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Conserved domains on  [gi|694097646|ref|WP_032441700|]
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MULTISPECIES: class 1 integron integrase IntI1, partial [Gammaproteobacteria]

Protein Classification

site-specific integrase( domain architecture ID 332)

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:  10577069|10047575|9278480
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_BRE_C super family cl00213
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 1-305 0e+00

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.


The actual alignment was detected with superfamily member PRK15417:

Pssm-ID: 469662 [Multi-domain]  Cd Length: 337  Bit Score: 596.64  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   1 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 80
Cdd:PRK15417  31 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  81 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:PRK15417 111 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 161 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:PRK15417 191 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 270

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 694097646 241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDALPPLTS 305
Cdd:PRK15417 271 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDALPPLTS 335
 
Name Accession Description Interval E-value
PRK15417 PRK15417
integron integrase;
1-305 0e+00

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 596.64  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   1 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 80
Cdd:PRK15417  31 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  81 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:PRK15417 111 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 161 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:PRK15417 191 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 270

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 694097646 241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDALPPLTS 305
Cdd:PRK15417 271 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDALPPLTS 335
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 1-300 0e+00

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: 521.57  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646    1 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 80
Cdd:TIGR02249  16 KRTEEAYLHWIKRFIRFHNKRHPSTMGDTEVEAFLSDLAVDGKVAASTQNQALNALLFLYKEILKTPLSLMERFVRAKRP 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   81 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:TIGR02249  96 RKLPVVLTREEVRRLLEHLEGKYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTVTLPKELIPPLRE 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  161 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:TIGR02249 176 QIELARAYHEADLAEGYGGVYLPHALARKYPNAPKEWGWQYLFPSHRLSRDPESGVIRRHHINETTIQRAVRRAVERAGI 255

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDAL 300
Cdd:TIGR02249 256 EKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLNRGASGVLSPLDRL 315
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 82-285 6.68e-91

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: 267.99  E-value: 6.68e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  82 RLPVVLTPDEVVRILGFL-EGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:cd01193    1 KLPVVLSPDEVRRILGALtELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 161 QLSRARAWWLKDQAEGRSGValpdalerkypraghswpwfwvfaqhthsTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:cd01193   81 YLKSARPKEELDPAEGRAGV-----------------------------LDPRTGVERRHHISETTVQRALKKAVEQAGI 131

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 694097646 241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:cd01193  132 TKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-285 1.61e-73

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 227.95  E-value: 1.61e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   2 RTEQAYVHWVRAFIRF---HGVRHPATLGSSEVEAFLSWLAnERKVSVSTHRQALAALLFFYGKV----LCTDLPWLQeI 74
Cdd:COG4974   23 NTIKAYRRDLRRFLRFleeLGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYAvregLLEDNPAAK-V 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  75 GRPRPSRRLPVVLTPDEVVRILGFLEGE------HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRAL 148
Cdd:COG4974  101 KLPKKPRKLPRVLTEEEIEALLEALDTEtpeglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTV 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 149 MLPESLAPSLREQLSRARawwlkdqaegrsgvalpdalerkypraghSWPWFWVFAQHthstdprsgvvRRHHMYDQTFQ 228
Cdd:COG4974  181 PLSPEALEALREYLEERR-----------------------------PRDSDYLFPTR-----------RGRPLSRRAIR 220

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 694097646 229 RAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:COG4974  221 KILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 86-287 1.39e-54

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: 175.20  E-value: 1.39e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   86 VLTPDEVVRILGFLEGE-----HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsirDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  161 QLSRarawwlkdqaegrsgvalpdaleRKYPRAGHSWpwfwVFAQHthstdprsgvvRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:pfam00589  81 WLSK-----------------------RLLEAPKSDY----LFASK-----------RGKPLSRQTVRKIFKRAGKEAGL 122

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 694097646  241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLK 287
Cdd:pfam00589 123 ELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
 
Name Accession Description Interval E-value
PRK15417 PRK15417
integron integrase;
1-305 0e+00

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 596.64  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   1 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 80
Cdd:PRK15417  31 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  81 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:PRK15417 111 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 161 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:PRK15417 191 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 270

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 694097646 241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDALPPLTS 305
Cdd:PRK15417 271 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDALPPLTS 335
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 1-300 0e+00

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: 521.57  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646    1 LRTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPS 80
Cdd:TIGR02249  16 KRTEEAYLHWIKRFIRFHNKRHPSTMGDTEVEAFLSDLAVDGKVAASTQNQALNALLFLYKEILKTPLSLMERFVRAKRP 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   81 RRLPVVLTPDEVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:TIGR02249  96 RKLPVVLTREEVRRLLEHLEGKYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTVTLPKELIPPLRE 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  161 QLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:TIGR02249 176 QIELARAYHEADLAEGYGGVYLPHALARKYPNAPKEWGWQYLFPSHRLSRDPESGVIRRHHINETTIQRAVRRAVERAGI 255

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLKVGGAGVRSPLDAL 300
Cdd:TIGR02249 256 EKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHVLNRGASGVLSPLDRL 315
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 82-285 6.68e-91

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: 267.99  E-value: 6.68e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  82 RLPVVLTPDEVVRILGFL-EGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:cd01193    1 KLPVVLSPDEVRRILGALtELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 161 QLSRARAWWLKDQAEGRSGValpdalerkypraghswpwfwvfaqhthsTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:cd01193   81 YLKSARPKEELDPAEGRAGV-----------------------------LDPRTGVERRHHISETTVQRALKKAVEQAGI 131

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 694097646 241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:cd01193  132 TKRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYTHV 176
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-285 1.61e-73

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 227.95  E-value: 1.61e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   2 RTEQAYVHWVRAFIRF---HGVRHPATLGSSEVEAFLSWLAnERKVSVSTHRQALAALLFFYGKV----LCTDLPWLQeI 74
Cdd:COG4974   23 NTIKAYRRDLRRFLRFleeLGKIPLAEITPEDIRAYLNYLR-ERGLSPSTINRYLAALRSFFRYAvregLLEDNPAAK-V 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  75 GRPRPSRRLPVVLTPDEVVRILGFLEGE------HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRAL 148
Cdd:COG4974  101 KLPKKPRKLPRVLTEEEIEALLEALDTEtpeglrDRALLLLLYATGLRVSELLGLKWSDIDLDRGTIRVRRGKGGKERTV 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 149 MLPESLAPSLREQLSRARawwlkdqaegrsgvalpdalerkypraghSWPWFWVFAQHthstdprsgvvRRHHMYDQTFQ 228
Cdd:COG4974  181 PLSPEALEALREYLEERR-----------------------------PRDSDYLFPTR-----------RGRPLSRRAIR 220

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 694097646 229 RAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:COG4974  221 KILKRLAKRAGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHV 277
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 86-287 1.39e-54

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: 175.20  E-value: 1.39e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   86 VLTPDEVVRILGFLEGE-----HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLRE 160
Cdd:pfam00589   1 RLTEDEVERLLDAAETGplsirDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  161 QLSRarawwlkdqaegrsgvalpdaleRKYPRAGHSWpwfwVFAQHthstdprsgvvRRHHMYDQTFQRAFKRAVEQAGI 240
Cdd:pfam00589  81 WLSK-----------------------RLLEAPKSDY----LFASK-----------RGKPLSRQTVRKIFKRAGKEAGL 122

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 694097646  241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLK 287
Cdd:pfam00589 123 ELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIYTHVAD 169
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 3-287 3.37e-51

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: 170.46  E-value: 3.37e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646    3 TEQAYVHWVRAFIRF--HGVRHPATLGSSEVEAFLSWLAnERKVSVSTHRQALAALLFFYG-----KVLCTDlPWLQeIG 75
Cdd:TIGR02225  17 TLEAYRRDLEKFLEFleERGIDLEEVDRGDIVDFLAELK-EAGLSARSIARALSALRSFYRfllreGIREDD-PSAL-IE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   76 RPRPSRRLPVVLTPDEVVRILGFLEGEH----RLFA--QLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDRALM 149
Cdd:TIGR02225  94 PPKVARKLPKVLTVEEVEALLAAPDVDTplglRDRAmlELLYATGLRVSELVGLRLEDVNLDEGFVRVR-GKGNKERLVP 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  150 LPESLAPSLREQLSRARawwlkdqaegrsgvalPDALERKYPRAGhswpwfWVFAQHthstdprsgvvRRHHMYDQTFQR 229
Cdd:TIGR02225 173 LGEEAIEALERYLKEAR----------------PLLLKKKVKESD------ALFLNR-----------RGGPLSRQGVWK 219

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 694097646  230 AFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLK 287
Cdd:TIGR02225 220 ILKEYAKRAGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVAR 277
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
2-285 3.31e-47

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 160.13  E-value: 3.31e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   2 RTEQAYVHWVRAFIRFHGVRH--PATLGSSEVEAFLSWLAnERKVSVSTHRQALAALLFFYGkvlctdlpWLQEIG---- 75
Cdd:COG4973   23 KTLEAYRRDLRRLIPLLGDADlpLEELTPADVRRFLARLH-RRGLSPRTLNRRLSALRSFFN--------WAVREGllea 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  76 -------RPRPSRRLPVVLTPDEVVRILGFLEGEH-----RLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGS 143
Cdd:COG4973   94 npaagvkAPKAPRKLPRALTVDELAQLLDALADDPlavrdRAIVELLYSTGLRLGELVGLDWEDVDLDAGEVRVR-GKTG 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 144 KDRALMLPESLAPSLREQLSRARAWWLKDQAegrsgvalpdalerkypraghswpwfWVFAqhthstdprsgVVRRHHMY 223
Cdd:COG4973  173 KSRTVPLGPKALAALREWLAVRPELAAPDEG--------------------------ALFP-----------SRRGTRLS 215

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 694097646 224 DQTFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:COG4973  216 PRNVQKRLRRLAKKAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHL 277
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 2-285 6.64e-47

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 159.55  E-value: 6.64e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   2 RTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERK--VSVSTHRQALAALLFFY----GKVLCTDLPwLQEIG 75
Cdd:PRK00236  26 HTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLARRRRqgLSARSLARRLSALRSFYrwlvRRGLLKANP-AAGLR 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  76 RPRPSRRLPVVLTPDEVVRILGFLEGEHRLFAQ------LLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDRalM 149
Cdd:PRK00236 105 APKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRdraileLLYGSGLRLSELVGLDIDDLDLASGTLRVL-GKGNKER--T 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 150 LPesLAPSLREQLSRarawWLKdqaegrsgvALPDALERKYPraghswpwfwVFaqhthstdpRSgvVRRHHMYDQTFQR 229
Cdd:PRK00236 182 VP--LGRAAREALEA----YLA---------LRPLFLPDDDA----------LF---------LG--ARGGRLSPRVVQR 225

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 694097646 230 AFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:PRK00236 226 RVKKLGKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHV 281
xerD PRK00283
tyrosine recombinase;
3-287 3.79e-45

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 154.96  E-value: 3.79e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   3 TEQAYVHWVRAFIRFHGVRH--PATLGSSEVEAFLSWLANERKVSVSTHRqALAALLFFYG-----KVLCTDLPWLQEIg 75
Cdd:PRK00283  26 TLSSYRRDLELFAEWLAARGlsLAEATRDDLQAFLAELAEGGYKATSSAR-RLSALRRFFQfllreGLREDDPSALLDS- 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  76 rPRPSRRLPVVLTPDEVVRILGFLEGEH----RLFA--QLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDRALM 149
Cdd:PRK00283 104 -PKLPRRLPKTLSEAQVEALLDAPDIDTplglRDRAmlELLYATGLRVSELVGLTLDDVSLRQGVVRVT-GKGNKERLVP 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 150 LPESLAPSLREQLSRARAWWLKDQAEGrsgvalpdalerkypraghswpwfWVFAQHthstdprsgvvRRHHMYDQTFQR 229
Cdd:PRK00283 182 LGEEAVYAIERYLERGRPALLNGRSSD------------------------ALFPSA-----------RGGQLTRQTFWH 226

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 694097646 230 AFKRAVEQAGI-TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVLK 287
Cdd:PRK00283 227 RIKHYAKRAGIdPKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVAT 285
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 2-285 8.27e-45

tyrosine recombinase XerC; 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 XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). 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 homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 153.92  E-value: 8.27e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646    2 RTEQAYVHWVRAFIRF----HGVRHPATLGSSEVEAFLSWLAnERKVSVSTHRQALAALLFFYG----KVLCTDLPwLQE 73
Cdd:TIGR02224  16 HTVRAYRRDLEAFLEFleeeGGLASLAEVTAADLRSFLAELH-ARGLSRRSLARKLSALRSFYRfllrRGLIDANP-AAG 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   74 IGRPRPSRRLPVVLTPDEVVRILGFLEGEHRLFAQ--------LLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKD 145
Cdd:TIGR02224  94 VRAPKQPKKLPKFLSEDEMEALLDAPEEDDEDWLAlrdraileLLYSSGLRVSELVGLDLSDLDLDFGEVRVR-GKGNKE 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  146 RALMLpeslapslreqLSRARAW---WLKdqaegrsgvALPDALERKYPRAGhswpwfwVF-AQHTHSTDPRSgvvrrhh 221
Cdd:TIGR02224 173 RIVPF-----------GPYARDAlqaYLE---------ARRSPLLASEGQDA-------LFlNRRGGRLTPRG------- 218

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 694097646  222 mydqtFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:TIGR02224 219 -----VQYRLQQLRAKAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHV 277
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 90-285 1.25e-43

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: 146.89  E-value: 1.25e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  90 DEVVRILGFLEGEHRLFA------QLLYGTGMRISEGLQLRVKDLDFDHGTIIVReGKGSKDRALMLPESLAPSLREQLS 163
Cdd:cd00798    2 DEVERLLDAPDTDTPLGLrdrailELLYASGLRVSELVGLDLSDVDLDEGLVRVT-GKGNKERLVPFGSYAVEALEEYLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 164 RARAWWLKDQAegrsgvalPDALerkypraghswpwfwvFAQHthstdprsgvvRRHHMYDQTFQRAFKRAVEQAGITKP 243
Cdd:cd00798   81 ERRPLLLKKKP--------PDAL----------------FLNK-----------RGKRLSRRGVWRILKKYAERAGLPKH 125

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 694097646 244 ATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:cd00798  126 VSPHTLRHSFATHLLEGGADLRVVQELLGHASLSTTQIYTHV 167
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 103-283 2.44e-36

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: 127.98  E-value: 2.44e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 103 HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGK--GSKDRALMLPESLAPSLREQLSRARAWWLKDQaegrsgv 180
Cdd:cd00397   19 DRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkGGKERTVPLPKELAEELKEYLKERRDKRGPLL------- 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 181 alpdalerkypraghswpwfwvfaqHTHSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGitKPATPHTLRHSFATALLRS 260
Cdd:cd00397   92 -------------------------KSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAG--RKITPHSLRHTFATNLLEN 144

                        170       180
                 ....*....|....*....|...
gi 694097646 261 GYDIRTVQDLLGHSDVSTTMIYT 283
Cdd:cd00397  145 GVDIKVVQKLLGHSSISTTQRYL 167
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 2-285 4.06e-29

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 114.07  E-value: 4.06e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646   2 RTEQAYVHWVRAFIRF---HGVRHPATLGSSEVEAFLSWLANERK-----VSVSTHRQALAALLFFYGkvlctdlpWL-- 71
Cdd:PRK01287  40 RTLKVYTEHLYPFILWceeRGLYYAADVTLPVLERYQRYLYGYRKangepLSTRTQRTQLSPLRVWFR--------WLlk 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  72 ---------QEIGRPRPSRRLPV-VLTPDEVVRILGFLEGE------HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTI 135
Cdd:PRK01287 112 rhhilynpaEDLELPKEEKRLPRqILSEAETEQVLASPDLTtlqglrDRALLELLWSTGIRRGELARLDLYDVDASRGVV 191

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 136 IVREGKGSKDRALMLPEslapslreqlsRARAWWLKDQAEGRsgvalPDALERkyPRAGHswpwfwVFAQHTHSTDPRSG 215
Cdd:PRK01287 192 TVRQGKGNKDRVVPVGE-----------RALAWLQRYLQDVR-----PQLAVR--PDSGA------LFVAMDGDGLARNT 247

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 216 VVRRhhmydqtfqraFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 285
Cdd:PRK01287 248 LTNM-----------VGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRV 306
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 87-284 5.46e-25

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: 98.17  E-value: 5.46e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  87 LTPDEVVRILGFLEGEH----RLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPEslapslreql 162
Cdd:cd00796    5 LTEDEEARLLAALEESTnphlRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSD---------- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 163 sRARAWwLKDQAEGRSGVALPdalerkypraghswpwfwvfaqhthstdprsGVVRRHHMYDQTFQRAFKRAVEQAGITK 242
Cdd:cd00796   75 -EAIAI-LKELKRKRGKDGFF-------------------------------VDGRFFGIPIASLRRAFKKARKRAGLED 121

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 694097646 243 pATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTH 284
Cdd:cd00796  122 -LRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRYAH 162
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
2-70 2.98e-24

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 93.83  E-value: 2.98e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 694097646    2 RTEQAYVHWVRAFIRFHGVRHPATLGSSEVEAFLSWLANERKVSVSTHRQALAALLFFYGKVLctDLPW 70
Cdd:pfam13495  17 RTIKAYLRWIRRFLRFHDKKHPEELTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWVL--EREL 83
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 89-284 1.99e-22

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: 90.70  E-value: 1.99e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  89 PDEVVRILGFLEGE---HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREgkgskdralmlpeslapslreQLSRA 165
Cdd:cd01189    1 PEELKKLLEALKKRgdrYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINR---------------------TLVRK 59

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 166 RA-WWLKDQAEGRSG---VALPDALERkypraghswpwfwvfaqhthstdprsgVVRRHhmydqtfqRAFKRAVEQAGIt 241
Cdd:cd01189   60 KKgGYVIKPPKTKSSirtIPLPDELIE---------------------------LLKEL--------KAFKKLLKKAGL- 103

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 694097646 242 KPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTM-IYTH 284
Cdd:cd01189  104 PRITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTLdVYAH 147
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 88-282 3.01e-22

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: 91.53  E-value: 3.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  88 TPDEVVRILGF----LEGEHRLFA--QLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPEslapslreQ 161
Cdd:cd01188    1 SPDEVRRLLAAidrlTPVGLRDYAilLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTE--------P 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 162 LSRARAWWLKDqaeGRsgvalpdalerkyPRAGHSWpwfwVFAQHTHStdprsgvvRRHHMYDQTFQRAFKRAVEQAGIT 241
Cdd:cd01188   73 VGEALADYLRD---GR-------------PRTDSRE----VFLRARAP--------YRPLSSTSQISSIVRRYLRKAGIE 124

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 694097646 242 KPAT-PHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 282
Cdd:cd01188  125 PSHRgTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIY 166
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 225-286 1.56e-19

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: 83.47  E-value: 1.56e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 694097646 225 QTFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHVL 286
Cdd:cd01185   96 QKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIV 157
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 103-283 4.64e-18

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: 80.40  E-value: 4.64e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 103 HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRalmlpesLAPSLREQLSRARAWWlkdqaegrsgval 182
Cdd:cd01182   23 DHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKER-------TVPLWKETVAALKAYL------------- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 183 pdaleRKYPRAGHSWPWFWVFAQHTHSTDPRSGVvrrhhmydqtfQRAFKRAVEQAGITKPA-----TPHTLRHSFATAL 257
Cdd:cd01182   83 -----QEFHLTPDPKQLFPLFPNRRGQPLTRDGV-----------AYILNKYVALASNRCPSlpkriTPHTLRHTKAMHL 146

                        170       180
                 ....*....|....*....|....*.
gi 694097646 258 LRSGYDIRTVQDLLGHSDVSTTMIYT 283
Cdd:cd01182  147 LQAGVDLTVIRDWLGHESVETTQIYA 172
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 86-285 7.50e-18

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: 79.77  E-value: 7.50e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  86 VLTPDEVVRILgflEGEH----RLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVregkgsKDRalmlpESLAPSLREQ 161
Cdd:cd01186    1 VLTPREVQELI---NACNnlrdKFLLALLYETGLRIGEALGLRIEDIDMADNQIEL------VPR-----EDNTNEARAK 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 162 LSRARawwlkdqaegrsGVALPDALERKYPRAGHSWPWFWVFAQHTHSTDPRSGVVRrHHMYDQTFQRAFKRAVEQAGIT 241
Cdd:cd01186   67 SMRER------------RIPVSQDLIDLYADYLTYIYCEEAEFSITVFVNVKGGNQG-KAMNYSDVYDLVRRLKKRTGID 133

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 694097646 242 kpATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTM-IYTHV 285
Cdd:cd01186  134 --FTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTTLnTYGHL 176
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 109-285 1.79e-16

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 78.81  E-value: 1.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 109 LLYGTGMRISEGLQLRVKDLDFDHGTI-IVREGkGSKDRALMLPESLaPSLREQLsrarawwlkDQAEGRSGVAlpdale 187
Cdd:PRK05084 203 LILGSGLRVSELVNLDLSDLNLKQMTIdVTRKG-GKRDSVNIAPFAL-PYLEEYL---------KIRASRYKAE------ 265

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 188 rKYPRAghswpwfwVFAqhthsTDPRsGVVRRhhMYDQTFQRAFKRAVEQAGitKPATPHTLRHSFATALLRSGYDIRTV 267
Cdd:PRK05084 266 -KQEKA--------LFL-----TKYR-GKPNR--ISARAIEKMVAKYSEAFG--VRLTPHKLRHTLATRLYDATKDQVLV 326

                        170
                 ....*....|....*...
gi 694097646 268 QDLLGHSDVSTTMIYTHV 285
Cdd:PRK05084 327 ADQLGHTSTETTDLYTHI 344
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 109-284 1.01e-14

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: 70.58  E-value: 1.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 109 LLYGTGMRISEGLQLRVKDLDFDHGTIIvREGKGSKDRALMlpeSLAPSLREQLsrarAWWLKDQAEGRSgvalpdaler 188
Cdd:cd01195   28 LLLDNALRRSEAVALDVEDLEKEHRRLR-ILGKGKKQREVV---TLPPTTREAL----AAWLAARGEAEG---------- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 189 kypraghswPWFwvfaqhtHSTDPRSgvvRRHHMYDQTFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYD-IRTV 267
Cdd:cd01195   90 ---------PLF-------VSLDRAS---RGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGlIRKV 150

                        170
                 ....*....|....*..
gi 694097646 268 QDLLGHSDVSTTMIYTH 284
Cdd:cd01195  151 QDFSRHADLRTLQVYDD 167
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 87-284 2.81e-14

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 72.38  E-value: 2.81e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  87 LTPDEVVRILGFLEGEH-----RLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREG--KGSKDRALMLPeslapslr 159
Cdd:COG0582  206 LTPEELPELLRALDAYRgspvtRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAErmKTRRPHIVPLS-------- 277

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 160 eqlsrarawwlkDQAegrsgVALpdaLERKYPRAGHSwpwFWVFaqhthsTDPRSgvvRRHHMYDQTFQRAFKRAveqaG 239
Cdd:COG0582  278 ------------RQA-----LEI---LKELKPLTGDS---EYVF------PSRRG---PKKPMSENTLNKALRRM----G 321

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 694097646 240 ITKpATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTM-IYTH 284
Cdd:COG0582  322 YGR-FTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaAYNR 366
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 113-284 1.86e-13

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: 67.40  E-value: 1.86e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 113 TGMRISEGLQLRVKDLDF-DHGTIIVREGKG--SKDRALMLPESLAPSLREQLsRARawwlkdqaegrsgvalpDALERK 189
Cdd:cd01194   34 EGLRTVEIVRADVGDLRQeGEGTILYVQGKGktSKDDFVYLRPDVLKALQAYL-KAR-----------------GKLDFE 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 190 YPraghswpwfwVFAQHTHSTdprsgvvRRHHMYDQTFQRAFKRAVEQAGITKPA-TPHTLRHSFATALLRSGYDIRTVQ 268
Cdd:cd01194   96 EP----------LFTSLSNNS-------KGQRLTTRSIRRIIKKYLRKAGLDDDRlTAHSLRHTAGTLALKAGKSLREVQ 158

                        170
                 ....*....|....*.
gi 694097646 269 DLLGHSDVSTTMIYTH 284
Cdd:cd01194  159 QLLRHSDPNTTMIYAH 174
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 109-283 5.11e-13

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


Pssm-ID: 271197 [Multi-domain]  Cd Length: 181  Bit Score: 66.38  E-value: 5.11e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 109 LLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKdralmlpeSLAPSLREQLSRARAWWLKDQAEGRsgvalpdaler 188
Cdd:cd01197   34 LAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGF--------STTHPLRFDEREALEAWLKERANWK----------- 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 189 kypraGHSWPWFWVFAQhthstdpRSGVVRrhhmydQTFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQ 268
Cdd:cd01197   95 -----GADTDWIFLSRR-------GGPLSR------QQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQ 156

                        170
                 ....*....|....*
gi 694097646 269 DLLGHSDVSTTMIYT 283
Cdd:cd01197  157 DYLGHRNIRHTVIYT 171
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 87-284 8.24e-12

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: 63.09  E-value: 8.24e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  87 LTPDEVVRILGF---LEGEHRLFAQ-------LLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRalMLPesLAP 156
Cdd:cd00797    1 YTDAEIRRLLAAadqLPPESPLRPLtyatlfgLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSR--LVP--LHP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 157 SLREQLSRARAwwlkdqaegrsgvalpdalERKYPRAGHSWPWFWVFAQHThstdprsgvvRRHHmydQTFQRAFKRAVE 236
Cdd:cd00797   77 STVGALRDYLA-------------------RRDRLLPSPSSSYFFVSQQGG----------RLTG---GGVYRVFRRLLR 124

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 694097646 237 QAGItKPAT------PHTLRHSFATALL----RSGYDIRT----VQDLLGHSDVSTTMIYTH 284
Cdd:cd00797  125 RIGL-RGAGdgrgprLHDLRHTFAVNRLtrwyREGADVERklpvLSTYLGHVNVTDTYWYLT 185
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 113-282 1.50e-11

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: 61.92  E-value: 1.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 113 TGMRISEGLQLRVKDLDF-DHGTIIvrEGKGSKDRALmlpeSLAPSLREQLSRaRAWWLKDQaegrsgvalpdalerkyp 191
Cdd:cd01192   36 TGLRISDLLSLKVEDVTNkDKLSIK--EQKTGKQKTF----PLNPTLVKALKE-YIDDLDLK------------------ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 192 ragHSWPWFWVFAQHthstdpRSGVVRRHHmydqtFQRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLL 271
Cdd:cd01192   91 ---RNDYLFKSLKQG------PEKPISRKQ-----AYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLL 156

                        170
                 ....*....|.
gi 694097646 272 GHSDVSTTMIY 282
Cdd:cd01192  157 NHSSPSITLRY 167
int PHA02601
integrase; Provisional
 87-284 3.18e-11

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 63.21  E-value: 3.18e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  87 LTPDEVVRILGFLEG----EHRLFAQLLYGTGMRISEGLQLRVKDLDfdHGTIIVREGKGSKDRALMLPEslapslreql 162
Cdd:PHA02601 173 LTKEEIERLLDACDGsrspDLGLIAKICLATGARWSEAETLKRSQIS--PYKITFVKTKGKKNRTVPISE---------- 240

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 163 srarawWLKDQAEGRSGVALPDALERkypraghswpwfwvfaqhthstdprsgvvrrhhmydqtfqraFKRAVEQAGITK 242
Cdd:PHA02601 241 ------ELYKMLPKRRGRLFKDAYES------------------------------------------FERAVKRAGIDL 272

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 694097646 243 P---ATpHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTH 284
Cdd:PHA02601 273 PegqAT-HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYAH 316
PRK09871 PRK09871
tyrosine recombinase; Provisional
 109-283 1.06e-09

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 57.30  E-value: 1.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 109 LLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKG--SKDRALMLPESLAPslrEQLSRARAWWlkdqaegrSGVALPDAl 186
Cdd:PRK09871  34 LAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNgfSTVHPLRFDEREAV---ERWTQERANW--------KGADRTDA- 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 187 erkypraghswpwfwVFAQHthstdpRSGVVRRHHMYdqtfqRAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRT 266
Cdd:PRK09871 102 ---------------IFISR------RGSRLSRQQAY-----RIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRL 155

                        170
                 ....*....|....*..
gi 694097646 267 VQDLLGHSDVSTTMIYT 283
Cdd:PRK09871 156 IQDYLGHRNIRHTVRYT 172
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 111-283 1.49e-09

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: 56.54  E-value: 1.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 111 YGTGMRISEGLQLRVKDLDF--DHGTII-VREGKGSKDRAlmlPESLAPSLREQLSRARAW--WLKdqaegrsgvalpda 185
Cdd:cd00799   26 FAGALRRSELVALRVEDLTRfvDGGLLIrLRRSKTDQDGE---GEIKALPYGPETCPVRALraWLE-------------- 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 186 lerkyPRAGHSWPWFwvfaqhthSTDPRSGVVRRHHMYDQTFQRAFKRAVEQAGI-TKPATPHTLRHSFATALLRSGYDI 264
Cdd:cd00799   89 -----AAGIPSGPLF--------RRIRRGGSVGTTRLSDRSVARIVKRRAALAGLdPGDFSGHSLRRGFATEAARAGASL 155

                        170
                 ....*....|....*....
gi 694097646 265 RTVQDLLGHSDVSTTMIYT 283
Cdd:cd00799  156 PEIMAQGGHKSVATVMRYI 174
PRK09870 PRK09870
tyrosine recombinase; Provisional
 87-283 4.04e-09

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 55.33  E-value: 4.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  87 LTPDEVVRIL-----GFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTI-IVREGKGSkdralmlpESLAPSLRE 160
Cdd:PRK09870  13 LTHSEIESLLkaantGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIyIHRLKKGF--------STTHPLLNK 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 161 QLSRARAWWlkdqaegrsgvalpdALERKYPRAGHSWPWFwvfaqhTHSTDPRSgvvrrhhmyDQTFQRAFKRAVEQAGI 240
Cdd:PRK09870  85 EIQALKNWL---------------SIRTSYPHAESEWVFL------SRKGNPLS---------RQQFYHIISTSGGNAGL 134

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 694097646 241 TKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYT 283
Cdd:PRK09870 135 SLEIHPHMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYT 177
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 104-283 9.52e-09

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: 53.50  E-value: 9.52e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 104 RLFAQLLYGTGMRISEGLQLRVKDLDFDHgtIIVREGKGSKDraLMLPesLAPSLREQLSRARAwwlkdqaegRSGVALp 183
Cdd:cd00800   15 RLAMELALLTGQRQGDLLRLKWSDITDGG--LLVEQSKTGKK--LLIP--WTPSLRALVDRIRA---------LPRKRS- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 184 dalerkypraghswpwFWVFaqHTHSTDPRSgvvrrhhmyDQTFQRAFKRAVEQAGITKPATP---HTLRHSFATALLRS 260
Cdd:cd00800   79 ----------------EYLI--NSRKGGPLS---------YDTLKSAWRRARKAAGLKGETEGftfHDLRAKAATDYAEQ 131

                        170       180
                 ....*....|....*....|...
gi 694097646 261 GyDIRTVQDLLGHSDVSTTMIYT 283
Cdd:cd00800  132 G-GSTDAQALLGHKSDAMTERYT 153
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 87-279 1.13e-07

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: 50.77  E-value: 1.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646  87 LTPDEVVRIL------GFLEGEHRLFAQLLYG--TGMRISEGLQLRVKDLDFDHGTIIVRegkgskdralmlpeslapsL 158
Cdd:cd01184    1 FTPEELAKIFssplytGCKKKDPALYWLPLIGlyTGARLNEICQLRVDDIKEEDGIWCID-------------------I 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 159 REQLSRARawwLKDQAEGRSgVALPDALerkyPRAGhswpwFWVFAQHTHSTD-PRSGVVRRHH--MYDQTFQRAFKRAV 235
Cdd:cd01184   62 NDDAEGRR---LKTKASRRL-VPIHPRL----IELG-----FLDYVEALRADGkLFLFPEKRDKdgKYSKAASKWFNRLL 128

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 694097646 236 EQAGITKPA--TPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTT 279
Cdd:cd01184  129 RKLGIKDDErkSFHSFRHTFITALKRAGVPEELIAQIVGHSRGGVT 174
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 225-284 6.59e-07

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: 47.81  E-value: 6.59e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 225 QTFQRAFKRAVEQAGITKpATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTH 284
Cdd:cd01187   84 NELSELKNISDDHGERFR-FHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 104-280 7.58e-07

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: 48.42  E-value: 7.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 104 RLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPeslapslreqlsrarawwLKDQAegrsgVALP 183
Cdd:cd00801   22 KLALRLLLLTGQRIGELARARWSEIDLEEKTWTIPAERTKNKRPHRVP------------------LSDQA-----LEIL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 184 DALERKYPRAGhswpwfWVFAqhthstdprSGVVRRHHMYDQTFQRAFKRAveqAGITKPATPHTLRHSFATALLRSGYD 263
Cdd:cd00801   79 EELKEFTGDSG------YLFP---------SRRKKKKPISENTINKALKRL---GYKGKEFTPHDLRRTFSTLLNELGID 140

                        170
                 ....*....|....*..
gi 694097646 264 IRTVQDLLGHSDVSTTM 280
Cdd:cd00801  141 PEVIERLLNHVLGGVVR 157
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 88-163 7.16e-05

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


Pssm-ID: 271190  Cd Length: 150  Bit Score: 42.33  E-value: 7.16e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 694097646  88 TPDEVVRILGFLEG---EHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSkdRALMLPESLAPSLREQLS 163
Cdd:cd01190    1 EPPEILDLSSFYQGdflKGQLIALLILELGLTPSEIANLKWADFDLDFQVLTIEKGGIK--RVLPLPKKLLPFLEQHIK 77
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 110-282 1.64e-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: 271191  Cd Length: 176  Bit Score: 41.64  E-value: 1.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 110 LYGTGMRISEGLQLRVKDLDFDHGTIIvreGKGSKDRALMLPESLAPSLREqlsrarawWLKDQAEGRSGVALPDALERK 189
Cdd:cd01191   29 LAATGARVSELIKIKVEHVELGYFDIY---SKGGKLRRLYIPKKLRNEALE--------WLKSTNRKSGYIFLNRFGERI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694097646 190 YPRAghswpwfwvFAQHthstdprsgvvrrhhmydqtfqraFKRAVEQAGI-TKPATPHTLRHSFATALLRSGYDIRTVQ 268
Cdd:cd01191   98 TTRG---------IAQQ------------------------LKNYARKYGLnPKVVYPHSFRHRFAKNFLEKYNDIALLA 144

                        170
                 ....*....|....
gi 694097646 269 DLLGHSDVSTTMIY 282
Cdd:cd01191  145 DLMGHESIETTRIY 158
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 229-282 1.67e-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: 271196  Cd Length: 183  Bit Score: 41.70  E-value: 1.67e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 694097646 229 RAFKRAVEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 282
Cdd:cd01196  118 RMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQNMANHASTRTTQLY 171
xerD PRK02436
site-specific tyrosine recombinase XerD;
96-163 7.18e-03

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 37.28  E-value: 7.18e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 694097646  96 LGFLEGehRLFAQLLYGTGMRISEGLQLRVKDLDFDHGtiIVREGKGSKDRALMLPESLAPSLREQLS 163
Cdd:PRK02436 109 TPFPEG--QLIALLILELGLTPSEIAGLKVADIDLDFQ--VLTIEKAGGKRVLTLPEALLPFLEAILN 172
 
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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