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Conserved domains on  [gi|8347627|gb|AAF74726|]
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integrase [Bacteroides fragilis]

Protein Classification

site-specific integrase( domain architecture ID 18321758)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 238-417 4.80e-46

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: 156.27  E-value: 4.80e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  238 DELNKLKDYQIPkDKQYLERVRDVFLFCCFTSLRYSDVRNLKRSDVKSDH----IEITTVKTADSLTIELNKYSKAILDK 313
Cdd:cd01185   1 EELKRLMALELS-DTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEASgrtwIRYRRKKTGKPVTVPLLPVAREILEK 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  314 YKDIHFENYMaLPVISNQKMNDYLKELGELAEINEPvretyykgneridevtpkyalLSTHAGRRTFICNALALGIPAQV 393
Cdd:cd01185  80 YKDDRSEGKL-FPVLSNQKINRYLKEIAKIAGIDKH---------------------LTFHVARHTFATLLLLKGVDIET 137

                       170       180
                ....*....|....*....|....
gi 8347627  394 VMKWTGHSDYKAMKPYIDIADDIK 417
Cdd:cd01185 138 ISKLLGHSSIKTTQIYAKIVDSKK 161
Phage_int_SAM_5 super family cl44621
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 125-211 5.09e-04

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


The actual alignment was detected with superfamily member pfam13102:

Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 39.13  E-value: 5.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627    125 SFWEVFDEFVKECGNQNNwtASTYEKFAAVRNHLKEF--KEDATFNYFNEFGLNEYVNFLRDTKDMRNSTIGKQMGFLKW 202
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGS--KGTARNYKSTLKHLKKFlkKKDITFEEITVDFLEKFEEYLKKKKGLSENTISKYFRTLRA 78


                  ....*....
gi 8347627    203 FLRWSFKKG 211
Cdd:pfam13102  79 VLNKAIKEG 87
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 15-95 6.12e-04

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: 38.51  E-value: 6.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627     15 KKNGvpiveNVPIRMRVIFASQRIEFTTGYRIDVAKWDADKQRVKSGCTNKLkqsaaEINTDLLKYYAEIQNIFKEFEVQ 94
Cdd:pfam17293   9 NKNG-----EAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNAL-----ELNEQIDQERSKLEDIILELEQK 78


                  .
gi 8347627     95 E 95
Cdd:pfam17293  79 G 79
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 238-417 4.80e-46

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: 156.27  E-value: 4.80e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  238 DELNKLKDYQIPkDKQYLERVRDVFLFCCFTSLRYSDVRNLKRSDVKSDH----IEITTVKTADSLTIELNKYSKAILDK 313
Cdd:cd01185   1 EELKRLMALELS-DTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEASgrtwIRYRRKKTGKPVTVPLLPVAREILEK 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  314 YKDIHFENYMaLPVISNQKMNDYLKELGELAEINEPvretyykgneridevtpkyalLSTHAGRRTFICNALALGIPAQV 393
Cdd:cd01185  80 YKDDRSEGKL-FPVLSNQKINRYLKEIAKIAGIDKH---------------------LTFHVARHTFATLLLLKGVDIET 137

                       170       180
                ....*....|....*....|....
gi 8347627  394 VMKWTGHSDYKAMKPYIDIADDIK 417
Cdd:cd01185 138 ISKLLGHSSIKTTQIYAKIVDSKK 161
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
124-425 4.73e-32

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 123.18  E-value: 4.73e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  124 VSFWEVFDEFVKECGNQNNWTASTYEKFAAVRNHLKEFKEDATFNYFNEFG---LNEYVNFLRDtKDMRNSTIGKQMGFL 200
Cdd:COG4974   1 LTLADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEITpedIRAYLNYLRE-RGLSPSTINRYLAAL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  201 KWFLRWSFKKGHHQNIAYDTFKPKlKTTSKKVIFLTWDELNKLKDYqIPKDKQYLERVRDVFLFCCFTSLRYSDVRNLKR 280
Cdd:COG4974  80 RSFFRYAVREGLLEDNPAAKVKLP-KKPRKLPRVLTEEEIEALLEA-LDTETPEGLRDRALLLLLYATGLRVSELLGLKW 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  281 SDVKSDH--IEITTVKTADSLTIELNKYSKAILDKYKDIH--------FENYMALPvISNQKMNDYLKELGELAEINEPV 350
Cdd:COG4974 158 SDIDLDRgtIRVRRGKGGKERTVPLSPEALEALREYLEERrprdsdylFPTRRGRP-LSRRAIRKILKRLAKRAGIPKRV 236

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 8347627  351 retyykgneridevtpkyallSTHAGRRTFICNALALGIPAQVVMKWTGHSDYKAMKPYIDIADDIKANAMNKFN 425
Cdd:COG4974 237 ---------------------TPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 234-402 3.19e-06

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: 46.93  E-value: 3.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627    234 FLTWDELNKLkdYQIPKDKQYLERVRDVFLFCCFTSLRYSDVRNLKRSDV--KSDHIEITTVKTADSLTIELNKYS---- 307
Cdd:pfam00589   1 RLTEDEVERL--LDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIdfENGVIRVHRGKGNKERTVPLSDAAlell 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627    308 KAILDK------YKDIHFENYMALPvISNQKMNDYLKELGELAEINEPvretyykgneridevtpkyalLSTHAGRRTFI 381
Cdd:pfam00589  79 KEWLSKrlleapKSDYLFASKRGKP-LSRQTVRKIFKRAGKEAGLELP---------------------LHPHMLRHSFA 136

                         170       180
                  ....*....|....*....|.
gi 8347627    382 CNALALGIPAQVVMKWTGHSD 402
Cdd:pfam00589 137 THLLEAGVDLRVVQKLLGHSS 157
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 125-211 5.09e-04

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 39.13  E-value: 5.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627    125 SFWEVFDEFVKECGNQNNwtASTYEKFAAVRNHLKEF--KEDATFNYFNEFGLNEYVNFLRDTKDMRNSTIGKQMGFLKW 202
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGS--KGTARNYKSTLKHLKKFlkKKDITFEEITVDFLEKFEEYLKKKKGLSENTISKYFRTLRA 78


                  ....*....
gi 8347627    203 FLRWSFKKG 211
Cdd:pfam13102  79 VLNKAIKEG 87
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 15-95 6.12e-04

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: 38.51  E-value: 6.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627     15 KKNGvpiveNVPIRMRVIFASQRIEFTTGYRIDVAKWDADKQRVKSGCTNKLkqsaaEINTDLLKYYAEIQNIFKEFEVQ 94
Cdd:pfam17293   9 NKNG-----EAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNAL-----ELNEQIDQERSKLEDIILELEQK 78


                  .
gi 8347627     95 E 95
Cdd:pfam17293  79 G 79
 
Name Accession Description Interval E-value
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 238-417 4.80e-46

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: 156.27  E-value: 4.80e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  238 DELNKLKDYQIPkDKQYLERVRDVFLFCCFTSLRYSDVRNLKRSDVKSDH----IEITTVKTADSLTIELNKYSKAILDK 313
Cdd:cd01185   1 EELKRLMALELS-DTSRLELVRDMFLFSCYTGLRFSDLKNLTWKNIVEASgrtwIRYRRKKTGKPVTVPLLPVAREILEK 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  314 YKDIHFENYMaLPVISNQKMNDYLKELGELAEINEPvretyykgneridevtpkyalLSTHAGRRTFICNALALGIPAQV 393
Cdd:cd01185  80 YKDDRSEGKL-FPVLSNQKINRYLKEIAKIAGIDKH---------------------LTFHVARHTFATLLLLKGVDIET 137

                       170       180
                ....*....|....*....|....
gi 8347627  394 VMKWTGHSDYKAMKPYIDIADDIK 417
Cdd:cd01185 138 ISKLLGHSSIKTTQIYAKIVDSKK 161
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
124-425 4.73e-32

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 123.18  E-value: 4.73e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  124 VSFWEVFDEFVKECGNQNNWTASTYEKFAAVRNHLKEFKEDATFNYFNEFG---LNEYVNFLRDtKDMRNSTIGKQMGFL 200
Cdd:COG4974   1 LTLADLLEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEITpedIRAYLNYLRE-RGLSPSTINRYLAAL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  201 KWFLRWSFKKGHHQNIAYDTFKPKlKTTSKKVIFLTWDELNKLKDYqIPKDKQYLERVRDVFLFCCFTSLRYSDVRNLKR 280
Cdd:COG4974  80 RSFFRYAVREGLLEDNPAAKVKLP-KKPRKLPRVLTEEEIEALLEA-LDTETPEGLRDRALLLLLYATGLRVSELLGLKW 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  281 SDVKSDH--IEITTVKTADSLTIELNKYSKAILDKYKDIH--------FENYMALPvISNQKMNDYLKELGELAEINEPV 350
Cdd:COG4974 158 SDIDLDRgtIRVRRGKGGKERTVPLSPEALEALREYLEERrprdsdylFPTRRGRP-LSRRAIRKILKRLAKRAGIPKRV 236

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 8347627  351 retyykgneridevtpkyallSTHAGRRTFICNALALGIPAQVVMKWTGHSDYKAMKPYIDIADDIKANAMNKFN 425
Cdd:COG4974 237 ---------------------TPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLH 290
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 234-409 4.62e-13

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: 66.58  E-value: 4.62e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  234 FLTWDELNKLKDYqIPKDKQylERVRDVFLFCCFTSLRYSDVRNLKRSDVKSDH--IEITTVKTADSLTIELNKYSKAIL 311
Cdd:cd00796   4 FLTEDEEARLLAA-LEESTN--PHLRLIVLLALYTGARRGEILSLRWDDIDLEVglIVLPETKNGKPRTVPLSDEAIAIL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  312 DKYKDIHFENYMALPVISNQKMNDYL----KELGELAEINEpvretyykgneridevtpkyalLSTHAGRRTFICNALAL 387
Cdd:cd00796  81 KELKRKRGKDGFFVDGRFFGIPIASLrrafKKARKRAGLED----------------------LRFHDLRHTFASRLVQA 138

                       170       180
                ....*....|....*....|..
gi 8347627  388 GIPAQVVMKWTGHSDYKAMKPY 409
Cdd:cd00796 139 GVPIKTVAKILGHSSIKMTMRY 160
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 239-410 9.22e-12

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: 63.27  E-value: 9.22e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  239 ELNKLKDyQIPKDKQYLERVRDVFLFCCFTSLRYSDVRNLKRSDVKSDHIEITTVKTADSL----TIELNKYSKAILDKY 314
Cdd:cd00397   1 ELEKLLD-AIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKTKGgkerTVPLPKELAEELKEY 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  315 KDIHFENYMAL--PVISNQKMNDYLKELGELAEINEPVRETYYKGNERIdevtpkyallSTHAGRRTFICNALALGIPAQ 392
Cdd:cd00397  80 LKERRDKRGPLlkSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRKI----------TPHSLRHTFATNLLENGVDIK 149

                       170
                ....*....|....*...
gi 8347627  393 VVMKWTGHSDYKAMKPYI 410
Cdd:cd00397 150 VVQKLLGHSSISTTQRYL 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
124-421 8.75e-11

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 62.29  E-value: 8.75e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  124 VSFWEVFDEFVKECGnQNNWTASTYEKFAAVRNHLKEFKEDATFNyFNEFGLNEYVNFLRDTKDMRNS--TIGKQMGFLK 201
Cdd:COG4973   2 LTLAEALEAYLEHLR-ERRLSPKTLEAYRRDLRRLIPLLGDADLP-LEELTPADVRRFLARLHRRGLSprTLNRRLSALR 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  202 WFLRWSFKKGH-HQNIAYDTFKPKLKTTSKKVifLTWDELNKLKDYqiPKDKQYLERVRDVFLFCCFTSLRYSDVRNLKR 280
Cdd:COG4973  80 SFFNWAVREGLlEANPAAGVKAPKAPRKLPRA--LTVDELAQLLDA--LADDPLAVRDRAIVELLYSTGLRLGELVGLDW 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  281 SDV--KSDHIEITTvKTADSLTIELNKYSKAILDKYKDI--HFENYMALPV--------ISNQKMNDYLKELGELAEINe 348
Cdd:COG4973 156 EDVdlDAGEVRVRG-KTGKSRTVPLGPKALAALREWLAVrpELAAPDEGALfpsrrgtrLSPRNVQKRLRRLAKKAGLP- 233

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 8347627  349 pvretyykgneriDEVTPkyallstHAGRRTFICNALALGIPAQVVMKWTGHSDYKAMKPYIDIADDIKANAM 421
Cdd:COG4973 234 -------------KHVHP-------HDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 247-418 2.38e-07

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: 50.37  E-value: 2.38e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  247 QIPKDKQYL----ERVRDVFLFCCFTSLRYSDVRNLKRSDVKS-DHIEITTVKTADSLTIELNKYSKAILDKY---KDIH 318
Cdd:cd01192  11 LIKEIKLYLkkanPRNYLLFIVGINTGLRISDLLSLKVEDVTNkDKLSIKEQKTGKQKTFPLNPTLVKALKEYiddLDLK 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  319 FENYMALP-------VISNQKMNDYLKELGELAEINEPvretyykgneridevtpkyalLSTHAGRRTF------ICNAL 385
Cdd:cd01192  91 RNDYLFKSlkqgpekPISRKQAYKILKKAADDLGLNYN---------------------IGTHSLRKTFgyhvykQGKDI 149

                       170       180       190
                ....*....|....*....|....*....|....
gi 8347627  386 ALgipaqvVMKWTGHSDYKAMKPYIDI-ADDIKA 418
Cdd:cd01192 150 EL------LMKLLNHSSPSITLRYLGIdQEDVDK 177
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 234-402 3.19e-06

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: 46.93  E-value: 3.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627    234 FLTWDELNKLkdYQIPKDKQYLERVRDVFLFCCFTSLRYSDVRNLKRSDV--KSDHIEITTVKTADSLTIELNKYS---- 307
Cdd:pfam00589   1 RLTEDEVERL--LDAAETGPLSIRDKALLELLYATGLRISELCSLRWSDIdfENGVIRVHRGKGNKERTVPLSDAAlell 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627    308 KAILDK------YKDIHFENYMALPvISNQKMNDYLKELGELAEINEPvretyykgneridevtpkyalLSTHAGRRTFI 381
Cdd:pfam00589  79 KEWLSKrlleapKSDYLFASKRGKP-LSRQTVRKIFKRAGKEAGLELP---------------------LHPHMLRHSFA 136

                         170       180
                  ....*....|....*....|.
gi 8347627    382 CNALALGIPAQVVMKWTGHSD 402
Cdd:pfam00589 137 THLLEAGVDLRVVQKLLGHSS 157
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 368-424 5.37e-06

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


Pssm-ID: 271180  Cd Length: 188  Bit Score: 46.91  E-value: 5.37e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 8347627  368 YALLSTHAGRRTFICNALALGIPAQVVMKWTGHSDYKAMKPYIDIADDIKANAMNKF 424
Cdd:cd00799 132 PGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVMRYIREADRFKDNAAAKL 188
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 116-402 1.42e-05

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 46.96  E-value: 1.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  116 EEQPEEAPVSFWEVFDEFVKEcgNQNNWTASTYEKfaaVRNHLKefkedatfNY-FNEFG--------LNEYVNFLRD-T 185
Cdd:COG0582  89 AAAAAAAANTFEEVAEEWLEE--KKPEWKEKTAAQ---VRRTLE--------KHiFPVLGdrpiaeitPPDLLAVLRPiE 155

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  186 KDMRNSTIGKQMGFLKWFLRWSFKKGH-HQNIAYDtFKPKLKTTSKKVI-FLTWDE----LNKLKDYQIPKDkqylerVR 259
Cdd:COG0582 156 ARGAPETARRVRQRLRQVFRYAVARGLiERNPAAD-LKGALPKPKVKHHpALTPEElpelLRALDAYRGSPV------TR 228

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  260 DVFLFCCFTSLRYSDVRNLKRSDVksD------HIEITTVKTADSLTIELNKYSKAILDKYKDIHFENYMALP------- 326
Cdd:COG0582 229 LALRLLLLTGVRPGELRGARWSEI--DleaalwTIPAERMKTRRPHIVPLSRQALEILKELKPLTGDSEYVFPsrrgpkk 306

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 8347627  327 VISNQKMNDYLKELGelaeinepvretyykgnerIDEVTPkyallstHAGRRTFICNALALGIPAQVVMKWTGHSD 402
Cdd:COG0582 307 PMSENTLNKALRRMG-------------------YGRFTP-------HGFRHTASTLLNEAGFPPDVIERQLAHKD 356
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 267-403 7.54e-05

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


Pssm-ID: 271187 [Multi-domain]  Cd Length: 142  Bit Score: 42.42  E-value: 7.54e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627  267 FTSLRYSDVRNLKRSDVKSD-HIEITTVKTADSLTIELNKYSKAILDKykdihfenyMALPVisnQKMNDYLKELGELAE 345
Cdd:cd01187  24 FTGARASELATLKFGCLHAQtSDDGTFLYWLKWENKGGKQLDIPISKK---------VAELI---KTINWTLNELSELKN 91

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 8347627  346 InepvretyykgnerIDEVTPKYaLLSTHAGRRTFICNALALGIPAQVVMKWTGHSDY 403
Cdd:cd01187  92 I--------------SDDHGERF-RFHTHRFRHTVATRLANSGMGILVLQQLLGHSSP 134
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 256-317 1.47e-04

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: 41.94  E-value: 1.47e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 8347627  256 ERVRDVFLFCCFTSLRYSDVRNLKRSDVKSDHIEITTVKTADSLTIELNKYSKAILDKYKDI 317
Cdd:cd00800  12 PLLRLAMELALLTGQRQGDLLRLKWSDITDGGLLVEQSKTGKKLLIPWTPSLRALVDRIRAL 73
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 125-211 5.09e-04

Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases.


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 39.13  E-value: 5.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627    125 SFWEVFDEFVKECGNQNNwtASTYEKFAAVRNHLKEF--KEDATFNYFNEFGLNEYVNFLRDTKDMRNSTIGKQMGFLKW 202
Cdd:pfam13102   1 DFLDYFKEYIEELKKKGS--KGTARNYKSTLKHLKKFlkKKDITFEEITVDFLEKFEEYLKKKKGLSENTISKYFRTLRA 78


                  ....*....
gi 8347627    203 FLRWSFKKG 211
Cdd:pfam13102  79 VLNKAIKEG 87
Arm-DNA-bind_5 pfam17293
Arm DNA-binding domain; This domain is the N-terminal Arm DNA-binding domain found in various ...
 15-95 6.12e-04

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: 38.51  E-value: 6.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8347627     15 KKNGvpiveNVPIRMRVIFASQRIEFTTGYRIDVAKWDADKQRVKSGCTNKLkqsaaEINTDLLKYYAEIQNIFKEFEVQ 94
Cdd:pfam17293   9 NKNG-----EAPLYLRIYKNGKRKYESLGLYITPEPWDKKKQKVKRKHPNAL-----ELNEQIDQERSKLEDIILELEQK 78


                  .
gi 8347627     95 E 95
Cdd:pfam17293  79 G 79
 
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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