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Conserved domains on  [gi|223692447|gb|ACN15730|]
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phage-specific recombinase/integrase XerD [Desulforapulum autotrophicum HRM2]

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; ...
 126-311 1.48e-97

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: 286.48  E-value: 1.48e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 206 YLQEHSLDKDWKRDYPLFINKQRNKLTKEGIAYIISQYVGPAKRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFL 285
Cdd:cd01182   81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                        170       180
                 ....*....|....*....|....*.
gi 223692447 286 GHQDVRTTEIYAKCDSELKRQAIANA 311
Cdd:cd01182  161 GHESVETTQIYAEADLEMKREALEKA 186
Phage_int_SAM_1 super family cl12235
Phage integrase, N-terminal SAM-like domain;
10-96 5.17e-07

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: 46.87  E-value: 5.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   10 LTEFLSvYLPRQKNASKNTIASYRDTFKLLLRFcLEQKDIPVEKLNMSMLShviitDFLEWLEEERKCCiATRNQRLAAI 89
Cdd:pfam02899   1 IDQFLE-YLSLERGLSPHTLRAYRRDLLAFLKF-LSEGGSSLEQITTSDVR-----AFLAELRAQGLSA-SSLARRLSAL 72


                  ....*..
gi 223692447   90 HSFFRYA 96
Cdd:pfam02899  73 RSFYQFL 79
 
Name Accession Description Interval E-value
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 126-311 1.48e-97

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: 286.48  E-value: 1.48e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 206 YLQEHSLDKDWKRDYPLFINKQRNKLTKEGIAYIISQYVGPAKRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFL 285
Cdd:cd01182   81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                        170       180
                 ....*....|....*....|....*.
gi 223692447 286 GHQDVRTTEIYAKCDSELKRQAIANA 311
Cdd:cd01182  161 GHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-313 2.84e-76

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 236.04  E-value: 2.84e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   4 TDFATHLTEFLSvYLPRQKNASKNTIASYRDTFKLLLRFCLEQKDIPVEKLNMSMlshviITDFLEWLEEeRKCCIATRN 83
Cdd:COG4974    1 LTLADLLEAFLE-ELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEITPED-----IRAYLNYLRE-RGLSPSTIN 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  84 QRLAAIHSFFRYAQYEepsGILHFQKIIALPIKKAPKPSVPHLTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQ 163
Cdd:COG4974   74 RYLAALRSFFRYAVRE---GLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 164 ELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEHSLDKdwkrDYPLFINKQRNKLTKEGIAYIISQY 243
Cdd:COG4974  151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRD----SDYLFPTRRGRPLSRRAIRKILKRL 226

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 244 vgpAKRmsASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYAKCDSELKRQAIANAYP 313
Cdd:COG4974  227 ---AKR--AGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 12-296 2.44e-57

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: 187.40  E-value: 2.44e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   12 EFLsVYLPRQKNASKNTIASYRDTFKLLLRFcLEQKDIPVEKLNMSMlshviITDFLEWLEEERKCCiATRNQRLAAIHS 91
Cdd:TIGR02225   2 QFL-DYLWVERGLSQNTLEAYRRDLEKFLEF-LEERGIDLEEVDRGD-----IVDFLAELKEAGLSA-RSIARALSALRS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   92 FFRYAQYE-----EPSGILHFQKIialpikKAPKPSVphLTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELI 166
Cdd:TIGR02225  74 FYRFLLREgiredDPSALIEPPKV------ARKLPKV--LTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELV 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  167 DLKIRNVILDNpAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEH---SLDKDWKRDYPLFINKQRNKLTKEGIAYIISQY 243
Cdd:TIGR02225 146 GLRLEDVNLDE-GFVRVRGKGNKERLVPLGEEAIEALERYLKEArplLLKKKVKESDALFLNRRGGPLSRQGVWKILKEY 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 223692447  244 vgpAKRmsASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIY 296
Cdd:TIGR02225 225 ---AKR--AGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-313 4.37e-54

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 179.19  E-value: 4.37e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   1 MKPTDFATHLTEFLSvYLPRQKNASKNTIASYRDTFKLLLRFCLEQKDIPVEKLNmsmlshviITDFLEWLEEERKCCIA 80
Cdd:PRK00236   1 MADADLPAALEAFLE-YLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLD--------AADLRSFLARRRRQGLS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  81 TRN--QRLAAIHSFFRYAQYEEpsgilhfqKIIALPIK--KAPK-----PSVphLTPETMKLLLSQPDKMTAKGRRDITL 151
Cdd:PRK00236  72 ARSlaRRLSALRSFYRWLVRRG--------LLKANPAAglRAPKipkrlPKP--LDVDQAKRLLDAIDEDDPLALRDRAI 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 152 LSVLYDSGCRVQELIDLKIRNVILDNpAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEHSLDKdwKRDYPLFINKQRNKL 231
Cdd:PRK00236 142 LELLYGSGLRLSELVGLDIDDLDLAS-GTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFL--PDDDALFLGARGGRL 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 232 TKEGIAYIISQYvgpakRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYAKCDSELKRQAIANA 311
Cdd:PRK00236 219 SPRVVQRRVKKL-----GKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293


                 ..
gi 223692447 312 YP 313
Cdd:PRK00236 294 HP 295
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 126-298 6.49e-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: 104.32  E-value: 6.49e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  126 LTPETMKLLLSQPDKMTAKgRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLS-IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  206 YLQEHSLDKDwKRDYpLFINKQRNKLTKEGIAYIISQYVGPAKRmsasmPKKVTPHMFRHSKAVHLLQADVNLIYIRDFL 285
Cdd:pfam00589  81 WLSKRLLEAP-KSDY-LFASKRGKPLSRQTVRKIFKRAGKEAGL-----ELPLHPHMLRHSFATHLLEAGVDLRVVQKLL 153

                         170
                  ....*....|...
gi 223692447  286 GHQDVRTTEIYAK 298
Cdd:pfam00589 154 GHSSISTTQIYTH 166
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
10-96 5.17e-07

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 46.87  E-value: 5.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   10 LTEFLSvYLPRQKNASKNTIASYRDTFKLLLRFcLEQKDIPVEKLNMSMLShviitDFLEWLEEERKCCiATRNQRLAAI 89
Cdd:pfam02899   1 IDQFLE-YLSLERGLSPHTLRAYRRDLLAFLKF-LSEGGSSLEQITTSDVR-----AFLAELRAQGLSA-SSLARRLSAL 72


                  ....*..
gi 223692447   90 HSFFRYA 96
Cdd:pfam02899  73 RSFYQFL 79
 
Name Accession Description Interval E-value
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 126-311 1.48e-97

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: 286.48  E-value: 1.48e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 206 YLQEHSLDKDWKRDYPLFINKQRNKLTKEGIAYIISQYVGPAKRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFL 285
Cdd:cd01182   81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                        170       180
                 ....*....|....*....|....*.
gi 223692447 286 GHQDVRTTEIYAKCDSELKRQAIANA 311
Cdd:cd01182  161 GHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-313 2.84e-76

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 236.04  E-value: 2.84e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   4 TDFATHLTEFLSvYLPRQKNASKNTIASYRDTFKLLLRFCLEQKDIPVEKLNMSMlshviITDFLEWLEEeRKCCIATRN 83
Cdd:COG4974    1 LTLADLLEAFLE-ELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEITPED-----IRAYLNYLRE-RGLSPSTIN 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  84 QRLAAIHSFFRYAQYEepsGILHFQKIIALPIKKAPKPSVPHLTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQ 163
Cdd:COG4974   74 RYLAALRSFFRYAVRE---GLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 164 ELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEHSLDKdwkrDYPLFINKQRNKLTKEGIAYIISQY 243
Cdd:COG4974  151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRPRD----SDYLFPTRRGRPLSRRAIRKILKRL 226

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 244 vgpAKRmsASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYAKCDSELKRQAIANAYP 313
Cdd:COG4974  227 ---AKR--AGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 12-296 2.44e-57

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: 187.40  E-value: 2.44e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   12 EFLsVYLPRQKNASKNTIASYRDTFKLLLRFcLEQKDIPVEKLNMSMlshviITDFLEWLEEERKCCiATRNQRLAAIHS 91
Cdd:TIGR02225   2 QFL-DYLWVERGLSQNTLEAYRRDLEKFLEF-LEERGIDLEEVDRGD-----IVDFLAELKEAGLSA-RSIARALSALRS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   92 FFRYAQYE-----EPSGILHFQKIialpikKAPKPSVphLTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELI 166
Cdd:TIGR02225  74 FYRFLLREgiredDPSALIEPPKV------ARKLPKV--LTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELV 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  167 DLKIRNVILDNpAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEH---SLDKDWKRDYPLFINKQRNKLTKEGIAYIISQY 243
Cdd:TIGR02225 146 GLRLEDVNLDE-GFVRVRGKGNKERLVPLGEEAIEALERYLKEArplLLKKKVKESDALFLNRRGGPLSRQGVWKILKEY 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 223692447  244 vgpAKRmsASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIY 296
Cdd:TIGR02225 225 ---AKR--AGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-313 4.37e-54

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 179.19  E-value: 4.37e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   1 MKPTDFATHLTEFLSvYLPRQKNASKNTIASYRDTFKLLLRFCLEQKDIPVEKLNmsmlshviITDFLEWLEEERKCCIA 80
Cdd:PRK00236   1 MADADLPAALEAFLE-YLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSLQDLD--------AADLRSFLARRRRQGLS 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  81 TRN--QRLAAIHSFFRYAQYEEpsgilhfqKIIALPIK--KAPK-----PSVphLTPETMKLLLSQPDKMTAKGRRDITL 151
Cdd:PRK00236  72 ARSlaRRLSALRSFYRWLVRRG--------LLKANPAAglRAPKipkrlPKP--LDVDQAKRLLDAIDEDDPLALRDRAI 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 152 LSVLYDSGCRVQELIDLKIRNVILDNpAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEHSLDKdwKRDYPLFINKQRNKL 231
Cdd:PRK00236 142 LELLYGSGLRLSELVGLDIDDLDLAS-GTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFL--PDDDALFLGARGGRL 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 232 TKEGIAYIISQYvgpakRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYAKCDSELKRQAIANA 311
Cdd:PRK00236 219 SPRVVQRRVKKL-----GKKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293


                 ..
gi 223692447 312 YP 313
Cdd:PRK00236 294 HP 295
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 11-313 5.10e-54

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: 178.96  E-value: 5.10e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   11 TEFLSvYLPRQKNASKNTIASYRDTFKLLLRFCLEQKDIpveklnmSMLSHVIITDFLEWLEEERKCCIATR--NQRLAA 88
Cdd:TIGR02224   1 EAFLE-YLRLERNYSPHTVRAYRRDLEAFLEFLEEEGGL-------ASLAEVTAADLRSFLAELHARGLSRRslARKLSA 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   89 IHSFFRYAQYEEPSGILHFQKIIAlpiKKAPKPsVPH-LTPETMKLLLSQPDKMTAK--GRRDITLLSVLYDSGCRVQEL 165
Cdd:TIGR02224  73 LRSFYRFLLRRGLIDANPAAGVRA---PKQPKK-LPKfLSEDEMEALLDAPEEDDEDwlALRDRAILELLYSSGLRVSEL 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  166 IDLKIRNVILDnPAVLILTGKGNKIRRVPLMRNTLVLLQNYLQE--HSLDKDWKRDyPLFINKQRNKLTKEGIAYIISQY 243
Cdd:TIGR02224 149 VGLDLSDLDLD-FGEVRVRGKGNKERIVPFGPYARDALQAYLEArrSPLLASEGQD-ALFLNRRGGRLTPRGVQYRLQQL 226

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  244 VGpakrmSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYAKCDSELKRQAIANAYP 313
Cdd:TIGR02224 227 RA-----KAGLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHP 291
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
10-312 3.60e-45

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 155.50  E-value: 3.60e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  10 LTEFLSVYLP--RQKNASKNTIASYRDTFKLLLRFClEQKDIPVEKLnmsmlSHVIITDFLEWLEEeRKCCIATRNQRLA 87
Cdd:COG4973    4 LAEALEAYLEhlRERRLSPKTLEAYRRDLRRLIPLL-GDADLPLEEL-----TPADVRRFLARLHR-RGLSPRTLNRRLS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  88 AIHSFFRYAQYEepsGILH---FQKIIALpikKAPKPSVPHLTPETMKLLLSQPDKmTAKGRRDITLLSVLYDSGCRVQE 164
Cdd:COG4973   77 ALRSFFNWAVRE---GLLEanpAAGVKAP---KAPRKLPRALTVDELAQLLDALAD-DPLAVRDRAIVELLYSTGLRLGE 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 165 LIDLKIRNVILDNPAVLIlTGKGNKIRRVPLMRNTLVLLQNYLqEHSLDKDWKRDYPLFINKQRNKLTKEGIAYIISQYv 244
Cdd:COG4973  150 LVGLDWEDVDLDAGEVRV-RGKTGKSRTVPLGPKALAALREWL-AVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRL- 226

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 223692447 245 gpAKRmsASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYAKCDselkRQAIANAY 312
Cdd:COG4973  227 --AKK--AGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLD----FQHLAEVY 286
xerD PRK00283
tyrosine recombinase;
11-296 1.72e-42

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 148.80  E-value: 1.72e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  11 TEFLSVylprQKNASKNTIASYRDTFKLLLRFcleqkdIPVEKLNMSMLSHVIITDFLEWLEEeRKCCIATRNQRLAAIH 90
Cdd:PRK00283  13 LDALWV----ERGLAENTLSSYRRDLELFAEW------LAARGLSLAEATRDDLQAFLAELAE-GGYKATSSARRLSALR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  91 SFFRYAqYEE------PSGIlhfqkiIALPIKKAPKPSVphLTPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQE 164
Cdd:PRK00283  82 RFFQFL-LREglreddPSAL------LDSPKLPRRLPKT--LSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 165 LIDLKIRNVILdNPAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEH--SLDKDWKRDYpLFINKQRNKLTKEGIAYIISQ 242
Cdd:PRK00283 153 LVGLTLDDVSL-RQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGrpALLNGRSSDA-LFPSARGGQLTRQTFWHRIKH 230

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 223692447 243 YvgpAKRmSASMPKKVTPHMFRHSKAVHLLQ--ADVNLiyIRDFLGHQDVRTTEIY 296
Cdd:PRK00283 231 Y---AKR-AGIDPKKLSPHVLRHAFATHLLNhgADLRV--VQELLGHSDISTTQIY 280
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 129-296 7.88e-42

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: 143.42  E-value: 7.88e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 129 ETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPaVLILTGKGNKIRRVPLMRNTLVLLQNYLQ 208
Cdd:cd00798    2 DEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEG-LVRVTGKGNKERLVPFGSYAVEALEEYLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 209 E--HSLDKDWKRDYpLFINKQRNKLTKEGIAYIISQYVgpakrMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLG 286
Cdd:cd00798   81 ErrPLLLKKKPPDA-LFLNKRGKRLSRRGVWRILKKYA-----ERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLG 154

                        170
                 ....*....|
gi 223692447 287 HQDVRTTEIY 296
Cdd:cd00798  155 HASLSTTQIY 164
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 132-297 1.17e-31

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: 116.81  E-value: 1.17e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 132 KLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGK--GNKIRRVPLMRNTLVLLQNYLQE 209
Cdd:cd00397    3 EKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkGGKERTVPLPKELAEELKEYLKE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 210 HSLDKDWKRDYPLFINKQRNKLTKEGIAYIISQYVgpaKRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQD 289
Cdd:cd00397   83 RRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIF---KKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSS 159


                 ....*...
gi 223692447 290 VRTTEIYA 297
Cdd:cd00397  160 ISTTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 126-298 6.49e-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: 104.32  E-value: 6.49e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  126 LTPETMKLLLSQPDKMTAKgRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:pfam00589   2 LTEDEVERLLDAAETGPLS-IRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  206 YLQEHSLDKDwKRDYpLFINKQRNKLTKEGIAYIISQYVGPAKRmsasmPKKVTPHMFRHSKAVHLLQADVNLIYIRDFL 285
Cdd:pfam00589  81 WLSKRLLEAP-KSDY-LFASKRGKPLSRQTVRKIFKRAGKEAGL-----ELPLHPHMLRHSFATHLLEAGVDLRVVQKLL 153

                         170
                  ....*....|...
gi 223692447  286 GHQDVRTTEIYAK 298
Cdd:pfam00589 154 GHSSISTTQIYTH 166
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 126-296 4.53e-26

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: 101.97  E-value: 4.53e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSqpdkmTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:cd01193    6 LSPDEVRRILG-----ALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 206 YLQEHslDKDWKRD---------YPLFINKQRNKLTKEGIAYIISQYVgpakrMSASMPKKVTPHMFRHSKAVHLLQADV 276
Cdd:cd01193   81 YLKSA--RPKEELDpaegragvlDPRTGVERRHHISETTVQRALKKAV-----EQAGITKRVTPHTLRHSFATHLLEAGT 153

                        170       180
                 ....*....|....*....|
gi 223692447 277 NLIYIRDFLGHQDVRTTEIY 296
Cdd:cd01193  154 DIRTIQELLGHSDLSTTMIY 173
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 20-296 1.28e-23

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: 99.00  E-value: 1.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   20 RQKNASKNTIASYRDTFKLLLRFcleqkdipVEKLNMSMLSHVIITDFLEWLEEERKCCIATRNQRLAAIHSFFRYAQYE 99
Cdd:TIGR02249  10 RTRHYAKRTEEAYLHWIKRFIRF--------HNKRHPSTMGDTEVEAFLSDLAVDGKVAASTQNQALNALLFLYKEILKT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  100 EPSGILHFQKiiALPIKKAPKPsvphLTPETMKLLLSQPDKmtakgrRDITLLSVLYDSGCRVQELIDLKIRNVILDNPA 179
Cdd:TIGR02249  82 PLSLMERFVR--AKRPRKLPVV----LTREEVRRLLEHLEG------KYRLIAKLLYGSGMRLMECLRLRIQDIDFDYGE 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  180 VLILTGKGNKIRRVPLMRNTLVLLQNYLQ------EHSLDKDW---------KRDYP----------LF------INKQR 228
Cdd:TIGR02249 150 IRIRQGKGGKDRTVTLPKELIPPLREQIElarayhEADLAEGYggvylphalARKYPnapkewgwqyLFpshrlsRDPES 229

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 223692447  229 NKLTKEGIAYIISQYVGPAKRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIY 296
Cdd:TIGR02249 230 GVIRRHHINETTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIY 297
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 10-296 3.37e-22

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 95.58  E-value: 3.37e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  10 LTEFLSVYLP--RQKNASKNTIASYRDTFKLLLRFClEQKDIpvekLNMSMLSHVIITDFLEWLEEERKC---CIATRNQ 84
Cdd:PRK01287  21 LRQLLERFLAwlQERNWSERTLKVYTEHLYPFILWC-EERGL----YYAADVTLPVLERYQRYLYGYRKAngePLSTRTQ 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  85 --RLAAIHSFFRYaqyeepsgILHFQKIIALP-----IKKAPKpSVPH--LTPETMKLLLSQPDKMTAKGRRDITLLSVL 155
Cdd:PRK01287  96 rtQLSPLRVWFRW--------LLKRHHILYNPaedleLPKEEK-RLPRqiLSEAETEQVLASPDLTTLQGLRDRALLELL 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 156 YDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEHSLDKDWKRDYP-LFINKQRNKLTKE 234
Cdd:PRK01287 167 WSTGIRRGELARLDLYDVDASRGVVTVRQGKGNKDRVVPVGERALAWLQRYLQDVRPQLAVRPDSGaLFVAMDGDGLARN 246

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 223692447 235 GiayiISQYVGPAKRMSAsMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIY 296
Cdd:PRK01287 247 T----LTNMVGRYIRAAG-IEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 127-306 5.01e-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: 88.45  E-value: 5.01e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 127 TPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQNY 206
Cdd:cd01188    1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEPVGEALADY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 207 LQehslDKDWKRDYP-LFINKQR--NKLTKE-GIAYIISQYVgpakRMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIR 282
Cdd:cd01188   81 LR----DGRPRTDSReVFLRARApyRPLSSTsQISSIVRRYL----RKAGIEPSHRGTHSLRHSLATRMLRAGTSLKVIA 152

                        170       180
                 ....*....|....*....|....
gi 223692447 283 DFLGHQDVRTTEIYAKCDSELKRQ 306
Cdd:cd01188  153 DLLGHRSIETTAIYAKIDVDDLRE 176
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 126-297 1.54e-19

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


Pssm-ID: 271194 [Multi-domain]  Cd Length: 174  Bit Score: 84.35  E-value: 1.54e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSQ-PDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIR--NVILDNpAVLILTGKG--NKIRRVPLMRNTL 200
Cdd:cd01194    1 LTLEQARQLLASlPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGdlRQEGEG-TILYVQGKGktSKDDFVYLRPDVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 201 VLLQNYLQEHSLDKDwkrDYPLFI----NKQRNKLTKEGIAYIISQYVgpakRMSASMPKKVTPHMFRHSKAVHLLQADV 276
Cdd:cd01194   80 KALQAYLKARGKLDF---EEPLFTslsnNSKGQRLTTRSIRRIIKKYL----RKAGLDDDRLTAHSLRHTAGTLALKAGK 152

                        170       180
                 ....*....|....*....|.
gi 223692447 277 NLIYIRDFLGHQDVRTTEIYA 297
Cdd:cd01194  153 SLREVQQLLRHSDPNTTMIYA 173
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 147-308 6.63e-18

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 83.43  E-value: 6.63e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 147 RDITLLSVLYDSGCRVQELIDLKIRNVILDNpAVLILTGKGNKIRRVPLMRNTLVLLQNYLQehsldkdwkrdyplfINK 226
Cdd:PRK05084 196 RDLAIIALILGSGLRVSELVNLDLSDLNLKQ-MTIDVTRKGGKRDSVNIAPFALPYLEEYLK---------------IRA 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 227 QRNKLTKEGIAYIISQYVGPAKRMSAS----MPKK--------VTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTE 294
Cdd:PRK05084 260 SRYKAEKQEKALFLTKYRGKPNRISARaiekMVAKyseafgvrLTPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTD 339

                        170
                 ....*....|....
gi 223692447 295 IYAKCDSELKRQAI 308
Cdd:PRK05084 340 LYTHIVNDEQKEAL 353
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 150-307 2.78e-15

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: 73.11  E-value: 2.78e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 150 TLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEHSLDKDWKRDYPLFINKQRN 229
Cdd:cd00797   29 TLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSYFFVSQQGG 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 230 KLTKEGIAYIISQYVGPAKRMSASMPKKVTPHMFRHSKAVHLLQA--------DVNLIYIRDFLGHQDVRTTEIYAKCDS 301
Cdd:cd00797  109 RLTGGGVYRVFRRLLRRIGLRGAGDGRGPRLHDLRHTFAVNRLTRwyregadvERKLPVLSTYLGHVNVTDTYWYLTATP 188


                 ....*.
gi 223692447 302 ELKRQA 307
Cdd:cd00797  189 ELMELA 194
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 126-297 2.81e-15

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: 72.36  E-value: 2.81e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSQPDKMTAKGRRDITLLsvLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:cd00796    5 LTEDEEARLLAALEESTNPHLRLIVLL--ALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAILKE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 206 YLQEHSLDKDWKrdyplfinkqrnkltkEGIAYIIsQYVGPAKRMSASMPK----KVTPHMFRHSKAVHLLQADVNLIYI 281
Cdd:cd00796   83 LKRKRGKDGFFV----------------DGRFFGI-PIASLRRAFKKARKRagleDLRFHDLRHTFASRLVQAGVPIKTV 145

                        170
                 ....*....|....*.
gi 223692447 282 RDFLGHQDVRTTEIYA 297
Cdd:cd00796  146 AKILGHSSIKMTMRYA 161
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 127-296 3.20e-14

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: 69.81  E-value: 3.20e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 127 TPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNpAVLILTGKGNKIR-RVPLMRNTLVLLQN 205
Cdd:cd01195    1 SREEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEH-RRLRILGKGKKQReVVTLPPTTREALAA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 206 YLQEHSldkdwKRDYPLFINKQRN----KLTKEGIAYII---SQYVGPAKRMSasmpkkvtPHMFRHSKAVHLLQADVNL 278
Cdd:cd01195   80 WLAARG-----EAEGPLFVSLDRAsrgrRLSPQAVYRIVrrlAERIGLGKRLS--------PHGLRHSAITLALDAGAGL 146

                        170
                 ....*....|....*....
gi 223692447 279 IY-IRDFLGHQDVRTTEIY 296
Cdd:cd01195  147 IRkVQDFSRHADLRTLQVY 165
PRK15417 PRK15417
integron integrase;
67-298 3.55e-12

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 66.22  E-value: 3.55e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  67 FLEWLEEERKCCIATRNQRLAAIHSFFRYAQYEEpsgiLHFQKIIALPIKKAPKPSVphLTP-ETMKLL--LSQPDKMTA 143
Cdd:PRK15417  64 FLSWLANERKVSVSTHRQALAALLFFYGKVLCTD----LPWLQEIGRPRPSRRLPVV--LTPdEVVRILgfLEGEHRLFA 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 144 KgrrditllsVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRV-------PLMRNTLVLLQNY-LQEHS---- 211
Cdd:PRK15417 138 Q---------LLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALmlpeslaPSLREQLSRARAWwLKDQAegrs 208

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 212 ---LDKDWKRDYP----------LFINKQRNKLTKEGIAYIISQYVGPAKRM------SASMPKKVTPHMFRHSKAVHLL 272
Cdd:PRK15417 209 gvaLPDALERKYPraghswpwfwVFAQHTHSTDPRSGVVRRHHMYDQTFQRAfkraveQAGITKPATPHTLRHSFATALL 288

                        250       260
                 ....*....|....*....|....*.
gi 223692447 273 QADVNLIYIRDFLGHQDVRTTEIYAK 298
Cdd:PRK15417 289 RSGYDIRTVQDLLGHSDVSTTMIYTH 314
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 147-304 6.07e-12

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: 63.05  E-value: 6.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 147 RDITLLSVLydSGCRVQELIDLKIRNVILDNPAVLIL--TGKGNKIRRVPLMRNTLVLLQNYlqehsldKDWKRDYPLFI 224
Cdd:cd01185   21 RDMFLFSCY--TGLRFSDLKNLTWKNIVEASGRTWIRyrRKKTGKPVTVPLLPVAREILEKY-------KDDRSEGKLFP 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 225 NKQR---NKLTKEgIAYIisqyvgpakrmsASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYAKCDS 301
Cdd:cd01185   92 VLSNqkiNRYLKE-IAKI------------AGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVD 158


                 ...
gi 223692447 302 ELK 304
Cdd:cd01185  159 SKK 161
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 125-302 7.57e-12

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: 63.30  E-value: 7.57e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 125 HLTPETMKLLLSQPdKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQ 204
Cdd:cd01197    6 YLTGKEVQALLQAA-CRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDEREALE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 205 NYLQEHS----LDKDWkrdypLFINKQRNKLTKEGIAYIISQYvgpakRMSASMPKKVTPHMFRHSKAVHLLQADVNLIY 280
Cdd:cd01197   85 AWLKERAnwkgADTDW-----IFLSRRGGPLSRQQAYRIIRDL-----GKEAGTVTQTHPHMLRHACGYALADRGADTRL 154

                        170       180
                 ....*....|....*....|..
gi 223692447 281 IRDFLGHQDVRTTEIYAKCDSE 302
Cdd:cd01197  155 IQDYLGHRNIRHTVIYTASNAA 176
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 126-293 1.21e-11

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: 62.82  E-value: 1.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSqpdkmTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLIL---------TGKGNKIRRVPLM 196
Cdd:cd01186    2 LTPREVQELIN-----ACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVpredntneaRAKSMRERRIPVS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 197 RNTLVLLQNYLQEhSLDKDWKRDYPLFIN-KQRNKLTKEGIAYIISQyvgpAKRMSASMPKKVTPHMFRHSKAVHLLQAD 275
Cdd:cd01186   77 QDLIDLYADYLTY-IYCEEAEFSITVFVNvKGGNQGKAMNYSDVYDL----VRRLKKRTGIDFTPHMFRHTHATALIRAG 151

                        170
                 ....*....|....*...
gi 223692447 276 VNLIYIRDFLGHQDVRTT 293
Cdd:cd01186  152 WSIEVVARRLGHAHVQTT 169
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 158-323 1.17e-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: 271191  Cd Length: 176  Bit Score: 59.75  E-value: 1.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 158 SGCRVQELIDLKIRNVILdnpAVLILTGKGNKIRRVPLMRNtlvlLQNYLQEHsLDKDWKRDYPLFINKQRNKLTKEGIA 237
Cdd:cd01191   32 TGARVSELIKIKVEHVEL---GYFDIYSKGGKLRRLYIPKK----LRNEALEW-LKSTNRKSGYIFLNRFGERITTRGIA 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 238 YIISQYvgpAKRMSASmPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYakcdseLKRQAIANAypDIVD 317
Cdd:cd01191  104 QQLKNY---ARKYGLN-PKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY------LRKTASEQQ--EIVD 171


                 ....*.
gi 223692447 318 nNLPDW 323
Cdd:cd01191  172 -KIVTW 176
PRK09870 PRK09870
tyrosine recombinase; Provisional
 126-296 1.66e-09

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 56.87  E-value: 1.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 126 LTPETMKLLLSQPDKMTAKGR-RDITLLSVLYdsGCRVQELIDLKIRNVILDNPAVLILTGKGNKIRRVPLMRNTLVLLQ 204
Cdd:PRK09870  13 LTHSEIESLLKAANTGPHAARnYCLTLLCFIH--GFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEIQALK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 205 NYLQ-----EHSlDKDWkrdypLFINKQRNKLTKEGIAYIISQYVGPAKrmsasMPKKVTPHMFRHSKAVHLLQADVNLI 279
Cdd:PRK09870  91 NWLSirtsyPHA-ESEW-----VFLSRKGNPLSRQQFYHIISTSGGNAG-----LSLEIHPHMLRHSCGFALANMGIDTR 159

                        170
                 ....*....|....*..
gi 223692447 280 YIRDFLGHQDVRTTEIY 296
Cdd:PRK09870 160 LIQDYLGHRNIRHTVWY 176
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 128-298 2.21e-09

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: 55.26  E-value: 2.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 128 PETMKLLLSQPDKmtaKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLI---LTGKGNK------------IRR 192
Cdd:cd01189    1 PEELKKLLEALKK---RGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRInrtLVRKKKGgyvikppktkssIRT 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 193 VPLmrnTLVLLQnYLQEHsldKDWKRDyplfinkqrnkLTKEGIAYIisqyvgpakrmsasmpkkvTPHMFRHSKAVHLL 272
Cdd:cd01189   78 IPL---PDELIE-LLKEL---KAFKKL-----------LKKAGLPRI-------------------TPHDLRHTFASLLL 120

                        170       180
                 ....*....|....*....|....*..
gi 223692447 273 QADVNLIYIRDFLGHQDVRTT-EIYAK 298
Cdd:cd01189  121 EAGVPLKVIAERLGHSDISTTlDVYAH 147
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 66-319 3.81e-09

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 57.36  E-value: 3.81e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  66 DFLEWLEE-ERKCCIATRNQRLAAIHSFFRYAqyeEPSGILHFQKIIALP--IKKAPKPSVPHLTPETMKLLLSQPDKMT 142
Cdd:COG0582  146 DLLAVLRPiEARGAPETARRVRQRLRQVFRYA---VARGLIERNPAADLKgaLPKPKVKHHPALTPEELPELLRALDAYR 222

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 143 AKGR-RDITLLSVLydSGCRVQELIDLKIRNVILDNpAVLILTG---KGNKIRRVPLMRNTLVLLQNyLQEHSLDKDWkr 218
Cdd:COG0582  223 GSPVtRLALRLLLL--TGVRPGELRGARWSEIDLEA-ALWTIPAermKTRRPHIVPLSRQALEILKE-LKPLTGDSEY-- 296

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 219 dypLFINKQRNK--LTKEGIAYIIsqyvgpaKRMSAsmpKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTE-I 295
Cdd:COG0582  297 ---VFPSRRGPKkpMSENTLNKAL-------RRMGY---GRFTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVRaA 363

                        250       260
                 ....*....|....*....|....
gi 223692447 296 YAKCDSELKRQAIANAYPDIVDNN 319
Cdd:COG0582  364 YNRADYLEERREMMQWWADYLDAL 387
PRK09871 PRK09871
tyrosine recombinase; Provisional
 143-296 8.29e-09

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 54.60  E-value: 8.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 143 AKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNpavliltGKGNkIRRV--------PLMRNTLVLLQNYLQEHSLDK 214
Cdd:PRK09871  23 ATGARDYCLILLAYRHGMRISELLDLHYQDLDLNE-------GRIN-IRRLkngfstvhPLRFDEREAVERWTQERANWK 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 215 DWKRDYPLFINKQRNKLTKEGiAYIISQYVGpakrMSASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTE 294
Cdd:PRK09871  95 GADRTDAIFISRRGSRLSRQQ-AYRIIRDAG----IEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTV 169


                 ..
gi 223692447 295 IY 296
Cdd:PRK09871 170 RY 171
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 127-308 9.43e-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: 54.41  E-value: 9.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 127 TPETMKLLLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLI-LTGKGNKIRRVPLMRNTLVLLQN 205
Cdd:cd01196    1 TAPEARRLLESIDSTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVrLAEKGGKQHEMPCHHDLEEYLRA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 206 YLQEHSLDKDwkRDYPLF--INKQRNKLTKEGIAYiisqyvGPAKRM------SASMPKKVTPHMFRHSKAVHLLQADVN 277
Cdd:cd01196   81 YLEAAEIEED--PKGPLFrtTRGGTRKLTHNPLTQ------ANAYRMvrrraiAADIPTAIGNHSFRATGITAYLKNGGT 152

                        170       180       190
                 ....*....|....*....|....*....|.
gi 223692447 278 LIYIRDFLGHQDVRTTEIYAKCDSELKRQAI 308
Cdd:cd01196  153 LEDAQNMANHASTRTTQLYDRRSDKITLDEV 183
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
10-96 5.17e-07

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 46.87  E-value: 5.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   10 LTEFLSvYLPRQKNASKNTIASYRDTFKLLLRFcLEQKDIPVEKLNMSMLShviitDFLEWLEEERKCCiATRNQRLAAI 89
Cdd:pfam02899   1 IDQFLE-YLSLERGLSPHTLRAYRRDLLAFLKF-LSEGGSSLEQITTSDVR-----AFLAELRAQGLSA-SSLARRLSAL 72


                  ....*..
gi 223692447   90 HSFFRYA 96
Cdd:pfam02899  73 RSFYQFL 79
int PHA02601
integrase; Provisional
 28-297 4.53e-06

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 47.80  E-value: 4.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447  28 TIASYRDTFKLLLRFCLEQKDIPVEKLNMSMLSHVIITDFLEWLEEERKCCI--ATRNQRLAAIHSFF-RYAQYEEPSGI 104
Cdd:PHA02601  75 TLEDGKARLAKLLILCKGLGDPIASEFTAKDFADYRARRLSGEFKVNKGRPIkpATVNRELAYLSAVFnELIKLGKWSGP 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 105 lhfQKIIALPIKKAPKPSVPHLTPETMKLLLsqpDKMTAKGRRDITLLSVL-YDSGCRVQELIDLKIRNVIldNPAVLIL 183
Cdd:PHA02601 155 ---NPLDGIRPFKEAEPELAFLTKEEIERLL---DACDGSRSPDLGLIAKIcLATGARWSEAETLKRSQIS--PYKITFV 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 184 TGKGNKIRRVPLMRNTLVLLQNylqehSLDKDWKRDYPLFinkqRNKLTKEGIayiisqyvgpakrmsaSMPKKVTPHMF 263
Cdd:PHA02601 227 KTKGKKNRTVPISEELYKMLPK-----RRGRLFKDAYESF----ERAVKRAGI----------------DLPEGQATHVL 281

                        250       260       270
                 ....*....|....*....|....*....|....
gi 223692447 264 RHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIYA 297
Cdd:PHA02601 282 RHTFASHFMMNGGNILVLQRILGHATIEMTMAYA 315
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 20-96 7.72e-06

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


Pssm-ID: 463787 [Multi-domain]  Cd Length: 99  Bit Score: 44.13  E-value: 7.72e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 223692447   20 RQKNASKNTIASYRDTFKLLLRFClEQKDIPVEKLNMSMlshviITDFLEWLEEERKCCIATRNQRLAAIHSFFRYA 96
Cdd:pfam13102  13 LKKKGSKGTARNYKSTLKHLKKFL-KKKDITFEEITVDF-----LEKFEEYLKKKKGLSENTISKYFRTLRAVLNKA 83
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 134-296 9.60e-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: 45.75  E-value: 9.60e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 134 LLSQPDKMTAKGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNPAVLILT---------GKGnKIRRVPLMRNTLVL-- 202
Cdd:cd00799    4 MLATLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLIRlrrsktdqdGEG-EIKALPYGPETCPVra 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 203 LQNYLqEHSLDKDWkrdyPLF--INKQRNK----LTKEGIAYIISQYVGPAkrmsASMPKKVTPHMFRHSKAVHLLQADV 276
Cdd:cd00799   83 LRAWL-EAAGIPSG----PLFrrIRRGGSVgttrLSDRSVARIVKRRAALA----GLDPGDFSGHSLRRGFATEAARAGA 153

                        170       180
                 ....*....|....*....|
gi 223692447 277 NLIYIRDFLGHQDVRTTEIY 296
Cdd:cd00799  154 SLPEIMAQGGHKSVATVMRY 173
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
20-100 2.95e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 39.13  E-value: 2.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447   20 RQKNASKNTIASYRDTFKLLLRFCleQKDIPVEklnmsmLSHVIITDFLEWLEEERKCCIATRNQRLAAIHSFFRYAQYE 99
Cdd:pfam13495  10 RLRGYAERTIKAYLRWIRRFLRFH--DKKHPEE------LTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWVLER 81


                  .
gi 223692447  100 E 100
Cdd:pfam13495  82 E 82
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 144-296 3.29e-03

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: 38.04  E-value: 3.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223692447 144 KGRRDITLLSVLYDSGCRVQELIDLKIRNVILDNpAVLILTGKGNKIRRVPLMRNTLVLLQNYLQEHSLDKDWkrDYPLF 223
Cdd:cd01192   22 ANPRNYLLFIVGINTGLRISDLLSLKVEDVTNKD-KLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLKRND--YLFKS 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 223692447 224 INKQRNKLTKEGIAYIISQYVGPAkrmsASMPKKVTPHMFRHSKAVHLLQADVNLIYIRDFLGHQDVRTTEIY 296
Cdd:cd01192   99 LKQGPEKPISRKQAYKILKKAADD----LGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
 
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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