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Conserved domains on  [gi|2055568642|ref|WP_216496691|]
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tyrosine-type recombinase/integrase, partial [Oscillibacter sp. MSJ-31]

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 ...
 4-91 9.23e-19

DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


The actual alignment was detected with superfamily member cd01191:

Pssm-ID: 469662  Cd Length: 176  Bit Score: 75.92  E-value: 9.23e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   4 GEIFLTMGRRSMDRRQIWSAMKRLCQKAGVAPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYLIESGAE 83
Cdd:cd01191    86 GYIFLNRFGERITTRGIAQQLKNYARKYGLNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASE 165


                  ....*...
gi 2055568642  84 HQRQLERL 91
Cdd:cd01191   166 QQEIVDKI 173
 
Name Accession Description Interval E-value
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 4-91 9.23e-19

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: 75.92  E-value: 9.23e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   4 GEIFLTMGRRSMDRRQIWSAMKRLCQKAGVAPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYLIESGAE 83
Cdd:cd01191    86 GYIFLNRFGERITTRGIAQQLKNYARKYGLNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASE 165


                  ....*...
gi 2055568642  84 HQRQLERL 91
Cdd:cd01191   166 QQEIVDKI 173
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-91 7.38e-17

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 72.72  E-value: 7.38e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   2 AHGEIFLTMGRRSMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYLIESG 81
Cdd:COG4974   201 DSDYLFPTRRGRPLSRRAIRKILKRLAKRAGI-PKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSD 279

                          90
                  ....*....|
gi 2055568642  82 AEHQRQLERL 91
Cdd:COG4974   280 EELREAVEKL 289
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 37-92 8.93e-14

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 64.94  E-value: 8.93e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2055568642  37 KVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYLIESGAEHQRQLERLG 92
Cdd:PRK05084  302 RLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEALDRLE 357
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 6-76 8.61e-13

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 61.83  E-value: 8.61e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVAPsKVFPHNLRHLFATayyrvyH------DIVKLADMLGHSSIETTRIY 76
Cdd:TIGR02225 203 LFLNRRGGPLSRQGVWKILKEYAKRAGIEK-PISPHTLRHSFAT------HllengaDLRVVQELLGHADISTTQIY 272
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 6-76 2.18e-12

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: 59.26  E-value: 2.18e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVAPsKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:pfam00589  95 LFASKRGKPLSRQTVRKIFKRAGKEAGLEL-PLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
 
Name Accession Description Interval E-value
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 4-91 9.23e-19

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: 75.92  E-value: 9.23e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   4 GEIFLTMGRRSMDRRQIWSAMKRLCQKAGVAPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYLIESGAE 83
Cdd:cd01191    86 GYIFLNRFGERITTRGIAQQLKNYARKYGLNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASE 165


                  ....*...
gi 2055568642  84 HQRQLERL 91
Cdd:cd01191   166 QQEIVDKI 173
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
2-91 7.38e-17

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 72.72  E-value: 7.38e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   2 AHGEIFLTMGRRSMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYLIESG 81
Cdd:COG4974   201 DSDYLFPTRRGRPLSRRAIRKILKRLAKRAGI-PKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSD 279

                          90
                  ....*....|
gi 2055568642  82 AEHQRQLERL 91
Cdd:COG4974   280 EELREAVEKL 289
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 2-77 2.04e-14

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: 64.57  E-value: 2.04e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2055568642   2 AHGEIFLTM---GRRSMDRRQIWSAMKRLCQKAGVAPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYL 77
Cdd:cd01188    89 DSREVFLRArapYRPLSSTSQISSIVRRYLRKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIADLLGHRSIETTAIYA 167
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
6-76 3.88e-14

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 65.37  E-value: 3.88e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:COG4973   205 LFPSRRGTRLSPRNVQKRLRRLAKKAGL-PKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIY 274
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 37-92 8.93e-14

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 64.94  E-value: 8.93e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2055568642  37 KVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYLIESGAEHQRQLERLG 92
Cdd:PRK05084  302 RLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQKEALDRLE 357
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 6-76 2.07e-13

XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 61.76  E-value: 2.07e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATayyrvyH------DIVKLADMLGHSSIETTRIY 76
Cdd:cd00798    95 LFLNKRGKRLSRRGVWRILKKYAERAGL-PKHVSPHTLRHSFAT------HlleggaDLRVVQELLGHASLSTTQIY 164
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 6-76 8.61e-13

tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274043 [Multi-domain]  Cd Length: 291  Bit Score: 61.83  E-value: 8.61e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVAPsKVFPHNLRHLFATayyrvyH------DIVKLADMLGHSSIETTRIY 76
Cdd:TIGR02225 203 LFLNRRGGPLSRQGVWKILKEYAKRAGIEK-PISPHTLRHSFAT------HllengaDLRVVQELLGHADISTTQIY 272
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 13-77 2.05e-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: 59.03  E-value: 2.05e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2055568642  13 RSMDRRQIWSAMKRLCQKAGVAPSKVF-PHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYL 77
Cdd:cd00397   102 TKLGERLSRRTLRRIFKKAGIEAGRKItPHSLRHTFATNLLENGVDIKVVQKLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 6-76 2.18e-12

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: 59.26  E-value: 2.18e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVAPsKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:pfam00589  95 LFASKRGKPLSRQTVRKIFKRAGKEAGLEL-PLHPHMLRHSFATHLLEAGVDLRVVQKLLGHSSISTTQIY 164
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 9-77 6.31e-12

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: 58.05  E-value: 6.31e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2055568642   9 TMGRRSMDRRQIWSAMKRLCQKAGVApSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYL 77
Cdd:cd01193   107 VERRHHISETTVQRALKKAVEQAGIT-KRVTPHTLRHSFATHLLEAGTDIRTIQELLGHSDLSTTMIYT 174
xerD PRK00283
tyrosine recombinase;
6-76 2.97e-11

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 57.51  E-value: 2.97e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVAPSKVFPHNLRHLFAT------AYYRVyhdivkLADMLGHSSIETTRIY 76
Cdd:PRK00283  210 LFPSARGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHVLRHAFAThllnhgADLRV------VQELLGHSDISTTQIY 280
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 10-76 8.05e-11

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: 56.25  E-value: 8.05e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2055568642  10 MGRRSMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:TIGR02249 232 IRRHHINETTIQRAVRRAVERAGI-EKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 11-76 1.06e-10

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 55.93  E-value: 1.06e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2055568642  11 GRRsMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:PRK00236  215 GGR-LSPRVVQRRVKKLGKKAGL-PSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIY 278
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 15-77 1.13e-09

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: 51.88  E-value: 1.13e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2055568642  15 MDRRQIWSAMKRLCQKAGVAPsKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYL 77
Cdd:cd01185    93 LSNQKINRYLKEIAKIAGIDK-HLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYA 154
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 6-77 1.48e-09

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: 51.61  E-value: 1.48e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2055568642   6 IFLTMGRRS----MDRRQIWSAMKRLCQKAGVAPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYL 77
Cdd:cd01194    98 LFTSLSNNSkgqrLTTRSIRRIIKKYLRKAGLDDDRLTAHSLRHTAGTLALKAGKSLREVQQLLRHSDPNTTMIYA 173
PRK15417 PRK15417
integron integrase;
12-76 6.70e-09

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 51.20  E-value: 6.70e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2055568642  12 RRSMDRRQIWSAMKRLCQKAGVAPSKVfPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:PRK15417  249 RHHMYDQTFQRAFKRAVEQAGITKPAT-PHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIY 312
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 11-76 1.84e-08

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: 48.48  E-value: 1.84e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2055568642  11 GRRSMDRRQIWSAMKRLCQKAGVapSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:cd00796    97 RFFGIPIASLRRAFKKARKRAGL--EDLRFHDLRHTFASRLVQAGVPIKTVAKILGHSSIKMTMRY 160
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 35-77 3.21e-08

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: 48.43  E-value: 3.21e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2055568642  35 PSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYL 77
Cdd:cd01182   130 PKRITPHTLRHTKAMHLLQAGVDLTVIRDWLGHESVETTQIYA 172
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 21-76 1.84e-07

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: 45.63  E-value: 1.84e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2055568642  21 WSAMKRLCQKAGVApsKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETT-RIY 76
Cdd:cd01189    91 LKAFKKLLKKAGLP--RITPHDLRHTFASLLLEAGVPLKVIAERLGHSDISTTlDVY 145
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 12-77 2.06e-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: 46.13  E-value: 2.06e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2055568642  12 RRSMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIYL 77
Cdd:cd01192   104 EKPISRKQAYKILKKAADDLGL-NYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYL 168
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 1-77 2.74e-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: 43.06  E-value: 2.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   1 IAHGEIFLTMGRRSMDRRQIWSA------MKRLCQKAGVAPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTR 74
Cdd:cd00799    92 IPSGPLFRRIRRGGSVGTTRLSDrsvariVKRRAALAGLDPGDFSGHSLRRGFATEAARAGASLPEIMAQGGHKSVATVM 171


                  ...
gi 2055568642  75 IYL 77
Cdd:cd00799   172 RYI 174
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 6-76 3.35e-05

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: 40.18  E-value: 3.35e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2055568642   6 IFLTMGRRSMDRRQIWSAMKRLCQKAGVaPSKVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:cd01197   101 IFLSRRGGPLSRQQAYRIIRDLGKEAGT-VTQTHPHMLRHACGYALADRGADTRLIQDYLGHRNIRHTVIY 170
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 20-73 9.95e-05

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


Pssm-ID: 271186 [Multi-domain]  Cd Length: 184  Bit Score: 38.94  E-value: 9.95e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2055568642  20 IWSAMKRLCQKAGVApskVFPHNLRHLFATAYYRVYHDIVKLADMLGHSSIETT 73
Cdd:cd01186   119 VYDLVRRLKKRTGID---FTPHMFRHTHATALIRAGWSIEVVARRLGHAHVQTT 169
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 2-76 5.00e-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: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 36.68  E-value: 5.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   2 AHGEIFLTMGRRSMDRR----QIWSAMKRLCQKAGVApSKVFPHNLRHLFATAYYRVYHDIVKLA-DMLGHSSIETTRIY 76
Cdd:cd01195    87 AEGPLFVSLDRASRGRRlspqAVYRIVRRLAERIGLG-KRLSPHGLRHSAITLALDAGAGLIRKVqDFSRHADLRTLQVY 165
int PHA02601
integrase; Provisional
 41-76 6.86e-04

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 36.63  E-value: 6.86e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2055568642  41 HNLRHLFATAYYRVYHDIVKLADMLGHSSIETTRIY 76
Cdd:PHA02601  279 HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAY 314
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 7-77 1.13e-03

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: 36.13  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2055568642   7 FLTMGRRSMDRRQIWSAMKRLCQKAGV--APSKVFP--HNLRHLFA----TAYYRVYHDIV----KLADMLGHSSIETTR 74
Cdd:cd00797   102 FVSQQGGRLTGGGVYRVFRRLLRRIGLrgAGDGRGPrlHDLRHTFAvnrlTRWYREGADVErklpVLSTYLGHVNVTDTY 181


                  ...
gi 2055568642  75 IYL 77
Cdd:cd00797   182 WYL 184
 
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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