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Conserved domains on  [gi|749938047|ref|WP_040324331|]
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site-specific integrase [Alkalihalobacillus alcalophilus]

Protein Classification

site-specific integrase( domain architecture ID 10315017)

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
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 126-312 1.13e-94

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: 279.16  E-value: 1.13e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 126 LTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 205
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 206 YMEEQNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVLiPEVLSCHCLRHSKAMHLLQAGVNLVYIRDI 285
Cdd:cd01182   81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSL-PKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                        170       180
                 ....*....|....*....|....*..
gi 749938047 286 LGHCSVQVTEIYAKTDSKQKREAIEKA 312
Cdd:cd01182  160 LGHESVETTQIYAEADLEMKREALEKA 186
Phage_int_SAM_1 super family cl12235
Phage integrase, N-terminal SAM-like domain;
10-100 6.68e-10

Phage integrase, N-terminal SAM-like domain;


The actual alignment was detected with superfamily member pfam02899:

Pssm-ID: 472283 [Multi-domain]  Cd Length: 83  Bit Score: 54.96  E-value: 6.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   10 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisvehLTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAAL 89
Cdd:pfam02899   1 IDQFL-EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGG------SSLEQITTSDVRAFLAELRAQGL-SASSLARRLSAL 72

                          90
                  ....*....|.
gi 749938047   90 HSFFKYLQYEN 100
Cdd:pfam02899  73 RSFYQFLIREG 83
 
Name Accession Description Interval E-value
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 126-312 1.13e-94

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: 279.16  E-value: 1.13e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 126 LTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 205
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 206 YMEEQNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVLiPEVLSCHCLRHSKAMHLLQAGVNLVYIRDI 285
Cdd:cd01182   81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSL-PKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                        170       180
                 ....*....|....*....|....*..
gi 749938047 286 LGHCSVQVTEIYAKTDSKQKREAIEKA 312
Cdd:cd01182  160 LGHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-312 6.37e-75

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 232.58  E-value: 6.37e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   4 TDFSYYLTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisveHLTLNKITKNLVVDYLDWTEdKRQCSPSTRN 83
Cdd:COG4974    1 LTLADLLEAFL-EELKREKGLSPNTIKAYRRDLRRFLRFLEELG-----KIPLAEITPEDIRAYLNYLR-ERGLSPSTIN 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  84 VRLAALHSFFKYLQYENpdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQ 163
Cdd:COG4974   74 RYLAALRSFFRYAVREG---LLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 164 EVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSanlyPLFFNKRKERLTRAGVNYIVEKY 243
Cdd:COG4974  151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRDSD----YLFPTRRGRPLSRRAIRKILKRL 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 749938047 244 KKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKA 312
Cdd:COG4974  227 AKRAG------IPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 17-297 4.18e-58

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: 189.33  E-value: 4.18e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   17 FLPGEIGASKNTIASYRDTFILFLRFLkDEKGISVEhltlnKITKNLVVDYLDWtEDKRQCSPSTRNVRLAALHSFFKYL 96
Cdd:TIGR02225   6 YLWVERGLSQNTLEAYRRDLEKFLEFL-EERGIDLE-----EVDRGDIVDFLAE-LKEAGLSARSIARALSALRSFYRFL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   97 QYEN--PDNLlewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIR 174
Cdd:TIGR02225  79 LREGirEDDP-----SALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVN 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  175 FDKPYtIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANLYP---LFFNKRKERLTRAGVNYIVekyKKLAREKN 251
Cdd:TIGR02225 154 LDEGF-VRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKEsdaLFLNRRGGPLSRQGVWKIL---KEYAKRAG 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 749938047  252 kvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 297
Cdd:TIGR02225 230 ---IEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-313 1.48e-52

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 175.34  E-value: 1.48e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   1 MKPTDFSYYLTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKGISVEHLTLNKITKNLVvdyldwTEDKRQCSPS 80
Cdd:PRK00236   1 MADADLPAALEAFL-EYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLA------RRRRQGLSAR 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  81 TRNVRLAALHSFFKYLQ-----YENPdnllewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLM 155
Cdd:PRK00236  74 SLARRLSALRSFYRWLVrrgllKANP--------AAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELL 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 156 YDTGARVQEVIDLTPSMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANlyPLFFNKRKERLTRAG 235
Cdd:PRK00236 146 YGSGLRLSELVGLDIDDLDLASG-TLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDD--ALFLGARGGRLSPRV 222

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 749938047 236 VNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKAY 313
Cdd:PRK00236 223 VQRRVKKLGKKAG------LPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAH 294
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 125-299 1.83e-27

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: 105.48  E-value: 1.83e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  125 YLTLDGIKLLLEMPDlNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVK 204
Cdd:pfam00589   1 RLTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  205 KYMEEQNLLRNSANLypLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRD 284
Cdd:pfam00589  80 EWLSKRLLEAPKSDY--LFASKRGKPLSRQTVRKIFKRAGKEAG------LELPLHPHMLRHSFATHLLEAGVDLRVVQK 151

                         170
                  ....*....|....*
gi 749938047  285 ILGHCSVQVTEIYAK 299
Cdd:pfam00589 152 LLGHSSISTTQIYTH 166
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
10-100 6.68e-10

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 54.96  E-value: 6.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   10 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisvehLTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAAL 89
Cdd:pfam02899   1 IDQFL-EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGG------SSLEQITTSDVRAFLAELRAQGL-SASSLARRLSAL 72

                          90
                  ....*....|.
gi 749938047   90 HSFFKYLQYEN 100
Cdd:pfam02899  73 RSFYQFLIREG 83
 
Name Accession Description Interval E-value
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 126-312 1.13e-94

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: 279.16  E-value: 1.13e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 126 LTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 205
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 206 YMEEQNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVLiPEVLSCHCLRHSKAMHLLQAGVNLVYIRDI 285
Cdd:cd01182   81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSL-PKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                        170       180
                 ....*....|....*....|....*..
gi 749938047 286 LGHCSVQVTEIYAKTDSKQKREAIEKA 312
Cdd:cd01182  160 LGHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-312 6.37e-75

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 232.58  E-value: 6.37e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   4 TDFSYYLTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisveHLTLNKITKNLVVDYLDWTEdKRQCSPSTRN 83
Cdd:COG4974    1 LTLADLLEAFL-EELKREKGLSPNTIKAYRRDLRRFLRFLEELG-----KIPLAEITPEDIRAYLNYLR-ERGLSPSTIN 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  84 VRLAALHSFFKYLQYENpdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQ 163
Cdd:COG4974   74 RYLAALRSFFRYAVREG---LLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 164 EVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSanlyPLFFNKRKERLTRAGVNYIVEKY 243
Cdd:COG4974  151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRDSD----YLFPTRRGRPLSRRAIRKILKRL 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 749938047 244 KKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKA 312
Cdd:COG4974  227 AKRAG------IPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 17-297 4.18e-58

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: 189.33  E-value: 4.18e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   17 FLPGEIGASKNTIASYRDTFILFLRFLkDEKGISVEhltlnKITKNLVVDYLDWtEDKRQCSPSTRNVRLAALHSFFKYL 96
Cdd:TIGR02225   6 YLWVERGLSQNTLEAYRRDLEKFLEFL-EERGIDLE-----EVDRGDIVDFLAE-LKEAGLSARSIARALSALRSFYRFL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   97 QYEN--PDNLlewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIR 174
Cdd:TIGR02225  79 LREGirEDDP-----SALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVN 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  175 FDKPYtIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANLYP---LFFNKRKERLTRAGVNYIVekyKKLAREKN 251
Cdd:TIGR02225 154 LDEGF-VRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKEsdaLFLNRRGGPLSRQGVWKIL---KEYAKRAG 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 749938047  252 kvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 297
Cdd:TIGR02225 230 ---IEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-313 1.48e-52

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 175.34  E-value: 1.48e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   1 MKPTDFSYYLTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKGISVEHLTLNKITKNLVvdyldwTEDKRQCSPS 80
Cdd:PRK00236   1 MADADLPAALEAFL-EYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLA------RRRRQGLSAR 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  81 TRNVRLAALHSFFKYLQ-----YENPdnllewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLM 155
Cdd:PRK00236  74 SLARRLSALRSFYRWLVrrgllKANP--------AAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELL 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 156 YDTGARVQEVIDLTPSMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANlyPLFFNKRKERLTRAG 235
Cdd:PRK00236 146 YGSGLRLSELVGLDIDDLDLASG-TLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDD--ALFLGARGGRLSPRV 222

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 749938047 236 VNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKAY 313
Cdd:PRK00236 223 VQRRVKKLGKKAG------LPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAH 294
xerD PRK00283
tyrosine recombinase;
21-297 3.43e-50

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 169.22  E-value: 3.43e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  21 EIGASKNTIASYRDTFILFLRFLkdekgiSVEHLTLNKITKNLVVDYLDWTEDkRQCSPSTRNVRLAALHSFFKYLQYEN 100
Cdd:PRK00283  19 ERGLAENTLSSYRRDLELFAEWL------AARGLSLAEATRDDLQAFLAELAE-GGYKATSSARRLSALRRFFQFLLREG 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 101 pdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPyT 180
Cdd:PRK00283  92 ---LREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQG-V 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 181 IKLIGKGNKARIVPLMEPTMRIVKKYMEE--QNLLRNSANLYpLFFNKRKERLTRAGVNYIVEKYKKLAReknkvLIPEV 258
Cdd:PRK00283 168 VRVTGKGNKERLVPLGEEAVYAIERYLERgrPALLNGRSSDA-LFPSARGGQLTRQTFWHRIKHYAKRAG-----IDPKK 241

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 749938047 259 LSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 297
Cdd:PRK00283 242 LSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIY 280
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 13-313 1.43e-49

tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274042 [Multi-domain]  Cd Length: 295  Bit Score: 167.40  E-value: 1.43e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   13 FLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKGISvehlTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAALHSF 92
Cdd:TIGR02224   3 FL-EYLRLERNYSPHTVRAYRRDLEAFLEFLEEEGGLA----SLAEVTAADLRSFLAELHARGL-SRRSLARKLSALRSF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   93 FKYLQYENpdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTE--AGRRNLALLTLMYDTGARVQEVIDLTP 170
Cdd:TIGR02224  77 YRFLLRRG---LIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDEdwLALRDRAILELLYSSGLRVSELVGLDL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  171 SMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQN-LLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKlare 249
Cdd:TIGR02224 154 SDLDLDFG-EVRVRGKGNKERIVPFGPYARDALQAYLEARRsPLLASEGQDALFLNRRGGRLTPRGVQYRLQQLRA---- 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 749938047  250 knKVLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKAY 313
Cdd:TIGR02224 229 --KAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAH 290
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
10-309 9.22e-48

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 162.44  E-value: 9.22e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  10 LTGFLTKFLP--GEIGASKNTIASYRDTFILFLRFLKDEkgisveHLTLNKITKNLVVDYLDWTEDKRqCSPSTRNVRLA 87
Cdd:COG4973    4 LAEALEAYLEhlRERRLSPKTLEAYRRDLRRLIPLLGDA------DLPLEELTPADVRRFLARLHRRG-LSPRTLNRRLS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  88 ALHSFFKYLQYE-----NPdnllewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDlNTEAGRRNLALLTLMYDTGARV 162
Cdd:COG4973   77 ALRSFFNWAVREglleaNP--------AAGVKAPKAPRKLPRALTVDELAQLLDALA-DDPLAVRDRAIVELLYSTGLRL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 163 QEVIDLTPSMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANlYPLFFNKRKERLTRAGVNyivEK 242
Cdd:COG4973  148 GELVGLDWEDVDLDAG-EVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPDE-GALFPSRRGTRLSPRNVQ---KR 222

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 749938047 243 YKKLAReknKVLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAI 309
Cdd:COG4973  223 LRRLAK---KAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 129-304 1.64e-43

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


Pssm-ID: 271179 [Multi-domain]  Cd Length: 172  Bit Score: 147.66  E-value: 1.64e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 129 DGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYtIKLIGKGNKARIVPLMEPTMRIVKKYME 208
Cdd:cd00798    2 DEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGL-VRVTGKGNKERLVPFGSYAVEALEEYLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 209 E-QNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVNLVYIRDILG 287
Cdd:cd00798   81 ErRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHV------SPHTLRHSFATHLLEGGADLRVVQELLG 154

                        170
                 ....*....|....*..
gi 749938047 288 HCSVQVTEIYAKTDSKQ 304
Cdd:cd00798  155 HASLSTTQIYTHVSFER 171
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 131-298 6.73e-30

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: 112.19  E-value: 6.73e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 131 IKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKpYTIKLIGKG---NKARIVPLMEPTMRIVKKYM 207
Cdd:cd00397    2 LEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDN-GTIRVRGKKtkgGKERTVPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 208 EE----QNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKnkvlipevLSCHCLRHSKAMHLLQAGVNLVYIR 283
Cdd:cd00397   81 KErrdkRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRK--------ITPHSLRHTFATNLLENGVDIKVVQ 152

                        170
                 ....*....|....*
gi 749938047 284 DILGHCSVQVTEIYA 298
Cdd:cd00397  153 KLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 125-299 1.83e-27

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: 105.48  E-value: 1.83e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  125 YLTLDGIKLLLEMPDlNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVK 204
Cdd:pfam00589   1 RLTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  205 KYMEEQNLLRNSANLypLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRD 284
Cdd:pfam00589  80 EWLSKRLLEAPKSDY--LFASKRGKPLSRQTVRKIFKRAGKEAG------LELPLHPHMLRHSFATHLLEAGVDLRVVQK 151

                         170
                  ....*....|....*
gi 749938047  285 ILGHCSVQVTEIYAK 299
Cdd:pfam00589 152 LLGHSSISTTQIYTH 166
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 73-329 2.81e-24

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 101.36  E-value: 2.81e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  73 DKRQCSPSTRNVRLAALHSFFKYLQYE-----NPDNLLEwqqvlsisVKKTEKKTINY-LTLDGIKLLLEMPDLNTEAGR 146
Cdd:PRK01287  86 NGEPLSTRTQRTQLSPLRVWFRWLLKRhhilyNPAEDLE--------LPKEEKRLPRQiLSEAETEQVLASPDLTTLQGL 157

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 147 RNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEE--QNLLRNSANLYpLFF 224
Cdd:PRK01287 158 RDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERALAWLQRYLQDvrPQLAVRPDSGA-LFV 236

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 225 NKRKERLTRAGVNYIVEKYKKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY------- 297
Cdd:PRK01287 237 AMDGDGLARNTLTNMVGRYIRAAGIEKAG------ACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYtrvsigh 310

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 749938047 298 -----AKTD-SKQKREAIEKAYVDVSPTDEPMWEKNED 329
Cdd:PRK01287 311 lqavhASTHpAERKADEKLRDADEVGLLADLYADDNAD 348
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 25-311 5.67e-22

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 94.99  E-value: 5.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  25 SKNTIASYRDTFILFLRFLKDEKGISVEHL------TLNKITKNLVVDYLDWTEDKRQC---------SPSTRNVRLAAL 89
Cdd:PRK05084  34 SPTTLYEYLTEYRRFFNWLISEGLSDASKIkdiplsTLENLTKKDVEAFILYLRERPLLnghstkkgnSQTTINRTLSAL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  90 HSFFKYL--QYENPD--NLLEWQQVLSISVKKtEKKTINY---------LTLDGIKLLLEMPD------LNTEAGR---- 146
Cdd:PRK05084 114 KSLFKYLteEAENEDgePYFYRNVMKKIELKK-KKETLAArahnlkqklFLGDEDYEFLDFIDneyeqkLSNRALSsfkk 192

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 147 ---RNLALLTLMYDTGARVQEVIDLTPSMIRFDKpYTIKLIGKGNKARIVPLMEPTMRIVKKYMEeqnlLRNS-----AN 218
Cdd:PRK05084 193 nkeRDLAIIALILGSGLRVSELVNLDLSDLNLKQ-MTIDVTRKGGKRDSVNIAPFALPYLEEYLK----IRASrykaeKQ 267

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 219 LYPLFFNKRK---ERLTRAGVNYIVEKYKKLAREKnkvlipevLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTE 295
Cdd:PRK05084 268 EKALFLTKYRgkpNRISARAIEKMVAKYSEAFGVR--------LTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTD 339

                        330
                 ....*....|....*.
gi 749938047 296 IYAKTDSKQKREAIEK 311
Cdd:PRK05084 340 LYTHIVNDEQKEALDR 355
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 126-298 3.43e-21

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: 88.97  E-value: 3.43e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 126 LTLDGIKLLLE-MPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLI-GKG--NKARIVPLMEPTMR 201
Cdd:cd01194    1 LTLEQARQLLAsLPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVqGKGktSKDDFVYLRPDVLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 202 IVKKYMEEQNLLRNSAnlyPLFF----NKRKERLTRAGVNYIVEKYKKLAREKnkvliPEVLSCHCLRHSKAMHLLQAGV 277
Cdd:cd01194   81 ALQAYLKARGKLDFEE---PLFTslsnNSKGQRLTTRSIRRIIKKYLRKAGLD-----DDRLTAHSLRHTAGTLALKAGK 152

                        170       180
                 ....*....|....*....|.
gi 749938047 278 NLVYIRDILGHCSVQVTEIYA 298
Cdd:cd01194  153 SLREVQQLLRHSDPNTTMIYA 173
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 126-297 3.98e-21

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: 88.87  E-value: 3.98e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 126 LTLDGIKLLLEmpdlNTEAGRRNLALLTLmYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 205
Cdd:cd01193    6 LSPDEVRRILG----ALTELRHRLILSLL-YGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 206 YMEEQN-----LLRNSANLYPLFFNKRKER--LTRAGVNYIVEKYKKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVN 278
Cdd:cd01193   81 YLKSARpkeelDPAEGRAGVLDPRTGVERRhhISETTVQRALKKAVEQAGITKRV------TPHTLRHSFATHLLEAGTD 154

                        170
                 ....*....|....*....
gi 749938047 279 LVYIRDILGHCSVQVTEIY 297
Cdd:cd01193  155 IRTIQELLGHSDLSTTMIY 173
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 127-307 9.59e-21

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: 87.68  E-value: 9.59e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 127 TLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPyTIKLIGKGNKA-RIVPLMEPTMRIVKK 205
Cdd:cd01188    1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSG-TITVRQKKTGRpVELPLTEPVGEALAD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 206 YMeeqnLLRNSANLYPLFFNKRK---ERLT-RAGVNYIVEKY-KKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVNLV 280
Cdd:cd01188   80 YL----RDGRPRTDSREVFLRARapyRPLSsTSQISSIVRRYlRKAGIEPSHR------GTHSLRHSLATRMLRAGTSLK 149

                        170       180
                 ....*....|....*....|....*..
gi 749938047 281 YIRDILGHCSVQVTEIYAKTDSKQKRE 307
Cdd:cd01188  150 VIADLLGHRSIETTAIYAKIDVDDLRE 176
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 125-298 2.18e-18

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: 80.83  E-value: 2.18e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 125 YLTLDGIKLLLEmpDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVK 204
Cdd:cd00796    4 FLTEDEEARLLA--ALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAILK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 205 KYMEEqnllrnsANLYPLFFNKRKERLTRAGVNYIVEKykklAREKNKVlipEVLSCHCLRHSKAMHLLQAGVNLVYIRD 284
Cdd:cd00796   82 ELKRK-------RGKDGFFVDGRFFGIPIASLRRAFKK----ARKRAGL---EDLRFHDLRHTFASRLVQAGVPIKTVAK 147

                        170
                 ....*....|....
gi 749938047 285 ILGHCSVQVTEIYA 298
Cdd:cd00796  148 ILGHSSIKMTMRYA 161
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 25-297 4.41e-18

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: 83.21  E-value: 4.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   25 SKNTIASYRDTFILFLRFLKdekgisVEHLTlnKITKNLVVDYLDWTEDKRQCSPSTRNVRLAALHSFFK-YLQYEnpdn 103
Cdd:TIGR02249  15 AKRTEEAYLHWIKRFIRFHN------KRHPS--TMGDTEVEAFLSDLAVDGKVAASTQNQALNALLFLYKeILKTP---- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  104 lLEWQQVLSISvkKTEKKTINYLTLDGIKLLLEMPDlnteaGRRNLaLLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKL 183
Cdd:TIGR02249  83 -LSLMERFVRA--KRPRKLPVVLTREEVRRLLEHLE-----GKYRL-IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIR 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  184 IGKGNKARIVP----LMEPTMRIVKK----YMEEQNLLRNSANL-------YP----------LFFNKRKERLTRAGV-- 236
Cdd:TIGR02249 154 QGKGGKDRTVTlpkeLIPPLREQIELarayHEADLAEGYGGVYLphalarkYPnapkewgwqyLFPSHRLSRDPESGVir 233

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 749938047  237 -NYIVEK-----YKKLAREKNkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 297
Cdd:TIGR02249 234 rHHINETtiqraVRRAVERAG---IEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
int PHA02601
integrase; Provisional
 57-298 6.11e-14

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 71.68  E-value: 6.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  57 NKITKNLVVDYLD-------WTEDKRQCSPSTRNVRLAALHSFFKYLQyenpdNLLEW--QQVLS-ISVKKTEKKTINYL 126
Cdd:PHA02601  99 SEFTAKDFADYRArrlsgefKVNKGRPIKPATVNRELAYLSAVFNELI-----KLGKWsgPNPLDgIRPFKEAEPELAFL 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 127 TLDGIKLLLEMPDLNTEAGRRNLALLTLmyDTGARVQEVIDLTPSMIrfdKPYTIKLIG-KGNKARIVPLMEPTMRIvkk 205
Cdd:PHA02601 174 TKEEIERLLDACDGSRSPDLGLIAKICL--ATGARWSEAETLKRSQI---SPYKITFVKtKGKKNRTVPISEELYKM--- 245

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 206 ymeeqnLLRNSANLYPLFFNKRKERLTRAGVNyivekykklareknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDI 285
Cdd:PHA02601 246 ------LPKRRGRLFKDAYESFERAVKRAGID-----------------LPEGQATHVLRHTFASHFMMNGGNILVLQRI 302

                        250
                 ....*....|...
gi 749938047 286 LGHCSVQVTEIYA 298
Cdd:PHA02601 303 LGHATIEMTMAYA 315
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 143-299 4.02e-13

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: 66.04  E-value: 4.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 143 EAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPY-----TIKLIGKG--------NKA--RIVPLMEPTMRIVKKYM 207
Cdd:cd01189   13 KRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTirinrTLVRKKKGgyvikppkTKSsiRTIPLPDELIELLKELK 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 208 EeqnllrnsanlyplfFNKRkerLTRAGVNYIvekykklareknkvlipevlSCHCLRHSKAMHLLQAGVNLVYIRDILG 287
Cdd:cd01189   93 A---------------FKKL---LKKAGLPRI--------------------TPHDLRHTFASLLLEAGVPLKVIAERLG 134

                        170
                 ....*....|...
gi 749938047 288 HCSVQVT-EIYAK 299
Cdd:cd01189  135 HSDISTTlDVYAH 147
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 127-297 4.15e-13

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271195 [Multi-domain]  Cd Length: 170  Bit Score: 66.34  E-value: 4.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 127 TLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKpYTIKLIGKGNKARIVPLMEP-TMRIVKK 205
Cdd:cd01195    1 SREEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEH-RRLRILGKGKKQREVVTLPPtTREALAA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 206 YMEeqnlLRNSANlYPLFF----NKRKERLTRAGVNYIVekyKKLAREknkVLIPEVLSCHCLRHSKAMHLLQAGVNLVY 281
Cdd:cd01195   80 WLA----ARGEAE-GPLFVsldrASRGRRLSPQAVYRIV---RRLAER---IGLGKRLSPHGLRHSAITLALDAGAGLIR 148

                        170
                 ....*....|....*..
gi 749938047 282 -IRDILGHCSVQVTEIY 297
Cdd:cd01195  149 kVQDFSRHADLRTLQVY 165
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 135-305 7.71e-13

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: 65.36  E-value: 7.71e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 135 LEMPDLNTEAGRRNLALLTlMYdTGARVQEVIDLTPSMIRFDKPYT-IKLI-GKGNKARIVPLMEPTMRIVKKYMEEqnl 212
Cdd:cd01185    9 LELSDTSRLELVRDMFLFS-CY-TGLRFSDLKNLTWKNIVEASGRTwIRYRrKKTGKPVTVPLLPVAREILEKYKDD--- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 213 lRNSANLYPLFFNKrkerltraGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQ 292
Cdd:cd01185   84 -RSEGKLFPVLSNQ--------KINRYLKEIAKIAG------IDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIK 148

                        170
                 ....*....|...
gi 749938047 293 VTEIYAKTDSKQK 305
Cdd:cd01185  149 TTQIYAKIVDSKK 161
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
10-100 6.68e-10

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 54.96  E-value: 6.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047   10 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisvehLTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAAL 89
Cdd:pfam02899   1 IDQFL-EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGG------SSLEQITTSDVRAFLAELRAQGL-SASSLARRLSAL 72

                          90
                  ....*....|.
gi 749938047   90 HSFFKYLQYEN 100
Cdd:pfam02899  73 RSFYQFLIREG 83
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 131-297 1.22e-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: 271192 [Multi-domain]  Cd Length: 178  Bit Score: 56.92  E-value: 1.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 131 IKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLiGKGNKARIVPLMEPTMRIVKKYMEEQ 210
Cdd:cd01192    9 KKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVTNKDKLSIKE-QKTGKQKTFPLNPTLVKALKEYIDDL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 211 NLLRNSaNLYPLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCS 290
Cdd:cd01192   88 DLKRND-YLFKSLKQGPEKPISRKQAYKILKKAADDLG------LNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSS 160


                 ....*..
gi 749938047 291 VQVTEIY 297
Cdd:cd01192  161 PSITLRY 167
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 132-309 2.43e-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: 271196  Cd Length: 183  Bit Score: 55.95  E-value: 2.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 132 KLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIdltpSMIRFD-----KPYTIKLIGKGNKARIVPLMEPTMRIVKKY 206
Cdd:cd01196    6 RRLLESIDSTHPVGLRDRALIALMVYSFARIGAVL----AMRVEDvydqgRRLWVRLAEKGGKQHEMPCHHDLEEYLRAY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 207 MEEQNLlrNSANLYPLFFNKRKE-------RLTRAGVnyivekYKKLAREKNKVLIPEVLSCHCLRHSKAMHLLQAGVNL 279
Cdd:cd01196   82 LEAAEI--EEDPKGPLFRTTRGGtrklthnPLTQANA------YRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTL 153

                        170       180       190
                 ....*....|....*....|....*....|
gi 749938047 280 VYIRDILGHCSVQVTEIYAKTDSKQKREAI 309
Cdd:cd01196  154 EDAQNMANHASTRTTQLYDRRSDKITLDEV 183
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 125-304 3.32e-09

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: 55.59  E-value: 3.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 125 YLTLDGIKLLLEmpdlntEAGR-----RNLALLTLMYDTGARVQEVIDLTPSMIRF-DKPYTIKLIgKGNKARIVPLMEP 198
Cdd:cd01197    6 YLTGKEVQALLQ------AACRgrtpaRDYCLLLLAFRHGFRVSELCDLHLSDVDLeSRRLHIRRL-KNGFSTTHPLRFD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 199 TMRIVKKYMEEQNLLRNSANLYpLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVN 278
Cdd:cd01197   79 EREALEAWLKERANWKGADTDW-IFLSRRGGPLSRQQAYRIIRDLGKEAG------TVTQTHPHMLRHACGYALADRGAD 151

                        170       180
                 ....*....|....*....|....*.
gi 749938047 279 LVYIRDILGHCSVQVTEIYAKTDSKQ 304
Cdd:cd01197  152 TRLIQDYLGHRNIRHTVIYTASNAAR 177
PRK15417 PRK15417
integron integrase;
67-299 4.71e-08

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 53.90  E-value: 4.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  67 YLDWTEDKRQCSPSTRNVRLAALHSFF-KYLQYENPdnlleWQQvlSISVKKTEKKTINYLTLDGIKLLLEMpdlnTEAG 145
Cdd:PRK15417  64 FLSWLANERKVSVSTHRQALAALLFFYgKVLCTDLP-----WLQ--EIGRPRPSRRLPVVLTPDEVVRILGF----LEGE 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 146 RRNLAllTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLME---PTMR-----IVKKYMEEQNLLRNSA 217
Cdd:PRK15417 133 HRLFA--QLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPEslaPSLReqlsrARAWWLKDQAEGRSGV 210

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 218 NL-------YP----------LFFNKRKERLTRAGV-------NYIVEKYKKLAREKNKVLIPEvlSCHCLRHSKAMHLL 273
Cdd:PRK15417 211 ALpdalerkYPraghswpwfwVFAQHTHSTDPRSGVvrrhhmyDQTFQRAFKRAVEQAGITKPA--TPHTLRHSFATALL 288

                        250       260
                 ....*....|....*....|....*.
gi 749938047 274 QAGVNLVYIRDILGHCSVQVTEIYAK 299
Cdd:PRK15417 289 RSGYDIRTVQDLLGHSDVSTTMIYTH 314
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 151-297 1.23e-07

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: 51.15  E-value: 1.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 151 LLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANLYPLFFNKRKER 230
Cdd:cd00797   30 LFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSYFFVSQQGGR 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 231 LTRAGV-NYIVEKYKKL----AREKNKvliPEVlscHCLRHSKAMHLL----QAGVNLV----YIRDILGHCSVQVTEIY 297
Cdd:cd00797  110 LTGGGVyRVFRRLLRRIglrgAGDGRG---PRL---HDLRHTFAVNRLtrwyREGADVErklpVLSTYLGHVNVTDTYWY 183
PRK09870 PRK09870
tyrosine recombinase; Provisional
 117-302 1.39e-07

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 51.09  E-value: 1.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 117 KTEKKTINYLTLDGIKLLLEMPDLNTEAGRrNLALLTLMYDTGARVQEVIDLTPSMIRF-DKPYTIKLIGKGNkARIVPL 195
Cdd:PRK09870   4 KADNKKRNFLTHSEIESLLKAANTGPHAAR-NYCLTLLCFIHGFRASEICRLRISDIDLkAKCIYIHRLKKGF-STTHPL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 196 MEPTMRIVKKYMEEQNLLRNSANLYpLFFNKRKERLTRAgvnyivEKYKKLAREKNKVLIPEVLSCHCLRHSKAMHLLQA 275
Cdd:PRK09870  82 LNKEIQALKNWLSIRTSYPHAESEW-VFLSRKGNPLSRQ------QFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANM 154

                        170       180
                 ....*....|....*....|....*..
gi 749938047 276 GVNLVYIRDILGHCSVQVTEIYAKTDS 302
Cdd:PRK09870 155 GIDTRLIQDYLGHRNIRHTVWYTASNA 181
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 158-311 2.17e-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: 271191  Cd Length: 176  Bit Score: 50.12  E-value: 2.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 158 TGARVQEVIDLTPSMIRFDkpyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSanlypLFFNKRKERLTRAGvn 237
Cdd:cd01191   32 TGARVSELIKIKVEHVELG---YFDIYSKGGKLRRLYIPKKLRNEALEWLKSTNRKSGY-----IFLNRFGERITTRG-- 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 749938047 238 yIVEKYKKLAREKNkvLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEK 311
Cdd:cd01191  102 -IAQQLKNYARKYG--LNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASEQQEIVDK 172
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 140-294 2.66e-07

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: 50.11  E-value: 2.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 140 LNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYtIKLIGKGN----------KARIVPLMEPTMRIVKKYMEE 209
Cdd:cd01186   11 INACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQ-IELVPREDntnearaksmRERRIPVSQDLIDLYADYLTY 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 210 QNLLRNSANLYplFFNKRKERLTRAGVNYIvEKYKKLAREKNKVLIPevLSCHCLRHSKAMHLLQAGVNLVYIRDILGHC 289
Cdd:cd01186   90 IYCEEAEFSIT--VFVNVKGGNQGKAMNYS-DVYDLVRRLKKRTGID--FTPHMFRHTHATALIRAGWSIEVVARRLGHA 164


                 ....*
gi 749938047 290 SVQVT 294
Cdd:cd01186  165 HVQTT 169
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 53-315 5.31e-07

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 50.81  E-value: 5.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047  53 HLTLNKITKNLVVDYLDWTEDKRqcSPST-RNVRlAALHSFFKY------LQYeNPdnllewQQVLSISVKKTEKKTINY 125
Cdd:COG0582  136 DRPIAEITPPDLLAVLRPIEARG--APETaRRVR-QRLRQVFRYavarglIER-NP------AADLKGALPKPKVKHHPA 205

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 126 LTLDGIKLLLEmpDLNTEAGRRN--LALLTLMYdTGARVQEVIDLTPSMIRFDKpytiKLI------GKGNKARIVPLME 197
Cdd:COG0582  206 LTPEELPELLR--ALDAYRGSPVtrLALRLLLL-TGVRPGELRGARWSEIDLEA----ALWtipaerMKTRRPHIVPLSR 278

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 198 PTMRIVKKymeeqnlLRNSANLYPLFF---NKRKERLTRAGVNYIVekyKKLAREKnkvlipevLSCHCLRHSKAMHLLQ 274
Cdd:COG0582  279 QALEILKE-------LKPLTGDSEYVFpsrRGPKKPMSENTLNKAL---RRMGYGR--------FTPHGFRHTASTLLNE 340

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 749938047 275 AGVNLVYIRDILGHCSVQVTE-IYAKTDS-KQKREAIEK--AYVD 315
Cdd:COG0582  341 AGFPPDVIERQLAHKDGNKVRaAYNRADYlEERREMMQWwaDYLD 385
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 139-297 2.69e-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: 47.29  E-value: 2.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 139 DLNTEAGRRNLALLTLMYDTGARVQEVI-----DLTpsmiRFDKPYTIKLIG--KGN---KARIVPLME----PTMRIVK 204
Cdd:cd00799    9 DDTTLRGLRDRALLLLGFAGALRRSELValrveDLT----RFVDGGLLIRLRrsKTDqdgEGEIKALPYgpetCPVRALR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 205 KYMEEQNLLRNsanlyPLF--FNKR----KERLTRAGVNYIVEKYKKLAreknkVLIPEVLSCHCLRHSKAMHLLQAGVN 278
Cdd:cd00799   85 AWLEAAGIPSG-----PLFrrIRRGgsvgTTRLSDRSVARIVKRRAALA-----GLDPGDFSGHSLRRGFATEAARAGAS 154

                        170
                 ....*....|....*....
gi 749938047 279 LVYIRDILGHCSVQVTEIY 297
Cdd:cd00799  155 LPEIMAQGGHKSVATVMRY 173
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 145-299 2.83e-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: 43.57  E-value: 2.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 145 GRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKP------YTIKLIGKGNKARIVPLMEPTMRIVKKYmeeqnllrnsan 218
Cdd:cd01187   12 LPQPIPVVQAAVFTGARASELATLKFGCLHAQTSddgtflYWLKWENKGGKQLDIPISKKVAELIKTI------------ 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 219 lyplffNKRKERLTRagvnyivekykkLAREKNKVLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYA 298
Cdd:cd01187   80 ------NWTLNELSE------------LKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYA 141


                 .
gi 749938047 299 K 299
Cdd:cd01187  142 L 142
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
23-96 1.32e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 39.90  E-value: 1.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 749938047   23 GASKNTIASYRDTFILFLRFLkDEKGISvehltlnKITKNLVVDYLDWTEDKRQCSPSTRNVRLAALHSFFKYL 96
Cdd:pfam13495  13 GYAERTIKAYLRWIRRFLRFH-DKKHPE-------ELTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWV 78
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 158-299 1.93e-04

Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity.


Pssm-ID: 271184 [Multi-domain]  Cd Length: 180  Bit Score: 41.52  E-value: 1.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 749938047 158 TGARVQEVIDLTPSMIRFDK--PY-TIKLIGKG----NKA--RIVPLMEPTMRI-VKKYMEEqnllRNSANLYPLFFNKR 227
Cdd:cd01184   35 TGARLNEICQLRVDDIKEEDgiWCiDINDDAEGrrlkTKAsrRLVPIHPRLIELgFLDYVEA----LRADGKLFLFPEKR 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 749938047 228 KERLTRAGvnyiveKY-KKLAREKNKVLIPEV--LSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTE-IYAK 299
Cdd:cd01184  111 DKDGKYSK------AAsKWFNRLLRKLGIKDDerKSFHSFRHTFITALKRAGVPEELIAQIVGHSRGGVTHdTYGK 180
 
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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