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Conserved domains on  [gi|1841703226|gb|QJT41637|]
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IntN1 [Cloning vector pMT406]

Protein Classification

site-specific integrase( domain architecture ID 13879611)

tyrosine based site-specific recombinase (integrase) containing an Arm DNA-binding domain, 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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 259-437 3.69e-39

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: 138.55  E-value: 3.69e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 259 EERDRIFNADLSATPQLAIQRDIFIFQTLIGCRVSDLYRMTKLNVVN----EAIEYIPKKTKegnpVTVRVPLNDKAKEI 334
Cdd:cd01185     1 EELKRLMALELSDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTG----KPVTVPLLPVAREI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 335 LERYK--EYEGKLLPFISEQKYNDAIKKIFKLAGVDRIVTildplthneikrpiyevasSHLARRTFIGNIYKKVKDPNL 412
Cdd:cd01185    77 LEKYKddRSEGKLFPVLSNQKINRYLKEIAKIAGIDKHLT-------------------FHVARHTFATLLLLKGVDIET 137

                         170       180
                  ....*....|....*....|....*
gi 1841703226 413 VSALSGHKEGsKAFRRYRDIDEEMK 437
Cdd:cd01185   138 ISKLLGHSSI-KTTQIYAKIVDSKK 161
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 5-91 8.99e-03

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


:

Pssm-ID: 465401  Cd Length: 87  Bit Score: 35.43  E-value: 8.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226   5 FIIKKaaKRYDTESMATIYVRFRNGRQlDSVAPTQLAINPNLWDDKDECVKTKAVCNEEMRTHINEEIRQLKTYIEKVYQ 84
Cdd:pfam17293   1 VYLRK--KKLNKNGEAPLYLRIYKNGK-RKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILELEQ 77


                  ....*..
gi 1841703226  85 QEKEAID 91
Cdd:pfam17293  78 KGKLSAE 84
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 259-437 3.69e-39

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: 138.55  E-value: 3.69e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 259 EERDRIFNADLSATPQLAIQRDIFIFQTLIGCRVSDLYRMTKLNVVN----EAIEYIPKKTKegnpVTVRVPLNDKAKEI 334
Cdd:cd01185     1 EELKRLMALELSDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTG----KPVTVPLLPVAREI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 335 LERYK--EYEGKLLPFISEQKYNDAIKKIFKLAGVDRIVTildplthneikrpiyevasSHLARRTFIGNIYKKVKDPNL 412
Cdd:cd01185    77 LEKYKddRSEGKLFPVLSNQKINRYLKEIAKIAGIDKHLT-------------------FHVARHTFATLLLLKGVDIET 137

                         170       180
                  ....*....|....*....|....*
gi 1841703226 413 VSALSGHKEGsKAFRRYRDIDEEMK 437
Cdd:cd01185   138 ISKLLGHSSI-KTTQIYAKIVDSKK 161
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
119-445 5.85e-22

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 95.45  E-value: 5.85e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 119 TIGELFDEFLNKHPLSEVRKKN-FRVVKRALLRYELYVRATKrgqkgfILDVDLVTPDTLRDMWDFFQNeyqyyelypsi 197
Cdd:COG4974     2 TLADLLEAFLEELKREKGLSPNtIKAYRRDLRRFLRFLEELG------KIPLAEITPEDIRAYLNYLRE----------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 198 yeaipekrtpQPRSKNTLIDCFSRIRTFFLWCFDNKRTTNRPFDKFPIEECTYGTPYYITLEERDRIFNADLSATPQLAi 277
Cdd:COG4974    65 ----------RGLSPSTINRYLAALRSFFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGL- 133

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 278 qRDIFIFQTLI--GCRVSDLYRMTK--LNVVNEAIEYIPKKTKEgnpvTVRVPLNDKAKEILERYKEY-----EGKLLP- 347
Cdd:COG4974   134 -RDRALLLLLYatGLRVSELLGLKWsdIDLDRGTIRVRRGKGGK----ERTVPLSPEALEALREYLEErrprdSDYLFPt 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 348 ----FISEQKYNDAIKKIFKLAGVDRIVTIldplthneikrpiyevassHLARRTFIGNIYKKVKDPNLVSALSGHKEgS 423
Cdd:COG4974   209 rrgrPLSRRAIRKILKRLAKRAGIPKRVTP-------------------HSLRHTFATHLLEAGVDLRTVQELLGHSS-I 268

                         330       340
                  ....*....|....*....|..
gi 1841703226 424 KAFRRYRDIDEEMKKDLVKLLD 445
Cdd:COG4974   269 STTQIYTHVSDEELREAVEKLH 290
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 255-434 4.12e-04

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: 40.77  E-value: 4.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 255 YITLEERDRIFNAdlSATPQLAIqRDIFIFQTLIGC--RVSDLYRMTKLNV-VNEAIEYIP--KKTKEgnpvtVRVPLND 329
Cdd:pfam00589   1 RLTEDEVERLLDA--AETGPLSI-RDKALLELLYATglRISELCSLRWSDIdFENGVIRVHrgKGNKE-----RTVPLSD 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 330 KAKEILERYKEYEGKLLP-----F-------ISEQKYNDAIKKIFKLAGvdrivtildplthneikrpIYEVASSHLARR 397
Cdd:pfam00589  73 AALELLKEWLSKRLLEAPksdylFaskrgkpLSRQTVRKIFKRAGKEAG-------------------LELPLHPHMLRH 133

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1841703226 398 TFIGNIYKKVKDPNLVSALSGHKEGSKAfRRYRDIDE 434
Cdd:pfam00589 134 SFATHLLEAGVDLRVVQKLLGHSSISTT-QIYTHVAD 169
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 5-91 8.99e-03

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


Pssm-ID: 465401  Cd Length: 87  Bit Score: 35.43  E-value: 8.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226   5 FIIKKaaKRYDTESMATIYVRFRNGRQlDSVAPTQLAINPNLWDDKDECVKTKAVCNEEMRTHINEEIRQLKTYIEKVYQ 84
Cdd:pfam17293   1 VYLRK--KKLNKNGEAPLYLRIYKNGK-RKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILELEQ 77


                  ....*..
gi 1841703226  85 QEKEAID 91
Cdd:pfam17293  78 KGKLSAE 84
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 259-437 3.69e-39

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: 138.55  E-value: 3.69e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 259 EERDRIFNADLSATPQLAIQRDIFIFQTLIGCRVSDLYRMTKLNVVN----EAIEYIPKKTKegnpVTVRVPLNDKAKEI 334
Cdd:cd01185     1 EELKRLMALELSDTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEasgrTWIRYRRKKTG----KPVTVPLLPVAREI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 335 LERYK--EYEGKLLPFISEQKYNDAIKKIFKLAGVDRIVTildplthneikrpiyevasSHLARRTFIGNIYKKVKDPNL 412
Cdd:cd01185    77 LEKYKddRSEGKLFPVLSNQKINRYLKEIAKIAGIDKHLT-------------------FHVARHTFATLLLLKGVDIET 137

                         170       180
                  ....*....|....*....|....*
gi 1841703226 413 VSALSGHKEGsKAFRRYRDIDEEMK 437
Cdd:cd01185   138 ISKLLGHSSI-KTTQIYAKIVDSKK 161
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
119-445 5.85e-22

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 95.45  E-value: 5.85e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 119 TIGELFDEFLNKHPLSEVRKKN-FRVVKRALLRYELYVRATKrgqkgfILDVDLVTPDTLRDMWDFFQNeyqyyelypsi 197
Cdd:COG4974     2 TLADLLEAFLEELKREKGLSPNtIKAYRRDLRRFLRFLEELG------KIPLAEITPEDIRAYLNYLRE----------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 198 yeaipekrtpQPRSKNTLIDCFSRIRTFFLWCFDNKRTTNRPFDKFPIEECTYGTPYYITLEERDRIFNADLSATPQLAi 277
Cdd:COG4974    65 ----------RGLSPSTINRYLAALRSFFRYAVREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGL- 133

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 278 qRDIFIFQTLI--GCRVSDLYRMTK--LNVVNEAIEYIPKKTKEgnpvTVRVPLNDKAKEILERYKEY-----EGKLLP- 347
Cdd:COG4974   134 -RDRALLLLLYatGLRVSELLGLKWsdIDLDRGTIRVRRGKGGK----ERTVPLSPEALEALREYLEErrprdSDYLFPt 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 348 ----FISEQKYNDAIKKIFKLAGVDRIVTIldplthneikrpiyevassHLARRTFIGNIYKKVKDPNLVSALSGHKEgS 423
Cdd:COG4974   209 rrgrPLSRRAIRKILKRLAKRAGIPKRVTP-------------------HSLRHTFATHLLEAGVDLRTVQELLGHSS-I 268

                         330       340
                  ....*....|....*....|..
gi 1841703226 424 KAFRRYRDIDEEMKKDLVKLLD 445
Cdd:COG4974   269 STTQIYTHVSDEELREAVEKLH 290
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 255-429 3.51e-09

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: 55.41  E-value: 3.51e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 255 YITLEERDRIFNA-DLSATPQLaiqRDIFIFQTLIGCRVSDLYRMTkLNVVNEAIEYIP-KKTKEGNPVTVrvPLNDKAK 332
Cdd:cd00796     4 FLTEDEEARLLAAlEESTNPHL---RLIVLLALYTGARRGEILSLR-WDDIDLEVGLIVlPETKNGKPRTV--PLSDEAI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 333 EILERYKEYEGKLLPF-------ISEQKYNDAIKKIFKLAGVDRIVTildplthneikrpiyevassHLARRTFIGNIYK 405
Cdd:cd00796    78 AILKELKRKRGKDGFFvdgrffgIPIASLRRAFKKARKRAGLEDLRF--------------------HDLRHTFASRLVQ 137

                         170       180
                  ....*....|....*....|....
gi 1841703226 406 KVKDPNLVSALSGHKEgSKAFRRY 429
Cdd:cd00796   138 AGVPIKTVAKILGHSS-IKMTMRY 160
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 260-420 7.25e-06

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: 45.93  E-value: 7.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 260 ERDRIFNADLSATPQlaIQRDIFIFQTLI--GCRVSDLYRMTKLNVVNEAIEYIPKKTKEGNPVTVRVPLNDKAKEILER 337
Cdd:cd00397     1 ELEKLLDAIDEDKKI--DLRDRAILLLLLetGLRISELLALKVKDIDLDNGTIRVRGKKTKGGKERTVPLPKELAEELKE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 338 YKEYEGKLLPFISEQKYNDAIKKIFKlaGVDRIVTILDPLThNEIKRPIYEVASSHLARRTFIGNIYKKVKDPNLVSALS 417
Cdd:cd00397    79 YLKERRDKRGPLLKSLYLNKLFGTKL--GERLSRRTLRRIF-KKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLL 155


                  ...
gi 1841703226 418 GHK 420
Cdd:cd00397   156 GHS 158
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 278-420 5.46e-05

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: 43.77  E-value: 5.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 278 QRDIFIFQTLI--GCRVSDLYRMTKLNV--VNEAIEYIPKKTkeGNPVTVrvPLNDKAKEILERY-----KEYEGKLL-- 346
Cdd:cd01188    20 LRDYAILLLLArlGLRAGDVAGLRLDDIdwRSGTITVRQKKT--GRPVEL--PLTEPVGEALADYlrdgrPRTDSREVfl 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 347 -------PFISEQKYNDAIKKIFKLAGVDRIVTildplthneikrpiyevaSSHLARRTFIGNIYKKVKDPNLVSALSGH 419
Cdd:cd01188    96 rarapyrPLSSTSQISSIVRRYLRKAGIEPSHR------------------GTHSLRHSLATRMLRAGTSLKVIADLLGH 157


                  .
gi 1841703226 420 K 420
Cdd:cd01188   158 R 158
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 263-438 5.79e-05

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: 43.80  E-value: 5.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 263 RIFNADLSATPQLAIQRDIFIFQTLIGCRVSDLYRMTKLNV-VNEAIEYIPK-KTKEGNPVtvRVPLNDKAKEILERYKE 340
Cdd:cd00801     6 PELWRALDTANLSPPTKLALRLLLLTGQRIGELARARWSEIdLEEKTWTIPAeRTKNKRPH--RVPLSDQALEILEELKE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 341 Y--EGKLL--------PFISEQKYNDAIKKIFKLAgvdrivtildplthneikrpiyEVASSHLARRTFIGNIYKKVKDP 410
Cdd:cd00801    84 FtgDSGYLfpsrrkkkKPISENTINKALKRLGYKG----------------------KEFTPHDLRRTFSTLLNELGIDP 141

                         170       180       190
                  ....*....|....*....|....*....|
gi 1841703226 411 NLVSALSGHKEGSKAFRRYR--DIDEEMKK 438
Cdd:cd00801   142 EVIERLLNHVLGGVVRAAYNryDYLEERRE 171
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 118-430 1.89e-04

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 43.49  E-value: 1.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 118 PTIGELFDEFLNKHpLSEVRKKNFRVVKRALlryELYVRAtkrgqkgFI--LDVDLVTPDTLRDmwdffqneyqyyelyp 195
Cdd:COG0582    97 NTFEEVAEEWLEEK-KPEWKEKTAAQVRRTL---EKHIFP-------VLgdRPIAEITPPDLLA---------------- 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 196 sIYEAIPEKRTPqprskNTLIDCFSRIRTFFLWCFDNKRTTNRPFD--KFPIEECTYGTPYYITLEERDRIFNAdLSATP 273
Cdd:COG0582   150 -VLRPIEARGAP-----ETARRVRQRLRQVFRYAVARGLIERNPAAdlKGALPKPKVKHHPALTPEELPELLRA-LDAYR 222

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 274 QLAIQRDIFIFQTLIGCRVSDLYRMTKLNV-VNEAIEYIPK-KTKEGNPVtvRVPLNDKAKEILERYKEYEGK---LLPF 348
Cdd:COG0582   223 GSPVTRLALRLLLLTGVRPGELRGARWSEIdLEAALWTIPAeRMKTRRPH--IVPLSRQALEILKELKPLTGDseyVFPS 300

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 349 ISEQK---YNDAIKKIFKLAGVDRIV------TildplthneikrpiyevASSHLARRTFigniykkvkDPNLVSALSGH 419
Cdd:COG0582   301 RRGPKkpmSENTLNKALRRMGYGRFTphgfrhT-----------------ASTLLNEAGF---------PPDVIERQLAH 354

                         330
                  ....*....|.
gi 1841703226 420 KEGSKAFRRYR 430
Cdd:COG0582   355 KDGNKVRAAYN 365
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 255-434 4.12e-04

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: 40.77  E-value: 4.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 255 YITLEERDRIFNAdlSATPQLAIqRDIFIFQTLIGC--RVSDLYRMTKLNV-VNEAIEYIP--KKTKEgnpvtVRVPLND 329
Cdd:pfam00589   1 RLTEDEVERLLDA--AETGPLSI-RDKALLELLYATglRISELCSLRWSDIdFENGVIRVHrgKGNKE-----RTVPLSD 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226 330 KAKEILERYKEYEGKLLP-----F-------ISEQKYNDAIKKIFKLAGvdrivtildplthneikrpIYEVASSHLARR 397
Cdd:pfam00589  73 AALELLKEWLSKRLLEAPksdylFaskrgkpLSRQTVRKIFKRAGKEAG-------------------LELPLHPHMLRH 133

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1841703226 398 TFIGNIYKKVKDPNLVSALSGHKEGSKAfRRYRDIDE 434
Cdd:pfam00589 134 SFATHLLEAGVDLRVVQKLLGHSSISTT-QIYTHVAD 169
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 5-91 8.99e-03

Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases.


Pssm-ID: 465401  Cd Length: 87  Bit Score: 35.43  E-value: 8.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1841703226   5 FIIKKaaKRYDTESMATIYVRFRNGRQlDSVAPTQLAINPNLWDDKDECVKTKAVCNEEMRTHINEEIRQLKTYIEKVYQ 84
Cdd:pfam17293   1 VYLRK--KKLNKNGEAPLYLRIYKNGK-RKYESLGLYITPEPWDKKKQKVKRKHPNALELNEQIDQERSKLEDIILELEQ 77


                  ....*..
gi 1841703226  85 QEKEAID 91
Cdd:pfam17293  78 KGKLSAE 84
 
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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