 44-217 1.44e-25

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: 98.55  E-value: 1.44e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544   44 YLLAPEVSALLWYMPDQ----RHHMLFATMWNTGIRIGEARTLTPESFDLDGLRPFVRVLsekvraRRGRPpkdevRLVP 119
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsiRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG------KGNKE-----RTVP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  120 LTDASfVRQMESWMVTTRPRRRE--------PLWPVTDETMRNWLKQAVKRAEADGvhfsiPVTPHTFRHSYIMHMLYHR 191
Cdd:pfam00589  70 LSDAA-LELLKEWLSKRLLEAPKsdylfaskRGKPLSRQTVRKIFKRAGKEAGLEL-----PLHPHMLRHSFATHLLEAG 143

                         170       180
                  ....*....|....*....|....*.
gi 486141544  192 QPRKVIQALAGHKDPRSMEVYTRVFA 217
Cdd:pfam00589 144 VDLRVVQKLLGHSSISTTQIYTHVAD 169
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 49-213 3.14e-25

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: 97.55  E-value: 3.14e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  49 EVSALL-----WYMPDQRHHMLFATMWNTGIRIGEARTLTPESFDLDGlrPFVRVLSEKVRARRGRppkdEVRLVPLTDA 123
Cdd:cd00397    1 ELEKLLdaideDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDN--GTIRVRGKKTKGGKER----TVPLPKELAE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 124 SFVRQMESWMVTTRPRRREPLWPVTDETMR------NWLKQAVKRAeadGVHFSIPVTPHTFRHSYIMHMLYHRQPRKVI 197
Cdd:cd00397   75 ELKEYLKERRDKRGPLLKSLYLNKLFGTKLgerlsrRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVV 151

                        170
                 ....*....|....*.
gi 486141544 198 QALAGHKDPRSMEVYT 213
Cdd:cd00397  152 QKLLGHSSISTTQRYL 167
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 45-215 1.99e-13

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: 67.99  E-value: 1.99e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544   45 LLAPEVSALLWympdQRHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVlsekvrarRGRPPKDevRLVPLTDAS 124
Cdd:TIGR02225 114 LAAPDVDTPLG----LRDRAMLELLYATGLRVSELVGLRLEDVNLD--EGFVRV--------RGKGNKE--RLVPLGEEA 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  125 fVRQMESWMVTTRP----------------RRREPLwpvTDETMRNWLKQAVKRAeadgvhfSI--PVTPHTFRHSYIMH 186
Cdd:TIGR02225 178 -IEALERYLKEARPlllkkkvkesdalflnRRGGPL---SRQGVWKILKEYAKRA-------GIekPISPHTLRHSFATH 246

                         170       180
                  ....*....|....*....|....*....
gi 486141544  187 MLYHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:TIGR02225 247 LLENGADLRVVQELLGHADISTTQIYTHV 275
xerD PRK00283
tyrosine recombinase;
42-215 5.23e-10

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 58.28  E-value: 5.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYmPDQ------RHHMLFATMWNTGIRIGEARTLTPESFDLDGLrpFVRVlsekvrarRGRPPKDev 115
Cdd:PRK00283 111 PKTLSEAQVEALLDA-PDIdtplglRDRAMLELLYATGLRVSELVGLTLDDVSLRQG--VVRV--------TGKGNKE-- 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 116 RLVPLTDASfVRQMESWMVTTRP--------------RRREPLwpvTDETMRNWLKQAVKRAEADGVHfsipVTPHTFRH 181
Cdd:PRK00283 178 RLVPLGEEA-VYAIERYLERGRPallngrssdalfpsARGGQL---TRQTFWHRIKHYAKRAGIDPKK----LSPHVLRH 249

                        170       180       190
                 ....*....|....*....|....*....|....
gi 486141544 182 SYIMHMLYHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:PRK00283 250 AFATHLLNHGADLRVVQELLGHSDISTTQIYTHV 283
 
Name Accession Description Interval E-value
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
42-215 6.04e-29

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 110.47  E-value: 6.04e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYMPD-----QRHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVLSEKvrarrgrppKDEVR 116
Cdd:COG4974  110 PRVLTEEEIEALLEALDTetpegLRDRALLLLLYATGLRVSELLGLKWSDIDLD--RGTIRVRRGK---------GGKER 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 117 LVPLTDaSFVRQMESWMVTTRPRRREPLW------PVTDETMRNWLKQAVKRAEadgvhFSIPVTPHTFRHSYIMHMLYH 190
Cdd:COG4974  179 TVPLSP-EALEALREYLEERRPRDSDYLFptrrgrPLSRRAIRKILKRLAKRAG-----IPKRVTPHSLRHTFATHLLEA 252

                        170       180
                 ....*....|....*....|....*
gi 486141544 191 RQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:COG4974  253 GVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 44-217 1.44e-25

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: 98.55  E-value: 1.44e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544   44 YLLAPEVSALLWYMPDQ----RHHMLFATMWNTGIRIGEARTLTPESFDLDGLRPFVRVLsekvraRRGRPpkdevRLVP 119
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsiRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRG------KGNKE-----RTVP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  120 LTDASfVRQMESWMVTTRPRRRE--------PLWPVTDETMRNWLKQAVKRAEADGvhfsiPVTPHTFRHSYIMHMLYHR 191
Cdd:pfam00589  70 LSDAA-LELLKEWLSKRLLEAPKsdylfaskRGKPLSRQTVRKIFKRAGKEAGLEL-----PLHPHMLRHSFATHLLEAG 143

                         170       180
                  ....*....|....*....|....*.
gi 486141544  192 QPRKVIQALAGHKDPRSMEVYTRVFA 217
Cdd:pfam00589 144 VDLRVVQKLLGHSSISTTQIYTHVAD 169
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 49-213 3.14e-25

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: 97.55  E-value: 3.14e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  49 EVSALL-----WYMPDQRHHMLFATMWNTGIRIGEARTLTPESFDLDGlrPFVRVLSEKVRARRGRppkdEVRLVPLTDA 123
Cdd:cd00397    1 ELEKLLdaideDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDN--GTIRVRGKKTKGGKER----TVPLPKELAE 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 124 SFVRQMESWMVTTRPRRREPLWPVTDETMR------NWLKQAVKRAeadGVHFSIPVTPHTFRHSYIMHMLYHRQPRKVI 197
Cdd:cd00397   75 ELKEYLKERRDKRGPLLKSLYLNKLFGTKLgerlsrRTLRRIFKKA---GIEAGRKITPHSLRHTFATNLLENGVDIKVV 151

                        170
                 ....*....|....*.
gi 486141544 198 QALAGHKDPRSMEVYT 213
Cdd:cd00397  152 QKLLGHSSISTTQRYL 167
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 42-215 1.57e-20

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: 85.40  E-value: 1.57e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYMPDQRHHMLFATMWNTGIRIGEARTLTPEsfDLDGLRPFVRVlsekvraRRGRPPKDevRLVPLT 121
Cdd:cd01193    3 PVVLSPDEVRRILGALTELRHRLILSLLYGAGLRISELLRLRVK--DIDFERGVIRV-------RQGKGGKD--RVVPLP 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 122 DaSFVRQMESWMVTTRP--------------------RRREPLwpvTDETMRNWLKQAVKRAeadGVHfsIPVTPHTFRH 181
Cdd:cd01193   72 E-KLLEPLRRYLKSARPkeeldpaegragvldprtgvERRHHI---SETTVQRALKKAVEQA---GIT--KRVTPHTLRH 142

                        170       180       190
                 ....*....|....*....|....*....|....
gi 486141544 182 SYIMHMLYHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:cd01193  143 SFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
42-215 2.09e-15

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 73.84  E-value: 2.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYMPD----QRHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVLSeKVRARRgrppkdevrL 117
Cdd:COG4973  109 PRALTVDELAQLLDALADdplaVRDRAIVELLYSTGLRLGELVGLDWEDVDLD--AGEVRVRG-KTGKSR---------T 176

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 118 VPLTDASfVRQMESWMV---TTRPRRREPLWP------VTDETMRNWLKQAVKRAEadgvhFSIPVTPHTFRHSYIMHML 188
Cdd:COG4973  177 VPLGPKA-LAALREWLAvrpELAAPDEGALFPsrrgtrLSPRNVQKRLRRLAKKAG-----LPKHVHPHDLRHSFATHLL 250

                        170       180
                 ....*....|....*....|....*..
gi 486141544 189 YHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:COG4973  251 ESGGDLRAVQELLGHASISTTQIYTHL 277
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 59-213 2.19e-15

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: 70.67  E-value: 2.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  59 DQRHHMLFATMWNTGIRIGEARTLTPESFDLDGLRPFVR--VLSEKVRARRGRPPK--DEVRLVPLTDaSFVRQMESWMv 134
Cdd:cd01189   15 GDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINrtLVRKKKGGYVIKPPKtkSSIRTIPLPD-ELIELLKELK- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 135 ttrprrreplwpvtdetmrnWLKQAVKRAEADgvhfsiPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHKDPRS-MEVYT 213
Cdd:cd01189   93 --------------------AFKKLLKKAGLP------RITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTtLDVYA 146
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 45-215 7.48e-15

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: 70.38  E-value: 7.48e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  45 LLAPEVSALLwYMPD------QRHHMLFATMWNTGIRIGEARTLTPESFDLDGlRPFVRVlsekvrarRGRPPKDevRLV 118
Cdd:cd01182    1 LTREEMKALL-AAPDrntslgRRDHALLLLLYDTGARVQELADLTIRDLRLDD-PATVRL--------HGKGRKE--RTV 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 119 PLTDASfVRQMESWM----VTTRPRRREPLW------PVTDETMRNWLKQAVKRAEADGVHFSIPVTPHTFRHSYIMHML 188
Cdd:cd01182   69 PLWKET-VAALKAYLqefhLTPDPKQLFPLFpnrrgqPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLL 147

                        170       180
                 ....*....|....*....|....*..
gi 486141544 189 YHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:cd01182  148 QAGVDLTVIRDWLGHESVETTQIYAEA 174
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 45-215 1.99e-13

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: 67.99  E-value: 1.99e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544   45 LLAPEVSALLWympdQRHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVlsekvrarRGRPPKDevRLVPLTDAS 124
Cdd:TIGR02225 114 LAAPDVDTPLG----LRDRAMLELLYATGLRVSELVGLRLEDVNLD--EGFVRV--------RGKGNKE--RLVPLGEEA 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  125 fVRQMESWMVTTRP----------------RRREPLwpvTDETMRNWLKQAVKRAeadgvhfSI--PVTPHTFRHSYIMH 186
Cdd:TIGR02225 178 -IEALERYLKEARPlllkkkvkesdalflnRRGGPL---SRQGVWKILKEYAKRA-------GIekPISPHTLRHSFATH 246

                         170       180
                  ....*....|....*....|....*....
gi 486141544  187 MLYHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:TIGR02225 247 LLENGADLRVVQELLGHADISTTQIYTHV 275
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 49-215 2.32e-13

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: 66.00  E-value: 2.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  49 EVSALLwYMPDQ------RHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVlsekvrarRGRPPKDevRLVPLTD 122
Cdd:cd00798    3 EVERLL-DAPDTdtplglRDRAILELLYASGLRVSELVGLDLSDVDLD--EGLVRV--------TGKGNKE--RLVPFGS 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 123 ASfVRQMESWMVTTRP-----RRREPLW------PVTDETMRNWLKQAVKRAEADGvhfsiPVTPHTFRHSYIMHMLYHR 191
Cdd:cd00798   70 YA-VEALEEYLEERRPlllkkKPPDALFlnkrgkRLSRRGVWRILKKYAERAGLPK-----HVSPHTLRHSFATHLLEGG 143

                        170       180
                 ....*....|....*....|....
gi 486141544 192 QPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:cd00798  144 ADLRVVQELLGHASLSTTQIYTHV 167
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 44-214 1.11e-11

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: 61.19  E-value: 1.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  44 YLLAPEVSALLWYMPDQRHHMLFATMW---NTGIRIGEARTLTPESFDLDGLRPFvrvlseKVRARRGRPpkdevRLVPL 120
Cdd:cd00796    4 FLTEDEEARLLAALEESTNPHLRLIVLlalYTGARRGEILSLRWDDIDLEVGLIV------LPETKNGKP-----RTVPL 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 121 TDasFVRQMESWMVTTRPRRREPLWPVTDETMRNWLKQAVKRA-EADGVHFsipVTPHTFRHSYIMHMLYHRQPRKVIQA 199
Cdd:cd00796   73 SD--EAIAILKELKRKRGKDGFFVDGRFFGIPIASLRRAFKKArKRAGLED---LRFHDLRHTFASRLVQAGVPIKTVAK 147

                        170
                 ....*....|....*
gi 486141544 200 LAGHKDPRSMEVYTR 214
Cdd:cd00796  148 ILGHSSIKMTMRYAH 162
xerD PRK00283
tyrosine recombinase;
42-215 5.23e-10

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 58.28  E-value: 5.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYmPDQ------RHHMLFATMWNTGIRIGEARTLTPESFDLDGLrpFVRVlsekvrarRGRPPKDev 115
Cdd:PRK00283 111 PKTLSEAQVEALLDA-PDIdtplglRDRAMLELLYATGLRVSELVGLTLDDVSLRQG--VVRV--------TGKGNKE-- 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 116 RLVPLTDASfVRQMESWMVTTRP--------------RRREPLwpvTDETMRNWLKQAVKRAEADGVHfsipVTPHTFRH 181
Cdd:PRK00283 178 RLVPLGEEA-VYAIERYLERGRPallngrssdalfpsARGGQL---TRQTFWHRIKHYAKRAGIDPKK----LSPHVLRH 249

                        170       180       190
                 ....*....|....*....|....*....|....
gi 486141544 182 SYIMHMLYHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:PRK00283 250 AFATHLLNHGADLRVVQELLGHSDISTTQIYTHV 283
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 42-215 6.46e-09

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: 55.09  E-value: 6.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544   42 PAYLLAPEVSALLWYMpDQRHHMLFATMWNTGIRIGEARTLTPESFDLDGLrpfvrvlseKVRARRGRPPKDevRLVPLT 121
Cdd:TIGR02249  99 PVVLTREEVRRLLEHL-EGKYRLIAKLLYGSGMRLMECLRLRIQDIDFDYG---------EIRIRQGKGGKD--RTVTLP 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  122 D---ASFVRQMES----------------WMVTTRPRR-----REPLW------------PVTDETMRNWL-----KQAV 160
Cdd:TIGR02249 167 KeliPPLREQIELarayheadlaegyggvYLPHALARKypnapKEWGWqylfpshrlsrdPESGVIRRHHInettiQRAV 246

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 486141544  161 KRAeADGVHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:TIGR02249 247 RRA-VERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 45-220 2.04e-08

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: 52.42  E-value: 2.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  45 LLAPEVSALLWYMPDQRHHMLFATMWNTGIRIGEARTLTPESFDLDGlrPFVRVLSEKVRARRGRPPKDEVRLVPLTD-- 122
Cdd:cd01186    2 LTPREVQELINACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMAD--NQIELVPREDNTNEARAKSMRERRIPVSQdl 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 123 ---------ASFVRQME-SWMVTTRPRRREPLWPVTDETMRNWLKQAVKRAeadgvhfSIPVTPHTFRHSYIMHMLYHRQ 192
Cdd:cd01186   80 idlyadyltYIYCEEAEfSITVFVNVKGGNQGKAMNYSDVYDLVRRLKKRT-------GIDFTPHMFRHTHATALIRAGW 152

                        170       180
                 ....*....|....*....|....*....
gi 486141544 193 PRKVIQALAGHKDPR-SMEVYTRVFALDM 220
Cdd:cd01186  153 SIEVVARRLGHAHVQtTLNTYGHLSEEDI 181
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 72-216 7.06e-08

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: 50.73  E-value: 7.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  72 TGIRIGEARTLTPESFDLDGLRPFVRVLSEKVrarrgrppKDEVRlVPLTDAsfVRQ-MESWMVTtrpRRREPLWPV-TD 149
Cdd:cd01185   30 TGLRFSDLKNLTWKNIVEASGRTWIRYRRKKT--------GKPVT-VPLLPV--AREiLEKYKDD---RSEGKLFPVlSN 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 486141544 150 ETMRNWLKQAVKRAeadGVHFsiPVTPHTFRHSYIMHmLYHRQ-PRKVIQALAGHKDPRSMEVYTRVF 216
Cdd:cd01185   96 QKINRYLKEIAKIA---GIDK--HLTFHVARHTFATL-LLLKGvDIETISKLLGHSSIKTTQIYAKIV 157
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 61-215 1.71e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 51.29  E-value: 1.71e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  61 RHHMLFATMWNTGIRIGEARTLtpESFDLDGLRPFVRVlsekvraRRGRPPKDevRLVPLTDASFVrQMESWMVTTRPR- 139
Cdd:PRK01287 158 RDRALLELLWSTGIRRGELARL--DLYDVDASRGVVTV-------RQGKGNKD--RVVPVGERALA-WLQRYLQDVRPQl 225

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 140 ----RREPLWPVTDET--MRNWLKQAVKRA-EADGVhfSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHKDPRSMEVY 212
Cdd:PRK01287 226 avrpDSGALFVAMDGDglARNTLTNMVGRYiRAAGI--EKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303


                 ...
gi 486141544 213 TRV 215
Cdd:PRK01287 304 TRV 306
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 72-225 1.85e-07

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: 49.55  E-value: 1.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  72 TGIRIGEARTLTPESFDLDGLRPFVRV----------LSEKVRA------RRGRPPKDEVRLvpltdasFVRqmeswmvT 135
Cdd:cd01188   32 LGLRAGDVAGLRLDDIDWRSGTITVRQkktgrpvelpLTEPVGEaladylRDGRPRTDSREV-------FLR-------A 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 136 TRPRRReplwPVTDETMRNWLKQAVKRAEADGVHFSipvtPHTFRHSYIMHMLYHRQPRKVIQALAGHKDPRSMEVYTRV 215
Cdd:cd01188   98 RAPYRP----LSSTSQISSIVRRYLRKAGIEPSHRG----THSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYAKI 169

                        170
                 ....*....|
gi 486141544 216 fALDMAATLA 225
Cdd:cd01188  170 -DVDDLREVA 178
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 72-219 5.60e-07

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 49.65  E-value: 5.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  72 TGIRIGEARTLTPESFDLDglRPFVRVLSEKVRARRgrppkdeVRLVPLTDASfVRQMESWMVTTR------PRRREPLW 145
Cdd:COG0582  237 TGVRPGELRGARWSEIDLE--AALWTIPAERMKTRR-------PHIVPLSRQA-LEILKELKPLTGdseyvfPSRRGPKK 306

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 486141544 146 PVTDETMRnwlkQAVKRAEADgvhfsiPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHKDPRSME-VYTRVFALD 219
Cdd:COG0582  307 PMSENTLN----KALRRMGYG------RFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNRADYLE 371
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 60-215 8.09e-07

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 49.00  E-value: 8.09e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  60 QRHHMLFATMWNTGIRIGEARTLTPESFDLDglRPFVRVLsekvrarrGRPPKDevRLVPLTDAsfVRQ-MESWMvTTRP 138
Cdd:PRK00236 136 LRDRAILELLYGSGLRLSELVGLDIDDLDLA--SGTLRVL--------GKGNKE--RTVPLGRA--AREaLEAYL-ALRP 200

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 139 ------------RRREPLWP-VTDETMRNWLKQAvkraeadgvHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHKD 205
Cdd:PRK00236 201 lflpdddalflgARGGRLSPrVVQRRVKKLGKKA---------GLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHAS 271

                        170
                 ....*....|
gi 486141544 206 PRSMEVYTRV 215
Cdd:PRK00236 272 LSTTQIYTHV 281
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 61-214 1.04e-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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 44.38  E-value: 1.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  61 RHHMLFATMWNTGIRIGEARTLtpesfDLDGLRPFVRVLsekVRARRGRPPKDEVRLVPLTdasfvRQMESWMVTTRPRR 140
Cdd:cd01195   21 RDEALVRLLLDNALRRSEAVAL-----DVEDLEKEHRRL---RILGKGKKQREVVTLPPTT-----REALAAWLAARGEA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 141 REPLWPVTDETMR------NWLKQAVKR-AEADGVHFSIpvTPHTFRHSYIMHMLYHRQP--RKViQALAGHKDPRSMEV 211
Cdd:cd01195   88 EGPLFVSLDRASRgrrlspQAVYRIVRRlAERIGLGKRL--SPHGLRHSAITLALDAGAGliRKV-QDFSRHADLRTLQV 164


                 ...
gi 486141544 212 YTR 214
Cdd:cd01195  165 YDD 167
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 72-206 1.24e-05

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: 44.61  E-value: 1.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  72 TGIRIGEARTLTPESFDLDGLRPFVRVLSEKvrARRGRPPKDEVRLVPLTDA-------SFVRQMESwmvttrpRRREPL 144
Cdd:cd01184   35 TGARLNEICQLRVDDIKEEDGIWCIDINDDA--EGRRLKTKASRRLVPIHPRlielgflDYVEALRA-------DGKLFL 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 486141544 145 WPVTDE-------TMRNWLKQAVKRAE---ADGVHFsipvtpHTFRHSYIMHMLYHRQPRKVIQALAGHKDP 206
Cdd:cd01184  106 FPEKRDkdgkyskAASKWFNRLLRKLGikdDERKSF------HSFRHTFITALKRAGVPEELIAQIVGHSRG 171
PRK15417 PRK15417
integron integrase;
42-218 4.82e-05

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 43.88  E-value: 4.82e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  42 PAYLLAPEVSALLWYMpdQRHHMLFATM-WNTGIRIGEARTLTPESFDLD---------------------GLRPFVRVL 99
Cdd:PRK15417 114 PVVLTPDEVVRILGFL--EGEHRLFAQLlYGTGMRISEGLQLRVKDLDFDhgtiivregkgskdralmlpeSLAPSLREQ 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 100 SEKVRARRGRPPKDEVRLVPLTDA---SFVRQMESW---------MVTTRPR----RREPLWpvtDETMRNWLKQAVKRA 163
Cdd:PRK15417 192 LSRARAWWLKDQAEGRSGVALPDAlerKYPRAGHSWpwfwvfaqhTHSTDPRsgvvRRHHMY---DQTFQRAFKRAVEQA 268

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 486141544 164 eadgvHFSIPVTPHTFRHSYIMHMLYHRQPRKVIQALAGHKDPRSMEVYTRVFAL 218
Cdd:PRK15417 269 -----GITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKV 318
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 72-215 2.69e-03

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: 37.32  E-value: 2.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  72 TGIRIGEARTLTPESFDLDGLRpfvrVLSEKVRARRGRPPKDEVR-LVPLTDASFVRQMEsWMVTTRPRRreplwPVTDE 150
Cdd:cd00800   24 TGQRQGDLLRLKWSDITDGGLL----VEQSKTGKKLLIPWTPSLRaLVDRIRALPRKRSE-YLINSRKGG-----PLSYD 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 486141544 151 TMRNWLKQAVKRAEADGVHFsiPVTPHTFRHSYIMhmLYHRQPRKV-IQALAGHKDPRSMEVYTRV 215
Cdd:cd00800   94 TLKSAWRRARKAAGLKGETE--GFTFHDLRAKAAT--DYAEQGGSTdAQALLGHKSDAMTERYTRK 155
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 47-214 6.60e-03

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: 271196  Cd Length: 183  Bit Score: 36.69  E-value: 6.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  47 APEVSALLWYMPDQ-----RHHMLFATMWNTGIRIGEARTLTPESFDLDGLRPFVRvLSEKVRARRGRPP--KDEVRLVP 119
Cdd:cd01196    2 APEARRLLESIDSThpvglRDRALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVR-LAEKGGKQHEMPChhDLEEYLRA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544 120 LTDASFVRQMESWMVTTRPRRREPLWPVTDETMRNWLKQAVKRAEADGVhfSIPVTPHTFRHSYIMHMLYHRQPRKVIQA 199
Cdd:cd01196   81 YLEAAEIEEDPKGPLFRTTRGGTRKLTHNPLTQANAYRMVRRRAIAADI--PTAIGNHSFRATGITAYLKNGGTLEDAQN 158

                        170
                 ....*....|....*
gi 486141544 200 LAGHKDPRSMEVYTR 214
Cdd:cd01196  159 MANHASTRTTQLYDR 173
PBP1_ABC_HAAT-like cd06344
type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type ...
 81-132 9.95e-03

type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of hydrophobic amino acids or peptides; This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of hydrophobic amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally.


Pssm-ID: 380567 [Multi-domain]  Cd Length: 332  Bit Score: 36.43  E-value: 9.95e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486141544  81 TLTPESFDLDGLRPFVRVLSEKVRARRGRPPK-------DEVRL-----------VPLTDASFVRQMESW 132
Cdd:cd06344  240 VVVATVFDPDDPRPEVRAFVEAFRKKYGREPDvwaaqgyDAVKLlaeaiekagstVPAKIASALRFLENW 309
 
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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