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Conserved domains on  [gi|1622219690|gb|THG91348|]
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integrase [Alkalihalobacillus alcalophilus ATCC 27647 = CGMCC 1.3604]

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; ...
 137-323 2.32e-95

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: 281.47  E-value: 2.32e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 137 LTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 216
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 217 YMEEQNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVLiPEVLSCHCLRHSKAMHLLQAGVNLVYIRDI 296
Cdd:cd01182    81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSL-PKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                         170       180
                  ....*....|....*....|....*..
gi 1622219690 297 LGHCSVQVTEIYAKTDSKQKREAIEKA 323
Cdd:cd01182   160 LGHESVETTQIYAEADLEMKREALEKA 186
Phage_int_SAM_1 super family cl12235
Phage integrase, N-terminal SAM-like domain;
21-111 4.85e-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: 55.34  E-value: 4.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  21 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisvehLTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAAL 100
Cdd:pfam02899   1 IDQFL-EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGG------SSLEQITTSDVRAFLAELRAQGL-SASSLARRLSAL 72

                          90
                  ....*....|.
gi 1622219690 101 HSFFKYLQYEN 111
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; ...
 137-323 2.32e-95

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: 281.47  E-value: 2.32e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 137 LTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 216
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 217 YMEEQNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVLiPEVLSCHCLRHSKAMHLLQAGVNLVYIRDI 296
Cdd:cd01182    81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSL-PKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                         170       180
                  ....*....|....*....|....*..
gi 1622219690 297 LGHCSVQVTEIYAKTDSKQKREAIEKA 323
Cdd:cd01182   160 LGHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
15-323 1.87e-75

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 234.50  E-value: 1.87e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  15 TDFSYYLTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisveHLTLNKITKNLVVDYLDWTEdKRQCSPSTRN 94
Cdd:COG4974     1 LTLADLLEAFL-EELKREKGLSPNTIKAYRRDLRRFLRFLEELG-----KIPLAEITPEDIRAYLNYLR-ERGLSPSTIN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  95 VRLAALHSFFKYLQYENpdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQ 174
Cdd:COG4974    74 RYLAALRSFFRYAVREG---LLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 175 EVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSanlyPLFFNKRKERLTRAGVNYIVEKY 254
Cdd:COG4974   151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRDSD----YLFPTRRGRPLSRRAIRKILKRL 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622219690 255 KKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKA 323
Cdd:COG4974   227 AKRAG------IPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 28-308 2.18e-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: 190.49  E-value: 2.18e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  28 FLPGEIGASKNTIASYRDTFILFLRFLkDEKGISVEhltlnKITKNLVVDYLDWtEDKRQCSPSTRNVRLAALHSFFKYL 107
Cdd:TIGR02225   6 YLWVERGLSQNTLEAYRRDLEKFLEFL-EERGIDLE-----EVDRGDIVDFLAE-LKEAGLSARSIARALSALRSFYRFL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 108 QYEN--PDNLlewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIR 185
Cdd:TIGR02225  79 LREGirEDDP-----SALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVN 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 186 FDKPYtIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANLYP---LFFNKRKERLTRAGVNYIVekyKKLAREKN 262
Cdd:TIGR02225 154 LDEGF-VRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKEsdaLFLNRRGGPLSRQGVWKIL---KEYAKRAG 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1622219690 263 kvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 308
Cdd:TIGR02225 230 ---IEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 21-324 2.43e-52

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 174.96  E-value: 2.43e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  21 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKGISVEHLTLNKITKNLVvdyldwTEDKRQCSPSTRNVRLAAL 100
Cdd:PRK00236   10 LEAFL-EYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLA------RRRRQGLSARSLARRLSAL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 101 HSFFKYLQ-----YENPdnllewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQE 175
Cdd:PRK00236   83 RSFYRWLVrrgllKANP--------AAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSE 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 176 VIDLTPSMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANlyPLFFNKRKERLTRAGVNYIVEKYK 255
Cdd:PRK00236  155 LVGLDIDDLDLASG-TLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDD--ALFLGARGGRLSPRVVQRRVKKLG 231

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622219690 256 KLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKAY 324
Cdd:PRK00236  232 KKAG------LPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAH 294
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 136-310 1.20e-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: 106.25  E-value: 1.20e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 136 YLTLDGIKLLLEMPDlNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVK 215
Cdd:pfam00589   1 RLTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 216 KYMEEQNLLRNSANLypLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRD 295
Cdd:pfam00589  80 EWLSKRLLEAPKSDY--LFASKRGKPLSRQTVRKIFKRAGKEAG------LELPLHPHMLRHSFATHLLEAGVDLRVVQK 151

                         170
                  ....*....|....*
gi 1622219690 296 ILGHCSVQVTEIYAK 310
Cdd:pfam00589 152 LLGHSSISTTQIYTH 166
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
21-111 4.85e-10

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 55.34  E-value: 4.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  21 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisvehLTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAAL 100
Cdd:pfam02899   1 IDQFL-EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGG------SSLEQITTSDVRAFLAELRAQGL-SASSLARRLSAL 72

                          90
                  ....*....|.
gi 1622219690 101 HSFFKYLQYEN 111
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; ...
 137-323 2.32e-95

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: 281.47  E-value: 2.32e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 137 LTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 216
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 217 YMEEQNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVLiPEVLSCHCLRHSKAMHLLQAGVNLVYIRDI 296
Cdd:cd01182    81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSL-PKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                         170       180
                  ....*....|....*....|....*..
gi 1622219690 297 LGHCSVQVTEIYAKTDSKQKREAIEKA 323
Cdd:cd01182   160 LGHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
15-323 1.87e-75

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 234.50  E-value: 1.87e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  15 TDFSYYLTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisveHLTLNKITKNLVVDYLDWTEdKRQCSPSTRN 94
Cdd:COG4974     1 LTLADLLEAFL-EELKREKGLSPNTIKAYRRDLRRFLRFLEELG-----KIPLAEITPEDIRAYLNYLR-ERGLSPSTIN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  95 VRLAALHSFFKYLQYENpdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQ 174
Cdd:COG4974    74 RYLAALRSFFRYAVREG---LLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 175 EVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSanlyPLFFNKRKERLTRAGVNYIVEKY 254
Cdd:COG4974   151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRDSD----YLFPTRRGRPLSRRAIRKILKRL 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622219690 255 KKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKA 323
Cdd:COG4974   227 AKRAG------IPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKL 289
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 28-308 2.18e-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: 190.49  E-value: 2.18e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  28 FLPGEIGASKNTIASYRDTFILFLRFLkDEKGISVEhltlnKITKNLVVDYLDWtEDKRQCSPSTRNVRLAALHSFFKYL 107
Cdd:TIGR02225   6 YLWVERGLSQNTLEAYRRDLEKFLEFL-EERGIDLE-----EVDRGDIVDFLAE-LKEAGLSARSIARALSALRSFYRFL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 108 QYEN--PDNLlewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIR 185
Cdd:TIGR02225  79 LREGirEDDP-----SALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVN 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 186 FDKPYtIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANLYP---LFFNKRKERLTRAGVNYIVekyKKLAREKN 262
Cdd:TIGR02225 154 LDEGF-VRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKEsdaLFLNRRGGPLSRQGVWKIL---KEYAKRAG 229

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1622219690 263 kvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 308
Cdd:TIGR02225 230 ---IEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 21-324 2.43e-52

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 174.96  E-value: 2.43e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  21 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKGISVEHLTLNKITKNLVvdyldwTEDKRQCSPSTRNVRLAAL 100
Cdd:PRK00236   10 LEAFL-EYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLDAADLRSFLA------RRRRQGLSARSLARRLSAL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 101 HSFFKYLQ-----YENPdnllewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQE 175
Cdd:PRK00236   83 RSFYRWLVrrgllKANP--------AAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSE 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 176 VIDLTPSMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANlyPLFFNKRKERLTRAGVNYIVEKYK 255
Cdd:PRK00236  155 LVGLDIDDLDLASG-TLRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDD--ALFLGARGGRLSPRVVQRRVKKLG 231

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1622219690 256 KLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKAY 324
Cdd:PRK00236  232 KKAG------LPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAH 294
xerD PRK00283
tyrosine recombinase;
32-308 2.25e-50

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 169.99  E-value: 2.25e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  32 EIGASKNTIASYRDTFILFLRFLkdekgiSVEHLTLNKITKNLVVDYLDWTEDkRQCSPSTRNVRLAALHSFFKYLQYEN 111
Cdd:PRK00283   19 ERGLAENTLSSYRRDLELFAEWL------AARGLSLAEATRDDLQAFLAELAE-GGYKATSSARRLSALRRFFQFLLREG 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 112 pdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPyT 191
Cdd:PRK00283   92 ---LREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQG-V 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 192 IKLIGKGNKARIVPLMEPTMRIVKKYMEE--QNLLRNSANLYpLFFNKRKERLTRAGVNYIVEKYKKLAReknkvLIPEV 269
Cdd:PRK00283  168 VRVTGKGNKERLVPLGEEAVYAIERYLERgrPALLNGRSSDA-LFPSARGGQLTRQTFWHRIKHYAKRAG-----IDPKK 241

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1622219690 270 LSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 308
Cdd:PRK00283  242 LSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIY 280
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 24-324 9.78e-50

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: 168.17  E-value: 9.78e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  24 FLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKGISvehlTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAALHSF 103
Cdd:TIGR02224   3 FL-EYLRLERNYSPHTVRAYRRDLEAFLEFLEEEGGLA----SLAEVTAADLRSFLAELHARGL-SRRSLARKLSALRSF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 104 FKYLQYENpdnLLEWQQVLSISVKKTEKKTINYLTLDGIKLLLEMPDLNTE--AGRRNLALLTLMYDTGARVQEVIDLTP 181
Cdd:TIGR02224  77 YRFLLRRG---LIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDEdwLALRDRAILELLYSSGLRVSELVGLDL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 182 SMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQN-LLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKlare 260
Cdd:TIGR02224 154 SDLDLDFG-EVRVRGKGNKERIVPFGPYARDALQAYLEARRsPLLASEGQDALFLNRRGGRLTPRGVQYRLQQLRA---- 228

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622219690 261 knKVLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEKAY 324
Cdd:TIGR02224 229 --KAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAH 290
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
21-320 4.19e-48

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 163.59  E-value: 4.19e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  21 LTGFLTKFLP--GEIGASKNTIASYRDTFILFLRFLKDEkgisveHLTLNKITKNLVVDYLDWTEDKRqCSPSTRNVRLA 98
Cdd:COG4973     4 LAEALEAYLEhlRERRLSPKTLEAYRRDLRRLIPLLGDA------DLPLEELTPADVRRFLARLHRRG-LSPRTLNRRLS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  99 ALHSFFKYLQYE-----NPdnllewqqVLSISVKKTEKKTINYLTLDGIKLLLEMPDlNTEAGRRNLALLTLMYDTGARV 173
Cdd:COG4973    77 ALRSFFNWAVREglleaNP--------AAGVKAPKAPRKLPRALTVDELAQLLDALA-DDPLAVRDRAIVELLYSTGLRL 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 174 QEVIDLTPSMIRFDKPyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANlYPLFFNKRKERLTRAGVNyivEK 253
Cdd:COG4973   148 GELVGLDWEDVDLDAG-EVRVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPDE-GALFPSRRGTRLSPRNVQ---KR 222

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622219690 254 YKKLAReknKVLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAI 320
Cdd:COG4973   223 LRRLAK---KAGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAEVY 286
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 140-315 1.44e-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: 148.04  E-value: 1.44e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 140 DGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYtIKLIGKGNKARIVPLMEPTMRIVKKYME 219
Cdd:cd00798     2 DEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGL-VRVTGKGNKERLVPFGSYAVEALEEYLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 220 E-QNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVNLVYIRDILG 298
Cdd:cd00798    81 ErRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHV------SPHTLRHSFATHLLEGGADLRVVQELLG 154

                         170
                  ....*....|....*..
gi 1622219690 299 HCSVQVTEIYAKTDSKQ 315
Cdd:cd00798   155 HASLSTTQIYTHVSFER 171
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 142-309 4.04e-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: 112.96  E-value: 4.04e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 142 IKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKpYTIKLIGKG---NKARIVPLMEPTMRIVKKYM 218
Cdd:cd00397     2 LEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDN-GTIRVRGKKtkgGKERTVPLPKELAEELKEYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 219 EE----QNLLRNSANLYPLFFNKRKERLTRAGVNYIVEKYKKLAREKnkvlipevLSCHCLRHSKAMHLLQAGVNLVYIR 294
Cdd:cd00397    81 KErrdkRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRK--------ITPHSLRHTFATNLLENGVDIKVVQ 152

                         170
                  ....*....|....*
gi 1622219690 295 DILGHCSVQVTEIYA 309
Cdd:cd00397   153 KLLGHSSISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 136-310 1.20e-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: 106.25  E-value: 1.20e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 136 YLTLDGIKLLLEMPDlNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVK 215
Cdd:pfam00589   1 RLTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 216 KYMEEQNLLRNSANLypLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRD 295
Cdd:pfam00589  80 EWLSKRLLEAPKSDY--LFASKRGKPLSRQTVRKIFKRAGKEAG------LELPLHPHMLRHSFATHLLEAGVDLRVVQK 151

                         170
                  ....*....|....*
gi 1622219690 296 ILGHCSVQVTEIYAK 310
Cdd:pfam00589 152 LLGHSSISTTQIYTH 166
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 84-340 3.38e-24

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 101.36  E-value: 3.38e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  84 DKRQCSPSTRNVRLAALHSFFKYLQYE-----NPDNLLEwqqvlsisVKKTEKKTINY-LTLDGIKLLLEMPDLNTEAGR 157
Cdd:PRK01287   86 NGEPLSTRTQRTQLSPLRVWFRWLLKRhhilyNPAEDLE--------LPKEEKRLPRQiLSEAETEQVLASPDLTTLQGL 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 158 RNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEE--QNLLRNSANLYpLFF 235
Cdd:PRK01287  158 RDRALLELLWSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERALAWLQRYLQDvrPQLAVRPDSGA-LFV 236

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 236 NKRKERLTRAGVNYIVEKYKKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY------- 308
Cdd:PRK01287  237 AMDGDGLARNTLTNMVGRYIRAAGIEKAG------ACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYtrvsigh 310

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1622219690 309 -----AKTD-SKQKREAIEKAYVDVSPTDEPMWEKNED 340
Cdd:PRK01287  311 lqavhASTHpAERKADEKLRDADEVGLLADLYADDNAD 348
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 36-322 2.42e-22

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 96.14  E-value: 2.42e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  36 SKNTIASYRDTFILFLRFLKDEKGISVEHL------TLNKITKNLVVDYLDWTEDKRQC---------SPSTRNVRLAAL 100
Cdd:PRK05084   34 SPTTLYEYLTEYRRFFNWLISEGLSDASKIkdiplsTLENLTKKDVEAFILYLRERPLLnghstkkgnSQTTINRTLSAL 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 101 HSFFKYL--QYENPD--NLLEWQQVLSISVKKtEKKTINY---------LTLDGIKLLLEMPD------LNTEAGR---- 157
Cdd:PRK05084  114 KSLFKYLteEAENEDgePYFYRNVMKKIELKK-KKETLAArahnlkqklFLGDEDYEFLDFIDneyeqkLSNRALSsfkk 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 158 ---RNLALLTLMYDTGARVQEVIDLTPSMIRFDKpYTIKLIGKGNKARIVPLMEPTMRIVKKYMEeqnlLRNS-----AN 229
Cdd:PRK05084  193 nkeRDLAIIALILGSGLRVSELVNLDLSDLNLKQ-MTIDVTRKGGKRDSVNIAPFALPYLEEYLK----IRASrykaeKQ 267

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 230 LYPLFFNKRK---ERLTRAGVNYIVEKYKKLAREKnkvlipevLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTE 306
Cdd:PRK05084  268 EKALFLTKYRgkpNRISARAIEKMVAKYSEAFGVR--------LTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTD 339

                         330
                  ....*....|....*.
gi 1622219690 307 IYAKTDSKQKREAIEK 322
Cdd:PRK05084  340 LYTHIVNDEQKEALDR 355
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 137-309 2.16e-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: 89.74  E-value: 2.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 137 LTLDGIKLLLE-MPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLI-GKG--NKARIVPLMEPTMR 212
Cdd:cd01194     1 LTLEQARQLLAsLPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEGTILYVqGKGktSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 213 IVKKYMEEQNLLRNSAnlyPLFF----NKRKERLTRAGVNYIVEKYKKLAREKnkvliPEVLSCHCLRHSKAMHLLQAGV 288
Cdd:cd01194    81 ALQAYLKARGKLDFEE---PLFTslsnNSKGQRLTTRSIRRIIKKYLRKAGLD-----DDRLTAHSLRHTAGTLALKAGK 152

                         170       180
                  ....*....|....*....|.
gi 1622219690 289 NLVYIRDILGHCSVQVTEIYA 309
Cdd:cd01194   153 SLREVQQLLRHSDPNTTMIYA 173
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 137-308 3.07e-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: 89.26  E-value: 3.07e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 137 LTLDGIKLLLEmpdlNTEAGRRNLALLTLmYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKK 216
Cdd:cd01193     6 LSPDEVRRILG----ALTELRHRLILSLL-YGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 217 YMEEQN-----LLRNSANLYPLFFNKRKER--LTRAGVNYIVEKYKKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVN 289
Cdd:cd01193    81 YLKSARpkeelDPAEGRAGVLDPRTGVERRhhISETTVQRALKKAVEQAGITKRV------TPHTLRHSFATHLLEAGTD 154

                         170
                  ....*....|....*....
gi 1622219690 290 LVYIRDILGHCSVQVTEIY 308
Cdd:cd01193   155 IRTIQELLGHSDLSTTMIY 173
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 138-318 1.01e-20

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: 88.07  E-value: 1.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 138 TLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPyTIKLIGKGNKA-RIVPLMEPTMRIVKK 216
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSG-TITVRQKKTGRpVELPLTEPVGEALAD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 217 YMeeqnLLRNSANLYPLFFNKRK---ERLT-RAGVNYIVEKY-KKLAREKNKVlipevlSCHCLRHSKAMHLLQAGVNLV 291
Cdd:cd01188    80 YL----RDGRPRTDSREVFLRARapyRPLSsTSQISSIVRRYlRKAGIEPSHR------GTHSLRHSLATRMLRAGTSLK 149

                         170       180
                  ....*....|....*....|....*..
gi 1622219690 292 YIRDILGHCSVQVTEIYAKTDSKQKRE 318
Cdd:cd01188   150 VIADLLGHRSIETTAIYAKIDVDDLRE 176
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 136-309 1.69e-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: 81.60  E-value: 1.69e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 136 YLTLDGIKLLLEmpDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVK 215
Cdd:cd00796     4 FLTEDEEARLLA--ALEESTNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAILK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 216 KYMEEqnllrnsANLYPLFFNKRKERLTRAGVNYIVEKykklAREKNKVlipEVLSCHCLRHSKAMHLLQAGVNLVYIRD 295
Cdd:cd00796    82 ELKRK-------RGKDGFFVDGRFFGIPIASLRRAFKK----ARKRAGL---EDLRFHDLRHTFASRLVQAGVPIKTVAK 147

                         170
                  ....*....|....
gi 1622219690 296 ILGHCSVQVTEIYA 309
Cdd:cd00796   148 ILGHSSIKMTMRYA 161
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 36-308 2.74e-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: 83.98  E-value: 2.74e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  36 SKNTIASYRDTFILFLRFLKdekgisVEHLTlnKITKNLVVDYLDWTEDKRQCSPSTRNVRLAALHSFFK-YLQYEnpdn 114
Cdd:TIGR02249  15 AKRTEEAYLHWIKRFIRFHN------KRHPS--TMGDTEVEAFLSDLAVDGKVAASTQNQALNALLFLYKeILKTP---- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 115 lLEWQQVLSISvkKTEKKTINYLTLDGIKLLLEMPDlnteaGRRNLaLLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKL 194
Cdd:TIGR02249  83 -LSLMERFVRA--KRPRKLPVVLTREEVRRLLEHLE-----GKYRL-IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIR 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 195 IGKGNKARIVP----LMEPTMRIVKK----YMEEQNLLRNSANL-------YP----------LFFNKRKERLTRAGV-- 247
Cdd:TIGR02249 154 QGKGGKDRTVTlpkeLIPPLREQIELarayHEADLAEGYGGVYLphalarkYPnapkewgwqyLFPSHRLSRDPESGVir 233

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622219690 248 -NYIVEK-----YKKLAREKNkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIY 308
Cdd:TIGR02249 234 rHHINETtiqraVRRAVERAG---IEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
int PHA02601
integrase; Provisional
 68-309 3.68e-14

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 72.45  E-value: 3.68e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  68 NKITKNLVVDYLD-------WTEDKRQCSPSTRNVRLAALHSFFKYLQyenpdNLLEW--QQVLS-ISVKKTEKKTINYL 137
Cdd:PHA02601   99 SEFTAKDFADYRArrlsgefKVNKGRPIKPATVNRELAYLSAVFNELI-----KLGKWsgPNPLDgIRPFKEAEPELAFL 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 138 TLDGIKLLLEMPDlntEAGRRNLALLTLM-YDTGARVQEVIDLTPSMIrfdKPYTIKLIG-KGNKARIVPLMEPTMRIvk 215
Cdd:PHA02601  174 TKEEIERLLDACD---GSRSPDLGLIAKIcLATGARWSEAETLKRSQI---SPYKITFVKtKGKKNRTVPISEELYKM-- 245

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 216 kymeeqnLLRNSANLYPLFFNKRKERLTRAGVNyivekykklareknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRD 295
Cdd:PHA02601  246 -------LPKRRGRLFKDAYESFERAVKRAGID-----------------LPEGQATHVLRHTFASHFMMNGGNILVLQR 301

                         250
                  ....*....|....
gi 1622219690 296 ILGHCSVQVTEIYA 309
Cdd:PHA02601  302 ILGHATIEMTMAYA 315
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 154-310 2.49e-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: 66.43  E-value: 2.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 154 EAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPY-----TIKLIGKG--------NKA--RIVPLMEPTMRIVKKYM 218
Cdd:cd01189    13 KRGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTirinrTLVRKKKGgyvikppkTKSsiRTIPLPDELIELLKELK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 219 EeqnllrnsanlyplfFNKRkerLTRAGVNYIvekykklareknkvlipevlSCHCLRHSKAMHLLQAGVNLVYIRDILG 298
Cdd:cd01189    93 A---------------FKKL---LKKAGLPRI--------------------TPHDLRHTFASLLLEAGVPLKVIAERLG 134

                         170
                  ....*....|...
gi 1622219690 299 HCSVQVT-EIYAK 310
Cdd:cd01189   135 HSDISTTlDVYAH 147
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 138-308 4.48e-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: 4.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 138 TLDGIKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKpYTIKLIGKGNKARIVPLMEP-TMRIVKK 216
Cdd:cd01195     1 SREEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEH-RRLRILGKGKKQREVVTLPPtTREALAA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 217 YMEeqnlLRNSANlYPLFF----NKRKERLTRAGVNYIVekyKKLAREknkVLIPEVLSCHCLRHSKAMHLLQAGVNLVY 292
Cdd:cd01195    80 WLA----ARGEAE-GPLFVsldrASRGRRLSPQAVYRIV---RRLAER---IGLGKRLSPHGLRHSAITLALDAGAGLIR 148

                         170
                  ....*....|....*..
gi 1622219690 293 -IRDILGHCSVQVTEIY 308
Cdd:cd01195   149 kVQDFSRHADLRTLQVY 165
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 146-316 6.06e-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: 65.75  E-value: 6.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 146 LEMPDLNTEAGRRNLALLTlMYdTGARVQEVIDLTPSMIRFDKPYT-IKLI-GKGNKARIVPLMEPTMRIVKKYMEEqnl 223
Cdd:cd01185     9 LELSDTSRLELVRDMFLFS-CY-TGLRFSDLKNLTWKNIVEASGRTwIRYRrKKTGKPVTVPLLPVAREILEKYKDD--- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 224 lRNSANLYPLFFNKrkerltraGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQ 303
Cdd:cd01185    84 -RSEGKLFPVLSNQ--------KINRYLKEIAKIAG------IDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIK 148

                         170
                  ....*....|...
gi 1622219690 304 VTEIYAKTDSKQK 316
Cdd:cd01185   149 TTQIYAKIVDSKK 161
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
21-111 4.85e-10

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 55.34  E-value: 4.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  21 LTGFLtKFLPGEIGASKNTIASYRDTFILFLRFLKDEKgisvehLTLNKITKNLVVDYLDWTEDKRQcSPSTRNVRLAAL 100
Cdd:pfam02899   1 IDQFL-EYLSLERGLSPHTLRAYRRDLLAFLKFLSEGG------SSLEQITTSDVRAFLAELRAQGL-SASSLARRLSAL 72

                          90
                  ....*....|.
gi 1622219690 101 HSFFKYLQYEN 111
Cdd:pfam02899  73 RSFYQFLIREG 83
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 142-308 9.13e-10

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: 57.30  E-value: 9.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 142 IKLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLiGKGNKARIVPLMEPTMRIVKKYMEEQ 221
Cdd:cd01192     9 KKLIKEIKLYLKKANPRNYLLFIVGINTGLRISDLLSLKVEDVTNKDKLSIKE-QKTGKQKTFPLNPTLVKALKEYIDDL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 222 NLLRNSaNLYPLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCS 301
Cdd:cd01192    88 DLKRND-YLFKSLKQGPEKPISRKQAYKILKKAADDLG------LNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSS 160


                  ....*..
gi 1622219690 302 VQVTEIY 308
Cdd:cd01192   161 PSITLRY 167
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 136-315 2.53e-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: 55.98  E-value: 2.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 136 YLTLDGIKLLLEmpdlntEAGR-----RNLALLTLMYDTGARVQEVIDLTPSMIRF-DKPYTIKLIgKGNKARIVPLMEP 209
Cdd:cd01197     6 YLTGKEVQALLQ------AACRgrtpaRDYCLLLLAFRHGFRVSELCDLHLSDVDLeSRRLHIRRL-KNGFSTTHPLRFD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 210 TMRIVKKYMEEQNLLRNSANLYpLFFNKRKERLTRAGVNYIVEKYKKLAReknkvlIPEVLSCHCLRHSKAMHLLQAGVN 289
Cdd:cd01197    79 EREALEAWLKERANWKGADTDW-IFLSRRGGPLSRQQAYRIIRDLGKEAG------TVTQTHPHMLRHACGYALADRGAD 151

                         170       180
                  ....*....|....*....|....*.
gi 1622219690 290 LVYIRDILGHCSVQVTEIYAKTDSKQ 315
Cdd:cd01197   152 TRLIQDYLGHRNIRHTVIYTASNAAR 177
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 143-320 2.56e-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: 2.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 143 KLLLEMPDLNTEAGRRNLALLTLMYDTGARVQEVIdltpSMIRFD-----KPYTIKLIGKGNKARIVPLMEPTMRIVKKY 217
Cdd:cd01196     6 RRLLESIDSTHPVGLRDRALIALMVYSFARIGAVL----AMRVEDvydqgRRLWVRLAEKGGKQHEMPCHHDLEEYLRAY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 218 MEEQNLlrNSANLYPLFFNKRKE-------RLTRAGVnyivekYKKLAREKNKVLIPEVLSCHCLRHSKAMHLLQAGVNL 290
Cdd:cd01196    82 LEAAEI--EEDPKGPLFRTTRGGtrklthnPLTQANA------YRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTL 153

                         170       180       190
                  ....*....|....*....|....*....|
gi 1622219690 291 VYIRDILGHCSVQVTEIYAKTDSKQKREAI 320
Cdd:cd01196   154 EDAQNMANHASTRTTQLYDRRSDKITLDEV 183
PRK15417 PRK15417
integron integrase;
78-310 3.88e-08

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 54.28  E-value: 3.88e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  78 YLDWTEDKRQCSPSTRNVRLAALHSFF-KYLQYENPdnlleWQQvlSISVKKTEKKTINYLTLDGIKLLLEMpdlnTEAG 156
Cdd:PRK15417   64 FLSWLANERKVSVSTHRQALAALLFFYgKVLCTDLP-----WLQ--EIGRPRPSRRLPVVLTPDEVVRILGF----LEGE 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 157 RRNLAllTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLME---PTMR-----IVKKYMEEQNLLRNSA 228
Cdd:PRK15417  133 HRLFA--QLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPEslaPSLReqlsrARAWWLKDQAEGRSGV 210

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 229 NL-------YP----------LFFNKRKERLTRAGV-------NYIVEKYKKLAREKNKVLIPEvlSCHCLRHSKAMHLL 284
Cdd:PRK15417  211 ALpdalerkYPraghswpwfwVFAQHTHSTDPRSGVvrrhhmyDQTFQRAFKRAVEQAGITKPA--TPHTLRHSFATALL 288

                         250       260
                  ....*....|....*....|....*.
gi 1622219690 285 QAGVNLVYIRDILGHCSVQVTEIYAK 310
Cdd:PRK15417  289 RSGYDIRTVQDLLGHSDVSTTMIYTH 314
PRK09870 PRK09870
tyrosine recombinase; Provisional
 128-313 1.14e-07

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 51.48  E-value: 1.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 128 KTEKKTINYLTLDGIKLLLEMPDLNTEAGRrNLALLTLMYDTGARVQEVIDLTPSMIRF-DKPYTIKLIGKGNkARIVPL 206
Cdd:PRK09870    4 KADNKKRNFLTHSEIESLLKAANTGPHAAR-NYCLTLLCFIHGFRASEICRLRISDIDLkAKCIYIHRLKKGF-STTHPL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 207 MEPTMRIVKKYMEEQNLLRNSANLYpLFFNKRKERLTRAgvnyivEKYKKLAREKNKVLIPEVLSCHCLRHSKAMHLLQA 286
Cdd:PRK09870   82 LNKEIQALKNWLSIRTSYPHAESEW-VFLSRKGNPLSRQ------QFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANM 154

                         170       180
                  ....*....|....*....|....*..
gi 1622219690 287 GVNLVYIRDILGHCSVQVTEIYAKTDS 313
Cdd:PRK09870  155 GIDTRLIQDYLGHRNIRHTVWYTASNA 181
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 162-308 1.27e-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: 1.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 162 LLTLMYDTGARVQEVIDLTPSMIRFDKPYTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSANLYPLFFNKRKER 241
Cdd:cd00797    30 LFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSYFFVSQQGGR 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 242 LTRAGV-NYIVEKYKKL----AREKNKvliPEVlscHCLRHSKAMHLL----QAGVNLV----YIRDILGHCSVQVTEIY 308
Cdd:cd00797   110 LTGGGVyRVFRRLLRRIglrgAGDGRG---PRL---HDLRHTFAVNRLtrwyREGADVErklpVLSTYLGHVNVTDTYWY 183
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 169-322 1.92e-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: 50.50  E-value: 1.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 169 TGARVQEVIDLTPSMIRFDkpyTIKLIGKGNKARIVPLMEPTMRIVKKYMEEQNLLRNSanlypLFFNKRKERLTRAGvn 248
Cdd:cd01191    32 TGARVSELIKIKVEHVELG---YFDIYSKGGKLRRLYIPKKLRNEALEWLKSTNRKSGY-----IFLNRFGERITTRG-- 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622219690 249 yIVEKYKKLAREKNkvLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYAKTDSKQKREAIEK 322
Cdd:cd01191   102 -IAQQLKNYARKYG--LNPKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIYLRKTASEQQEIVDK 172
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 64-326 2.16e-07

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 51.96  E-value: 2.16e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  64 HLTLNKITKNLVVDYLDWTEDKRqcSPST-RNVRlAALHSFFKY------LQYeNPdnllewQQVLSISVKKTEKKTINY 136
Cdd:COG0582   136 DRPIAEITPPDLLAVLRPIEARG--APETaRRVR-QRLRQVFRYavarglIER-NP------AADLKGALPKPKVKHHPA 205

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 137 LTLDGIKLLLEmpDLNTEAGRRN--LALLTLMYdTGARVQEVIDLTPSMIRFDKpytiKLI------GKGNKARIVPLME 208
Cdd:COG0582   206 LTPEELPELLR--ALDAYRGSPVtrLALRLLLL-TGVRPGELRGARWSEIDLEA----ALWtipaerMKTRRPHIVPLSR 278

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 209 PTMRIVKKymeeqnlLRNSANLYPLFF---NKRKERLTRAGVNYIVekyKKLAREKnkvlipevLSCHCLRHSKAMHLLQ 285
Cdd:COG0582   279 QALEILKE-------LKPLTGDSEYVFpsrRGPKKPMSENTLNKAL---RRMGYGR--------FTPHGFRHTASTLLNE 340

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1622219690 286 AGVNLVYIRDILGHCSVQVTE-IYAKTDS-KQKREAIEK--AYVD 326
Cdd:COG0582   341 AGFPPDVIERQLAHKDGNKVRaAYNRADYlEERREMMQWwaDYLD 385
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 151-305 2.38e-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: 50.49  E-value: 2.38e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 151 LNTEAGRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKPYtIKLIGKGN----------KARIVPLMEPTMRIVKKYMEE 220
Cdd:cd01186    11 INACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQ-IELVPREDntnearaksmRERRIPVSQDLIDLYADYLTY 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 221 QNLLRNSANLYplFFNKRKERLTRAGVNYIvEKYKKLAREKNKVLIPevLSCHCLRHSKAMHLLQAGVNLVYIRDILGHC 300
Cdd:cd01186    90 IYCEEAEFSIT--VFVNVKGGNQGKAMNYS-DVYDLVRRLKKRTGID--FTPHMFRHTHATALIRAGWSIEVVARRLGHA 164


                  ....*
gi 1622219690 301 SVQVT 305
Cdd:cd01186   165 HVQTT 169
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 150-308 2.82e-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: 2.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 150 DLNTEAGRRNLALLTLMYDTGARVQEVI-----DLTpsmiRFDKPYTIKLIG--KGN---KARIVPLME----PTMRIVK 215
Cdd:cd00799     9 DDTTLRGLRDRALLLLGFAGALRRSELValrveDLT----RFVDGGLLIRLRrsKTDqdgEGEIKALPYgpetCPVRALR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 216 KYMEEQNLLRNsanlyPLF--FNKR----KERLTRAGVNYIVEKYKKLAreknkVLIPEVLSCHCLRHSKAMHLLQAGVN 289
Cdd:cd00799    85 AWLEAAGIPSG-----PLFrrIRRGgsvgTTRLSDRSVARIVKRRAALA-----GLDPGDFSGHSLRRGFATEAARAGAS 154

                         170
                  ....*....|....*....
gi 1622219690 290 LVYIRDILGHCSVQVTEIY 308
Cdd:cd00799   155 LPEIMAQGGHKSVATVMRY 173
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 156-310 2.39e-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: 2.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 156 GRRNLALLTLMYDTGARVQEVIDLTPSMIRFDKP------YTIKLIGKGNKARIVPLMEPTMRIVKKYmeeqnllrnsan 229
Cdd:cd01187    12 LPQPIPVVQAAVFTGARASELATLKFGCLHAQTSddgtflYWLKWENKGGKQLDIPISKKVAELIKTI------------ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 230 lyplffNKRKERLTRagvnyivekykkLAREKNKVLIPEVLSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTEIYA 309
Cdd:cd01187    80 ------NWTLNELSE------------LKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYA 141


                  .
gi 1622219690 310 K 310
Cdd:cd01187   142 L 142
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
34-107 1.08e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 40.29  E-value: 1.08e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1622219690  34 GASKNTIASYRDTFILFLRFLkDEKGISvehltlnKITKNLVVDYLDWTEDKRQCSPSTRNVRLAALHSFFKYL 107
Cdd:pfam13495  13 GYAERTIKAYLRWIRRFLRFH-DKKHPE-------ELTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWV 78
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 169-310 2.20e-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: 2.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690 169 TGARVQEVIDLTPSMIRFDKPYT---IKLIGKG----NKA--RIVPLMEPTMRI-VKKYMEEqnllRNSANLYPLFFNKR 238
Cdd:cd01184    35 TGARLNEICQLRVDDIKEEDGIWcidINDDAEGrrlkTKAsrRLVPIHPRLIELgFLDYVEA----LRADGKLFLFPEKR 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622219690 239 KERLTRAGvnyiveKY-KKLAREKNKVLIPEV--LSCHCLRHSKAMHLLQAGVNLVYIRDILGHCSVQVTE-IYAK 310
Cdd:cd01184   111 DKDGKYSK------AAsKWFNRLLRKLGIKDDerKSFHSFRHTFITALKRAGVPEELIAQIVGHSRGGVTHdTYGK 180
PTZ00432 PTZ00432
falcilysin; Provisional
 105-270 9.00e-03

falcilysin; Provisional


Pssm-ID: 240416 [Multi-domain]  Cd Length: 1119  Bit Score: 38.24  E-value: 9.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  105 KYLQYENPDNLL-EWQQVLSISVKKTEKKTINYLTLD-GIKLL-LEMPDLNTEAGRRNLALLTLMydtGARVQEVIDltP 181
Cdd:PTZ00432   454 KETNEKRKDKVHyTFEKVVLNALTKVVTEGFNKSAVEaSLNNIeFVMKELNLGTYPKGLMLIFLM---QSRLQYGKD--P 528

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622219690  182 SMI-RFDK-------------PYTIKLIGK---GNKARIVPLMEPTMRivKKYMEEQNllrnsaNLYPLFFNKRKERLTR 244
Cdd:PTZ00432   529 FEIlRFEKllnelklridnesKYLEKLIEKhllNNNHRVTVHLEAVES--SKYEKEFN------KLVKDELKERLSHLTK 600

                          170       180
                   ....*....|....*....|....*.
gi 1622219690  245 AGVNYIVEKYKKLAREKNKVLIPEVL 270
Cdd:PTZ00432   601 EQVDEMEKAYEKFKKEREADDDPEHL 626
 
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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