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Conserved domains on  [gi|1774956731|dbj|BBO91002|]
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integrase [Desulfosarcina ovata subsp. ovata]

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

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 1.45e-94

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


:

Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 278.78  E-value: 1.45e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQH 205
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 206 YLQEHSLDKDWKKDYPLFVNKHRSKLTKEGIAYIISQYVVSAKKISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFL 285
Cdd:cd01182    81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                         170       180
                  ....*....|....*....|....*.
gi 1774956731 286 GHEDIKTTEIYAKCDTELKRQAIENA 311
Cdd:cd01182   161 GHESVETTQIYAEADLEMKREALEKA 186
Phage_int_SAM_1 super family cl12235
Phage integrase, N-terminal SAM-like domain;
10-96 1.95e-09

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: 53.80  E-value: 1.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  10 LTGFLSvYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPAEklnmgmLTHVMIADFLEWLEKKRKcSTATRNQRLAAI 89
Cdd:pfam02899   1 IDQFLE-YLSLERGLSPHTLRAYRRDLLAFLKFLSEGGSSLEQ------ITTSDVRAFLAELRAQGL-SASSLARRLSAL 72


                  ....*..
gi 1774956731  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 1.45e-94

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 278.78  E-value: 1.45e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQH 205
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 206 YLQEHSLDKDWKKDYPLFVNKHRSKLTKEGIAYIISQYVVSAKKISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFL 285
Cdd:cd01182    81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                         170       180
                  ....*....|....*....|....*.
gi 1774956731 286 GHEDIKTTEIYAKCDTELKRQAIENA 311
Cdd:cd01182   161 GHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-313 3.35e-78

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 241.05  E-value: 3.35e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731   4 TDFATHLTGFLSvYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPAEKLnmgmlTHVMIADFLEWLeKKRKCSTATRN 83
Cdd:COG4974     1 LTLADLLEAFLE-ELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEI-----TPEDIRAYLNYL-RERGLSPSTIN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  84 QRLAAIHSFFRYAQYEepsGILHFQKVIAIPVKKASKPSAPHLTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQ 163
Cdd:COG4974    74 RYLAALRSFFRYAVRE---GLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 164 ELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLdkdwKKDYPLFVNKHRSKLTKEGIAYIISQY 243
Cdd:COG4974   151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRP----RDSDYLFPTRRGRPLSRRAIRKILKRL 226

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 244 vvsAKKisASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCDTELKRQAIENAYP 313
Cdd:COG4974   227 ---AKR--AGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 17-313 3.32e-58

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: 189.74  E-value: 3.32e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  17 YLPRQKNASNNTIASYRDTFKLLLRYCQEEkdipAEKLNMGMLTHVMIADFLEWLeKKRKCSTATRNQRLAAIHSFFRYA 96
Cdd:TIGR02224   6 YLRLERNYSPHTVRAYRRDLEAFLEFLEEE----GGLASLAEVTAADLRSFLAEL-HARGLSRRSLARKLSALRSFYRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  97 QYEepsGILHFQKVIAIPVKKASKPSAPHLTPEAMKFLLSQPDKMTVK--GRRNLTLLSVLYDSGCRVQELADLRVRDVV 174
Cdd:TIGR02224  81 LRR---GLIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDEDwlALRDRAILELLYSSGLRVSELVGLDLSDLD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 175 VDnPALLILTGKGNKMRRVPLMKNTLTLLQHYLQE--HSLDKDWKKDyPLFVNKHRSKLTKEGIAYIISQYVvsakkISA 252
Cdd:TIGR02224 158 LD-FGEVRVRGKGNKERIVPFGPYARDALQAYLEArrSPLLASEGQD-ALFLNRRGGRLTPRGVQYRLQQLR-----AKA 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1774956731 253 SMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCDTELKRQAIENAYP 313
Cdd:TIGR02224 231 GLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHP 291
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-313 6.22e-55

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 181.12  E-value: 6.22e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731   1 MKPTDFATHLTGFLSvYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPaeklnmgmLTHVMIADFLEWLEKKRK--CS 78
Cdd:PRK00236    1 MADADLPAALEAFLE-YLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISS--------LQDLDAADLRSFLARRRRqgLS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  79 TATRNQRLAAIHSFFRYaqyeepsgiLHFQKVIAI-PVKKASKPSAPH-----LTPEAMKFLLSQPDKMTVKGRRNLTLL 152
Cdd:PRK00236   72 ARSLARRLSALRSFYRW---------LVRRGLLKAnPAAGLRAPKIPKrlpkpLDVDQAKRLLDAIDEDDPLALRDRAIL 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 153 SVLYDSGCRVQELADLRVRDVvvDNPA-LLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLDKdwKKDYPLFVNKHRSKL 231
Cdd:PRK00236  143 ELLYGSGLRLSELVGLDIDDL--DLASgTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFL--PDDDALFLGARGGRL 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 232 TKEGIAYIISQYVvsakkISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCDTELKRQAIENA 311
Cdd:PRK00236  219 SPRVVQRRVKKLG-----KKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293


                  ..
gi 1774956731 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 ...
 128-298 5.37e-29

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: 109.72  E-value: 5.37e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 128 PEAMKFLLSQPDKMtvkgrRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYL 207
Cdd:pfam00589   8 ERLLDAAETGPLSI-----RDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKEWL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 208 QEHSLDKDwKKDYpLFVNKHRSKLTKEGIAYIISQYVvsakkISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGH 287
Cdd:pfam00589  83 SKRLLEAP-KSDY-LFASKRGKPLSRQTVRKIFKRAG-----KEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGH 155

                         170
                  ....*....|.
gi 1774956731 288 EDIKTTEIYAK 298
Cdd:pfam00589 156 SSISTTQIYTH 166
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
10-96 1.95e-09

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 53.80  E-value: 1.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  10 LTGFLSvYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPAEklnmgmLTHVMIADFLEWLEKKRKcSTATRNQRLAAI 89
Cdd:pfam02899   1 IDQFLE-YLSLERGLSPHTLRAYRRDLLAFLKFLSEGGSSLEQ------ITTSDVRAFLAELRAQGL-SASSLARRLSAL 72


                  ....*..
gi 1774956731  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 1.45e-94

C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism.


Pssm-ID: 271183 [Multi-domain]  Cd Length: 186  Bit Score: 278.78  E-value: 1.45e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQH 205
Cdd:cd01182     1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPATVRLHGKGRKERTVPLWKETVAALKA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 206 YLQEHSLDKDWKKDYPLFVNKHRSKLTKEGIAYIISQYVVSAKKISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFL 285
Cdd:cd01182    81 YLQEFHLTPDPKQLFPLFPNRRGQPLTRDGVAYILNKYVALASNRCPSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDWL 160

                         170       180
                  ....*....|....*....|....*.
gi 1774956731 286 GHEDIKTTEIYAKCDTELKRQAIENA 311
Cdd:cd01182   161 GHESVETTQIYAEADLEMKREALEKA 186
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
4-313 3.35e-78

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 241.05  E-value: 3.35e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731   4 TDFATHLTGFLSvYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPAEKLnmgmlTHVMIADFLEWLeKKRKCSTATRN 83
Cdd:COG4974     1 LTLADLLEAFLE-ELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPLAEI-----TPEDIRAYLNYL-RERGLSPSTIN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  84 QRLAAIHSFFRYAQYEepsGILHFQKVIAIPVKKASKPSAPHLTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQ 163
Cdd:COG4974    74 RYLAALRSFFRYAVRE---GLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVS 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 164 ELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLdkdwKKDYPLFVNKHRSKLTKEGIAYIISQY 243
Cdd:COG4974   151 ELLGLKWSDIDLDRGTIRVRRGKGGKERTVPLSPEALEALREYLEERRP----RDSDYLFPTRRGRPLSRRAIRKILKRL 226

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 244 vvsAKKisASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCDTELKRQAIENAYP 313
Cdd:COG4974   227 ---AKR--AGIPKRVTPHSLRHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 17-313 3.32e-58

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: 189.74  E-value: 3.32e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  17 YLPRQKNASNNTIASYRDTFKLLLRYCQEEkdipAEKLNMGMLTHVMIADFLEWLeKKRKCSTATRNQRLAAIHSFFRYA 96
Cdd:TIGR02224   6 YLRLERNYSPHTVRAYRRDLEAFLEFLEEE----GGLASLAEVTAADLRSFLAEL-HARGLSRRSLARKLSALRSFYRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  97 QYEepsGILHFQKVIAIPVKKASKPSAPHLTPEAMKFLLSQPDKMTVK--GRRNLTLLSVLYDSGCRVQELADLRVRDVV 174
Cdd:TIGR02224  81 LRR---GLIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDDEDwlALRDRAILELLYSSGLRVSELVGLDLSDLD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 175 VDnPALLILTGKGNKMRRVPLMKNTLTLLQHYLQE--HSLDKDWKKDyPLFVNKHRSKLTKEGIAYIISQYVvsakkISA 252
Cdd:TIGR02224 158 LD-FGEVRVRGKGNKERIVPFGPYARDALQAYLEArrSPLLASEGQD-ALFLNRRGGRLTPRGVQYRLQQLR-----AKA 230

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1774956731 253 SMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCDTELKRQAIENAYP 313
Cdd:TIGR02224 231 GLPKHVHPHALRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHP 291
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 1-313 6.22e-55

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 181.12  E-value: 6.22e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731   1 MKPTDFATHLTGFLSvYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPaeklnmgmLTHVMIADFLEWLEKKRK--CS 78
Cdd:PRK00236    1 MADADLPAALEAFLE-YLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISS--------LQDLDAADLRSFLARRRRqgLS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  79 TATRNQRLAAIHSFFRYaqyeepsgiLHFQKVIAI-PVKKASKPSAPH-----LTPEAMKFLLSQPDKMTVKGRRNLTLL 152
Cdd:PRK00236   72 ARSLARRLSALRSFYRW---------LVRRGLLKAnPAAGLRAPKIPKrlpkpLDVDQAKRLLDAIDEDDPLALRDRAIL 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 153 SVLYDSGCRVQELADLRVRDVvvDNPA-LLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLDKdwKKDYPLFVNKHRSKL 231
Cdd:PRK00236  143 ELLYGSGLRLSELVGLDIDDL--DLASgTLRVLGKGNKERTVPLGRAAREALEAYLALRPLFL--PDDDALFLGARGGRL 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 232 TKEGIAYIISQYVvsakkISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCDTELKRQAIENA 311
Cdd:PRK00236  219 SPRVVQRRVKKLG-----KKAGLPSHITPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAA 293


                  ..
gi 1774956731 312 YP 313
Cdd:PRK00236  294 HP 295
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 13-296 1.70e-54

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: 180.09  E-value: 1.70e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  13 FLsVYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPAEklnmgmLTHVMIADFLEWLeKKRKCSTATRNQRLAAIHSF 92
Cdd:TIGR02225   3 FL-DYLWVERGLSQNTLEAYRRDLEKFLEFLEERGIDLEE------VDRGDIVDFLAEL-KEAGLSARSIARALSALRSF 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  93 FRYAQYE-----EPSGILHFQKViaipvkKASKPSAphLTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELAD 167
Cdd:TIGR02225  75 YRFLLREgiredDPSALIEPPKV------ARKLPKV--LTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVG 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 168 LRVRDVVVDNpALLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLDKDWKKDYP---LFVNKHRSKLTKEGIAYIISQYv 244
Cdd:TIGR02225 147 LRLEDVNLDE-GFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKEsdaLFLNRRGGPLSRQGVWKILKEY- 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1774956731 245 vsAKKisASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIY 296
Cdd:TIGR02225 225 --AKR--AGIEKPISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIY 272
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
10-300 1.56e-46

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 159.36  E-value: 1.56e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  10 LTGFLSVYLP--RQKNASNNTIASYRDTFKLLLRYCQEEKdipaekLNMGMLTHVMIADFLEWLEKkRKCSTATRNQRLA 87
Cdd:COG4973     4 LAEALEAYLEhlRERRLSPKTLEAYRRDLRRLIPLLGDAD------LPLEELTPADVRRFLARLHR-RGLSPRTLNRRLS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  88 AIHSFFRYAQYEepsGILHFQKVIAIPVKKASKPSAPHLTPEAMKFLLSQPDKmTVKGRRNLTLLSVLYDSGCRVQELAD 167
Cdd:COG4973    77 ALRSFFNWAVRE---GLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALAD-DPLAVRDRAIVELLYSTGLRLGELVG 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 168 LRVRDVVVDNPALLIlTGKGNKMRRVPLMKNTLTLLQHYLqEHSLDKDWKKDYPLFVNKHRSKLTKEGIAYIISQYvvsA 247
Cdd:COG4973   153 LDWEDVDLDAGEVRV-RGKTGKSRTVPLGPKALAALREWL-AVRPELAAPDEGALFPSRRGTRLSPRNVQKRLRRL---A 227

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1774956731 248 KKisASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCD 300
Cdd:COG4973   228 KK--AGLPKHVHPHDLRHSFATHLLESGGDLRAVQELLGHASISTTQIYTHLD 278
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 131-296 3.19e-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: 146.89  E-value: 3.19e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 131 MKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPaLLILTGKGNKMRRVPLMKNTLTLLQHYLQE- 209
Cdd:cd00798     4 VERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEG-LVRVTGKGNKERLVPFGSYAVEALEEYLEEr 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 210 -HSLDKDwKKDYPLFVNKHRSKLTKEGIAYIISQYVvsakkISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHE 288
Cdd:cd00798    83 rPLLLKK-KPPDALFLNKRGKRLSRRGVWRILKKYA-----ERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHA 156


                  ....*...
gi 1774956731 289 DIKTTEIY 296
Cdd:cd00798   157 SLSTTQIY 164
xerD PRK00283
tyrosine recombinase;
22-296 7.88e-42

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 147.26  E-value: 7.88e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  22 KNASNNTIASY-RDtfklLLRYCQEekdIPAEKLNMGMLTHVMIADFLEWL-EKKRKCSTATRnqRLAAIHSFFRYAqYE 99
Cdd:PRK00283   20 RGLAENTLSSYrRD----LELFAEW---LAARGLSLAEATRDDLQAFLAELaEGGYKATSSAR--RLSALRRFFQFL-LR 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 100 E------PSGILhfqkviaIPVKKASK-PSAphLTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRD 172
Cdd:PRK00283   90 EglreddPSALL-------DSPKLPRRlPKT--LSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 173 VVVdNPALLILTGKGNKMRRVPLMKNTLTLLQHYLQEH--SLDKDWKKDYpLFVNKHRSKLTKEGIAYIISQYVVSAKkI 250
Cdd:PRK00283  161 VSL-RQGVVRVTGKGNKERLVPLGEEAVYAIERYLERGrpALLNGRSSDA-LFPSARGGQLTRQTFWHRIKHYAKRAG-I 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1774956731 251 SasmPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIY 296
Cdd:PRK00283  238 D---PKKLSPHVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIY 280
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 134-297 1.83e-33

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: 121.43  E-value: 1.83e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 134 LLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGK--GNKMRRVPLMKNTLTLLQHYLQEHS 211
Cdd:cd00397     5 LLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkGGKERTVPLPKELAEELKEYLKERR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 212 LDKDWKKDYPLFVNKHRSKLTKEGIAYIISQYVvsaKKISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIK 291
Cdd:cd00397    85 DKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIF---KKAGIEAGRKITPHSLRHTFATNLLENGVDIKVVQKLLGHSSIS 161


                  ....*.
gi 1774956731 292 TTEIYA 297
Cdd:cd00397   162 TTQRYL 167
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 128-298 5.37e-29

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: 109.72  E-value: 5.37e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 128 PEAMKFLLSQPDKMtvkgrRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYL 207
Cdd:pfam00589   8 ERLLDAAETGPLSI-----RDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHRGKGNKERTVPLSDAALELLKEWL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 208 QEHSLDKDwKKDYpLFVNKHRSKLTKEGIAYIISQYVvsakkISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGH 287
Cdd:pfam00589  83 SKRLLEAP-KSDY-LFASKRGKPLSRQTVRKIFKRAG-----KEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGH 155

                         170
                  ....*....|.
gi 1774956731 288 EDIKTTEIYAK 298
Cdd:pfam00589 156 SSISTTQIYTH 166
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 126-296 9.13e-27

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: 103.89  E-value: 9.13e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSqpdkmTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQH 205
Cdd:cd01193     6 LSPDEVRRILG-----ALTELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRQGKGGKDRVVPLPEKLLEPLRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 206 YLQEHslDKDWKKD---------YPLFVNKHRSKLTKEGIAYIISQYVvsakkISASMPEKVTPHMFRHSKAMHLLQAGV 276
Cdd:cd01193    81 YLKSA--RPKEELDpaegragvlDPRTGVERRHHISETTVQRALKKAV-----EQAGITKRVTPHTLRHSFATHLLEAGT 153

                         170       180
                  ....*....|....*....|
gi 1774956731 277 SLIYIRDFLGHEDIKTTEIY 296
Cdd:cd01193   154 DIRTIQELLGHSDLSTTMIY 173
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 20-296 1.44e-25

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 105.21  E-value: 1.44e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  20 RQKNASNNTIASYRDTFKLLLRYCQEEKDIPAEKLNMGMLTHvmiadFLEWLEKKRKC-----STATRNQRLAAIHSFFR 94
Cdd:PRK01287   33 QERNWSERTLKVYTEHLYPFILWCEERGLYYAADVTLPVLER-----YQRYLYGYRKAngeplSTRTQRTQLSPLRVWFR 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  95 YaqyeepsgILHFQKVIAIPVKKASKPSAPH------LTPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADL 168
Cdd:PRK01287  108 W--------LLKRHHILYNPAEDLELPKEEKrlprqiLSEAETEQVLASPDLTTLQGLRDRALLELLWSTGIRRGELARL 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 169 RVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLDKDWKKDYP-LFVNKHRSKLTKEGIAYIISQYVVSA 247
Cdd:PRK01287  180 DLYDVDASRGVVTVRQGKGNKDRVVPVGERALAWLQRYLQDVRPQLAVRPDSGaLFVAMDGDGLARNTLTNMVGRYIRAA 259

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1774956731 248 --KKISASmpekvtpHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIY 296
Cdd:PRK01287  260 giEKAGAC-------HLFRHAMATQMLENGADTRHIQAILGHAKLETTQIY 303
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 67-296 4.32e-25

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: 102.86  E-value: 4.32e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  67 FLEWLEKKRKCSTATRNQRLAAIhSFFryaqYEEpsgILHFQKVIAIPVKKASKPS-APH-LTPEAMKFLLSQpdkmtVK 144
Cdd:TIGR02249  49 FLSDLAVDGKVAASTQNQALNAL-LFL----YKE---ILKTPLSLMERFVRAKRPRkLPVvLTREEVRRLLEH-----LE 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 145 GRRNLtLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPL-----------MKNTLTLLQHYLQE---- 209
Cdd:TIGR02249 116 GKYRL-IAKLLYGSGMRLMECLRLRIQDIDFDYGEIRIRQGKGGKDRTVTLpkelipplreqIELARAYHEADLAEgygg 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 210 ----HSLDK-------DWKKDYpLFVNKHRSKLTKEG------IAYIISQYVVSAKKISASMPEKVTPHMFRHSKAMHLL 272
Cdd:TIGR02249 195 vylpHALARkypnapkEWGWQY-LFPSHRLSRDPESGvirrhhINETTIQRAVRRAVERAGIEKPVTCHTLRHSFATHLL 273

                         250       260
                  ....*....|....*....|....
gi 1774956731 273 QAGVSLIYIRDFLGHEDIKTTEIY 296
Cdd:TIGR02249 274 ESGADIRTVQELLGHSDVKTTQIY 297
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 126-297 1.42e-23

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: 95.52  E-value: 1.42e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSQ-PDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDV-VVDNPALLILTGKG--NKMRRVPLMKNTLT 201
Cdd:cd01194     1 LTLEQARQLLASlPIDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLrQEGEGTILYVQGKGktSKDDFVYLRPDVLK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 202 LLQHYLQEHSLDKdwkKDYPLFVN-KHRSK---LTKEGIAYIISQYVvsakKISASMPEKVTPHMFRHSKAMHLLQAGVS 277
Cdd:cd01194    81 ALQAYLKARGKLD---FEEPLFTSlSNNSKgqrLTTRSIRRIIKKYL----RKAGLDDDRLTAHSLRHTAGTLALKAGKS 153

                         170       180
                  ....*....|....*....|
gi 1774956731 278 LIYIRDFLGHEDIKTTEIYA 297
Cdd:cd01194   154 LREVQQLLRHSDPNTTMIYA 173
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 127-306 1.03e-22

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: 93.08  E-value: 1.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 127 TPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHY 206
Cdd:cd01188     1 SPDEVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQKKTGRPVELPLTEPVGEALADY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 207 LQehslDKDWKKDYP-LFV---NKHRSKLTKEGIAYIISQYVVSAKkISasmPEKVTPHMFRHSKAMHLLQAGVSLIYIR 282
Cdd:cd01188    81 LR----DGRPRTDSReVFLrarAPYRPLSSTSQISSIVRRYLRKAG-IE---PSHRGTHSLRHSLATRMLRAGTSLKVIA 152

                         170       180
                  ....*....|....*....|....
gi 1774956731 283 DFLGHEDIKTTEIYAKCDTELKRQ 306
Cdd:cd01188   153 DLLGHRSIETTAIYAKIDVDDLRE 176
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 125-310 1.21e-17

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 82.66  E-value: 1.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 125 HLTPEAMKFLlsQPDKmtvkgRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNpALLILTGKGNKMRRVPLMKNTLTLLQ 204
Cdd:PRK05084  181 KLSNRALSSF--KKNK-----ERDLAIIALILGSGLRVSELVNLDLSDLNLKQ-MTIDVTRKGGKRDSVNIAPFALPYLE 252

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 205 HYLQ-EHSLDKDWKKDYPLFVNKHR---SKLTKEGIAYIISQYvvsakkiSASMPEKVTPHMFRHSKAMHLLQAGVSLIY 280
Cdd:PRK05084  253 EYLKiRASRYKAEKQEKALFLTKYRgkpNRISARAIEKMVAKY-------SEAFGVRLTPHKLRHTLATRLYDATKDQVL 325

                         170       180       190
                  ....*....|....*....|....*....|
gi 1774956731 281 IRDFLGHEDIKTTEIYAKCDTELKRQAIEN 310
Cdd:PRK05084  326 VADQLGHTSTETTDLYTHIVNDEQKEALDR 355
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 126-297 2.19e-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: 72.74  E-value: 2.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSQPDKMTVKGRRNLTLLsvLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQH 205
Cdd:cd00796     5 LTEDEEARLLAALEESTNPHLRLIVLL--ALYTGARRGEILSLRWDDIDLEVGLIVLPETKNGKPRTVPLSDEAIAILKE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 206 YLQEHSLDKDWKKdyPLFVNKHRSKLTKegiayiisqyVVSAKKISASMPeKVTPHMFRHSKAMHLLQAGVSLIYIRDFL 285
Cdd:cd00796    83 LKRKRGKDGFFVD--GRFFGIPIASLRR----------AFKKARKRAGLE-DLRFHDLRHTFASRLVQAGVPIKTVAKIL 149

                         170
                  ....*....|..
gi 1774956731 286 GHEDIKTTEIYA 297
Cdd:cd00796   150 GHSSIKMTMRYA 161
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 127-296 5.33e-15

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: 71.73  E-value: 5.33e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 127 TPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILtGKGNKMR-RVPLMKNTLTLLQH 205
Cdd:cd01195     1 SREEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRIL-GKGKKQReVVTLPPTTREALAA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 206 YLQEHSldkdwKKDYPLFVNKHRS----KLTKEGIAYIISQyvvSAKkiSASMPEKVTPHMFRHSKAMHLLQAGVSLIY- 280
Cdd:cd01195    80 WLAARG-----EAEGPLFVSLDRAsrgrRLSPQAVYRIVRR---LAE--RIGLGKRLSPHGLRHSAITLALDAGAGLIRk 149

                         170
                  ....*....|....*.
gi 1774956731 281 IRDFLGHEDIKTTEIY 296
Cdd:cd01195   150 VQDFSRHADLRTLQVY 165
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 159-304 7.99e-15

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: 71.14  E-value: 7.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 159 GCRVQELADLRVRDVVVDNPALLIL--TGKGNKMRRVPLMKNTLTLLQHYlqehsldKDWKKDYPLFVNKHRSKltkegi 236
Cdd:cd01185    31 GLRFSDLKNLTWKNIVEASGRTWIRyrRKKTGKPVTVPLLPVAREILEKY-------KDDRSEGKLFPVLSNQK------ 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 237 ayiISQYVvsaKKIS--ASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAKCDTELK 304
Cdd:cd01185    98 ---INRYL---KEIAkiAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIYAKIVDSKK 161
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 150-307 5.93e-14

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: 69.64  E-value: 5.93e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 150 TLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLDKDWKKDYPLFVNKHRS 229
Cdd:cd00797    29 TLFGLLYATGLRVGEALRLRLEDVDLDSGILTIRQTKFGKSRLVPLHPSTVGALRDYLARRDRLLPSPSSSYFFVSQQGG 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 230 KLTKEGIAYIISQYVVSAKKISAsmPEKVTP--HMFRHSKAMHLL----QAG----VSLIYIRDFLGHEDIKTTEIYAKC 299
Cdd:cd00797   109 RLTGGGVYRVFRRLLRRIGLRGA--GDGRGPrlHDLRHTFAVNRLtrwyREGadveRKLPVLSTYLGHVNVTDTYWYLTA 186


                  ....*...
gi 1774956731 300 DTELKRQA 307
Cdd:cd00797   187 TPELMELA 194
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 126-293 5.79e-13

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: 66.29  E-value: 5.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSqpdkmTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLIL---------TGKGNKMRRVPLM 196
Cdd:cd01186     2 LTPREVQELIN-----ACNNLRDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVpredntneaRAKSMRERRIPVS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 197 KNTLTLLQHYLQEhSLDKDWKKDYPLFVNKHRSKLTKeGIAYIISQYVVSAKKISASMpeKVTPHMFRHSKAMHLLQAGV 276
Cdd:cd01186    77 QDLIDLYADYLTY-IYCEEAEFSITVFVNVKGGNQGK-AMNYSDVYDLVRRLKKRTGI--DFTPHMFRHTHATALIRAGW 152

                         170
                  ....*....|....*..
gi 1774956731 277 SLIYIRDFLGHEDIKTT 293
Cdd:cd01186   153 SIEVVARRLGHAHVQTT 169
PRK15417 PRK15417
integron integrase;
67-298 8.28e-13

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 68.15  E-value: 8.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  67 FLEWLEKKRKCSTATRNQRLAAIHSFFRYAQYEEpsgiLHFQKVIAIPVKKASKPSAphLTPEAMKFLLSqpdkmTVKGR 146
Cdd:PRK15417   64 FLSWLANERKVSVSTHRQALAALLFFYGKVLCTD----LPWLQEIGRPRPSRRLPVV--LTPDEVVRILG-----FLEGE 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 147 RNLtLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYLQEH---------------S 211
Cdd:PRK15417  133 HRL-FAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALMLPESLAPSLREQLSRArawwlkdqaegrsgvA 211

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 212 LDKDWKKDYP----------LFVNKHRSKLTKEGIA---YIISQYVVSAKKIS---ASMPEKVTPHMFRHSKAMHLLQAG 275
Cdd:PRK15417  212 LPDALERKYPraghswpwfwVFAQHTHSTDPRSGVVrrhHMYDQTFQRAFKRAveqAGITKPATPHTLRHSFATALLRSG 291

                         250       260
                  ....*....|....*....|...
gi 1774956731 276 VSLIYIRDFLGHEDIKTTEIYAK 298
Cdd:PRK15417  292 YDIRTVQDLLGHSDVSTTMIYTH 314
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 127-308 2.44e-12

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: 64.81  E-value: 2.44e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 127 TPEAMKFLLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLI-LTGKGNKMRRVPLMKNTLTLLQH 205
Cdd:cd01196     1 TAPEARRLLESIDSTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVYDQGRRLWVrLAEKGGKQHEMPCHHDLEEYLRA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 206 YLQEHSLDKDwkKDYPLFVNKHRS--KLTKEGIAYIISQYVVSAKKISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRD 283
Cdd:cd01196    81 YLEAAEIEED--PKGPLFRTTRGGtrKLTHNPLTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTLEDAQN 158

                         170       180
                  ....*....|....*....|....*
gi 1774956731 284 FLGHEDIKTTEIYAKCDTELKRQAI 308
Cdd:cd01196   159 MANHASTRTTQLYDRRSDKITLDEV 183
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 125-296 1.36e-11

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: 62.52  E-value: 1.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 125 HLTPEAMKFLLSQPdKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQ 204
Cdd:cd01197     6 YLTGKEVQALLQAA-CRGRTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRLKNGFSTTHPLRFDEREALE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 205 HYLQEHS----LDKDWkkdypLFVNKHRSKLTKEGIAYIISQYvvsakKISASMPEKVTPHMFRHSKAMHLLQAGVSLIY 280
Cdd:cd01197    85 AWLKERAnwkgADTDW-----IFLSRRGGPLSRQQAYRIIRDL-----GKEAGTVTQTHPHMLRHACGYALADRGADTRL 154

                         170
                  ....*....|....*.
gi 1774956731 281 IRDFLGHEDIKTTEIY 296
Cdd:cd01197   155 IQDYLGHRNIRHTVIY 170
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 158-323 9.57e-11

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: 9.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 158 SGCRVQELADLRVRDVVVdnpALLILTGKGNKMRRVPLMKNtltllqhyLQEHS---LDKDWKKDYPLFVNKHRSKLTKE 234
Cdd:cd01191    32 TGARVSELIKIKVEHVEL---GYFDIYSKGGKLRRLYIPKK--------LRNEAlewLKSTNRKSGYIFLNRFGERITTR 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 235 GIAYIISQYvvsAKKISASmPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYakcdteLKRQAIENAypT 314
Cdd:cd01191   101 GIAQQLKNY---ARKYGLN-PKVVYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY------LRKTASEQQ--E 168


                  ....*....
gi 1774956731 315 LVDSnLPDW 323
Cdd:cd01191   169 IVDK-IVTW 176
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 144-298 1.24e-10

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: 58.72  E-value: 1.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 144 KGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLI---LTGKGNK------------MRRVPLMKNTLTLLQHYlq 208
Cdd:cd01189    14 RGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRInrtLVRKKKGgyvikppktkssIRTIPLPDELIELLKEL-- 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 209 ehsldKDWKKDyplfvnkhrskLTKEGIAYIisqyvvsakkisasmpekvTPHMFRHSKAMHLLQAGVSLIYIRDFLGHE 288
Cdd:cd01189    92 -----KAFKKL-----------LKKAGLPRI-------------------TPHDLRHTFASLLLEAGVPLKVIAERLGHS 136

                         170
                  ....*....|.
gi 1774956731 289 DIKTT-EIYAK 298
Cdd:cd01189   137 DISTTlDVYAH 147
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
10-96 1.95e-09

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 53.80  E-value: 1.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  10 LTGFLSvYLPRQKNASNNTIASYRDTFKLLLRYCQEEKDIPAEklnmgmLTHVMIADFLEWLEKKRKcSTATRNQRLAAI 89
Cdd:pfam02899   1 IDQFLE-YLSLERGLSPHTLRAYRRDLLAFLKFLSEGGSSLEQ------ITTSDVRAFLAELRAQGL-SASSLARRLSAL 72


                  ....*..
gi 1774956731  90 HSFFRYA 96
Cdd:pfam02899  73 RSFYQFL 79
PRK09870 PRK09870
tyrosine recombinase; Provisional
 126-296 5.62e-09

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 55.33  E-value: 5.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 126 LTPEAMKFLLSQPDKMTVKGR-RNLTLLSVLYdsGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQ 204
Cdd:PRK09870   13 LTHSEIESLLKAANTGPHAARnYCLTLLCFIH--GFRASEICRLRISDIDLKAKCIYIHRLKKGFSTTHPLLNKEIQALK 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 205 HYLQ-----EHSlDKDWkkdypLFVNKHRSKLTKEGIAYIISQyvvSAKKisASMPEKVTPHMFRHSKAMHLLQAGVSLI 279
Cdd:PRK09870   91 NWLSirtsyPHA-ESEW-----VFLSRKGNPLSRQQFYHIIST---SGGN--AGLSLEIHPHMLRHSCGFALANMGIDTR 159

                         170
                  ....*....|....*..
gi 1774956731 280 YIRDFLGHEDIKTTEIY 296
Cdd:PRK09870  160 LIQDYLGHRNIRHTVWY 176
PRK09871 PRK09871
tyrosine recombinase; Provisional
 145-296 1.80e-08

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 53.83  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 145 GRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLDKDWKKDYPLFV 224
Cdd:PRK09871   25 GARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRLKNGFSTVHPLRFDEREAVERWTQERANWKGADRTDAIFI 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1774956731 225 NKHRSKLTKEGiAYIIsqyvVSAKKISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIY 296
Cdd:PRK09871  105 SRRGSRLSRQQ-AYRI----IRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRY 171
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 134-311 1.17e-07

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: 51.15  E-value: 1.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 134 LLSQPDKMTVKGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNPALLILT---------GKGnkmRRVPLMKNTLTL-- 202
Cdd:cd00799     4 MLATLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLTRFVDGGLLIRlrrsktdqdGEG---EIKALPYGPETCpv 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 203 --LQHYLqEHSLDKDWkkdyPLF--VNKHRSK----LTKEGIAYIISQYVVSAKKIsasmPEKVTPHMFRHSKAMHLLQA 274
Cdd:cd00799    81 raLRAWL-EAAGIPSG----PLFrrIRRGGSVgttrLSDRSVARIVKRRAALAGLD----PGDFSGHSLRRGFATEAARA 151

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1774956731 275 GVSLIYIRDFLGHEDIKTTEIYakcdTELKRQAIENA 311
Cdd:cd00799   152 GASLPEIMAQGGHKSVATVMRY----IREADRFKDNA 184
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 149-298 1.67e-07

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: 50.77  E-value: 1.67e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 149 LTLLSvLYdSGCRVQELADLRVRDVVVD--------NPALLILTGK-GNKMRRVPLMKNTLTL-LQHYLQehSLDKDWKK 218
Cdd:cd01184    28 LPLIG-LY-TGARLNEICQLRVDDIKEEdgiwcidiNDDAEGRRLKtKASRRLVPIHPRLIELgFLDYVE--ALRADGKL 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 219 DYPLFVNKHRSKLTKEgIAYIISQYVVSAKKISAsmpEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHE-DIKTTEIYA 297
Cdd:cd01184   104 FLFPEKRDKDGKYSKA-ASKWFNRLLRKLGIKDD---ERKSFHSFRHTFITALKRAGVPEELIAQIVGHSrGGVTHDTYG 179


                  .
gi 1774956731 298 K 298
Cdd:cd01184   180 K 180
int PHA02601
integrase; Provisional
 28-297 4.21e-07

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 50.88  E-value: 4.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  28 TIASYRDTFKLLLRYCQEEKDIPAEKLNMGMLTH---VMIADFLEwLEKKRKCSTATRNQRLAAIHSFF-RYAQYEEPSG 103
Cdd:PHA02601   75 TLEDGKARLAKLLILCKGLGDPIASEFTAKDFADyraRRLSGEFK-VNKGRPIKPATVNRELAYLSAVFnELIKLGKWSG 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 104 ilhfQKVIA-IPVKKASKPSAPHLTPEAMKFLLSQPDKmtvKGRRNLTLLSVL-YDSGCRVQELADLRvRDVVVDNPALL 181
Cdd:PHA02601  154 ----PNPLDgIRPFKEAEPELAFLTKEEIERLLDACDG---SRSPDLGLIAKIcLATGARWSEAETLK-RSQISPYKITF 225

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 182 ILTgKGNKMRRVPLMKNTLTLLqhylqEHSLDKDWKKDYPLFVNkhrskltkegiayiisqyvvSAKKISASMPEKVTPH 261
Cdd:PHA02601  226 VKT-KGKKNRTVPISEELYKML-----PKRRGRLFKDAYESFER--------------------AVKRAGIDLPEGQATH 279

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1774956731 262 MFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYA 297
Cdd:PHA02601  280 VLRHTFASHFMMNGGNILVLQRILGHATIEMTMAYA 315
Phage_int_SAM_5 pfam13102
Phage integrase SAM-like domain; A family of uncharacterized proteins found by clustering ...
 20-96 6.80e-07

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: 46.83  E-value: 6.80e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1774956731  20 RQKNASNNTIASYRDTFKLLLRYCQEeKDIPaeklnMGMLTHVMIADFLEWLEKKRKCSTATRNQRLAAIHSFFRYA 96
Cdd:pfam13102  13 LKKKGSKGTARNYKSTLKHLKKFLKK-KDIT-----FEEITVDFLEKFEEYLKKKKGLSENTISKYFRTLRAVLNKA 83
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
20-100 3.05e-06

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 44.53  E-value: 3.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731  20 RQKNASNNTIASYRDTFKLLLRYCQEEKdiPAEklnmgmLTHVMIADFLEWLEKKRKCSTATRNQRLAAIHSFFRYAQYE 99
Cdd:pfam13495  10 RLRGYAERTIKAYLRWIRRFLRFHDKKH--PEE------LTEEDIEAYLSHLANERNVSASTQNQALNALSFFYRWVLER 81


                  .
gi 1774956731 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 1.46e-05

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: 44.98  E-value: 1.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774956731 144 KGRRNLTLLSVLYDSGCRVQELADLRVRDVVVDNpALLILTGKGNKMRRVPLMKNTLTLLQHYLQEHSLDKDWKKDYPLf 223
Cdd:cd01192    22 ANPRNYLLFIVGINTGLRISDLLSLKVEDVTNKD-KLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLKRNDYLFKSL- 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1774956731 224 vNKHRSKLTKEGIAYIISQYVvsakKISASMPEKVTPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIY 296
Cdd:cd01192   100 -KQGPEKPISRKQAYKILKKA----ADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRY 167
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 259-298 7.72e-03

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: 36.25  E-value: 7.72e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1774956731 259 TPHMFRHSKAMHLLQAGVSLIYIRDFLGHEDIKTTEIYAK 298
Cdd:cd01187   103 HTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
 
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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