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site-specific tyrosine recombinase XerD [Parabacteroides johnsonii]

Protein Classification

site-specific tyrosine recombinase( domain architecture ID 11493903)

site-specific tyrosine recombinase acts by catalyzing the cutting and rejoining of recombining DNA molecules

CATH:  1.10.443.10
Gene Ontology:  GO:0009037|GO:0003677|GO:0007049|GO:0051301|GO:0006313
PubMed:  10047575|9278480|10577069
SCOP:  4002347

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 9-297 4.50e-143

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: 404.27  E-value: 4.50e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495    9 ERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFLFL 88
Cdd:TIGR02225   1 EQFLDYLWVERGLSQNTLEAYRRDLEKFLEFLEERGIDLEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   89 DNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIK 168
Cdd:TIGR02225  81 EGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  169 VEGKGSKQRLVPISETAIKEIKNYLYDRNHVPV--KKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFR 246
Cdd:TIGR02225 161 VRGKGNKERLVPLGEEAIEALERYLKEARPLLLkkKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLR 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 495421495  247 HSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPRS 297
Cdd:TIGR02225 241 HSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
 
Name Accession Description Interval E-value
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 9-297 4.50e-143

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: 404.27  E-value: 4.50e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495    9 ERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFLFL 88
Cdd:TIGR02225   1 EQFLDYLWVERGLSQNTLEAYRRDLEKFLEFLEERGIDLEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   89 DNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIK 168
Cdd:TIGR02225  81 EGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  169 VEGKGSKQRLVPISETAIKEIKNYLYDRNHVPV--KKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFR 246
Cdd:TIGR02225 161 VRGKGNKERLVPLGEEAIEALERYLKEARPLLLkkKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLR 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 495421495  247 HSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPRS 297
Cdd:TIGR02225 241 HSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
xerD PRK00283
tyrosine recombinase;
8-297 5.98e-121

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 348.72  E-value: 5.98e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   8 VERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFLF 87
Cdd:PRK00283   9 IEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSALRRFFQFLL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  88 LDNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFI 167
Cdd:PRK00283  89 REGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQGVV 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 168 KVEGKGSKQRLVPISETAIKEIKNYLYDRNHVPVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGI-KKNVSPHTFR 246
Cdd:PRK00283 169 RVTGKGNKERLVPLGEEAVYAIERYLERGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIdPKKLSPHVLR 248

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495421495 247 HSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPRS 297
Cdd:PRK00283 249 HAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
8-295 8.99e-107

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 312.31  E-value: 8.99e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   8 VERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKY-ADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFL 86
Cdd:COG4974    7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPlAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  87 FLDNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGF 166
Cdd:COG4974   87 VREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 167 IKV-EGKGSKQRLVPISETAIKEIKNYLYDRNHVPvkkgfEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTF 245
Cdd:COG4974  167 IRVrRGKGGKERTVPLSPEALEALREYLEERRPRD-----SDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSL 241

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 495421495 246 RHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHP 295
Cdd:COG4974  242 RHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 115-286 2.70e-85

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: 253.20  E-value: 2.70e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 115 VNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEGKGSKQRLVPISETAIKEIKNYLY 194
Cdd:cd00798    1 VDEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 195 DRNHVPVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITT 274
Cdd:cd00798   81 ERRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                        170
                 ....*....|..
gi 495421495 275 TEIYTHIDRQFL 286
Cdd:cd00798  161 TQIYTHVSFERL 172
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 112-282 6.54e-50

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: 162.87  E-value: 6.54e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  112 VLTVNEINSILDTIDlTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVE-GKGSKQRLVPISETAIKEIK 190
Cdd:pfam00589   1 RLTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  191 NYLYDRNhvpVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHE 270
Cdd:pfam00589  80 EWLSKRL---LEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 495421495  271 KITTTEIYTHID 282
Cdd:pfam00589 157 SISTTQIYTHVA 168
 
Name Accession Description Interval E-value
recomb_XerD TIGR02225
tyrosine recombinase XerD; The phage integrase family describes a number of recombinases with ...
 9-297 4.50e-143

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: 404.27  E-value: 4.50e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495    9 ERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFLFL 88
Cdd:TIGR02225   1 EQFLDYLWVERGLSQNTLEAYRRDLEKFLEFLEERGIDLEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   89 DNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIK 168
Cdd:TIGR02225  81 EGIREDDPSALIEPPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVNLDEGFVR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  169 VEGKGSKQRLVPISETAIKEIKNYLYDRNHVPV--KKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFR 246
Cdd:TIGR02225 161 VRGKGNKERLVPLGEEAIEALERYLKEARPLLLkkKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLR 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 495421495  247 HSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPRS 297
Cdd:TIGR02225 241 HSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHPRA 291
xerD PRK00283
tyrosine recombinase;
8-297 5.98e-121

tyrosine recombinase;


Pssm-ID: 234713 [Multi-domain]  Cd Length: 299  Bit Score: 348.72  E-value: 5.98e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   8 VERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFLF 87
Cdd:PRK00283   9 IEQFLDALWVERGLAENTLSSYRRDLELFAEWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSALRRFFQFLL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  88 LDNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFI 167
Cdd:PRK00283  89 REGLREDDPSALLDSPKLPRRLPKTLSEAQVEALLDAPDIDTPLGLRDRAMLELLYATGLRVSELVGLTLDDVSLRQGVV 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 168 KVEGKGSKQRLVPISETAIKEIKNYLYDRNHVPVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGI-KKNVSPHTFR 246
Cdd:PRK00283 169 RVTGKGNKERLVPLGEEAVYAIERYLERGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIdPKKLSPHVLR 248

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495421495 247 HSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPRS 297
Cdd:PRK00283 249 HAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHPRA 299
xerC PRK00236
site-specific tyrosine recombinase XerC; Reviewed
 8-296 1.60e-108

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234698 [Multi-domain]  Cd Length: 297  Bit Score: 317.10  E-value: 1.60e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   8 VERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKY-ADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFL 86
Cdd:PRK00236  10 LEAFLEYLRVERGLSPHTLRAYRRDLRAFLAFLEEHGISSlQDLDAADLRSFLARRRRQGLSARSLARRLSALRSFYRWL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  87 FLDNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGF 166
Cdd:PRK00236  90 VRRGLLKANPAAGLRAPKIPKRLPKPLDVDQAKRLLDAIDEDDPLALRDRAILELLYGSGLRLSELVGLDIDDLDLASGT 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 167 IKVEGKGSKQRLVPISETAIKEIKNYLYDRNHVPVKKGFediLFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFR 246
Cdd:PRK00236 170 LRVLGKGNKERTVPLGRAAREALEAYLALRPLFLPDDDA---LFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLR 246

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 495421495 247 HSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPR 296
Cdd:PRK00236 247 HSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPR 296
recomb_XerC TIGR02224
tyrosine recombinase XerC; The phage integrase family describes a number of recombinases with ...
 9-298 1.59e-107

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: 314.55  E-value: 1.59e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495    9 ERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEG--KKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFL 86
Cdd:TIGR02224   1 EAFLEYLRLERNYSPHTVRAYRRDLEAFLEFLEEEGglASLAEVTAADLRSFLAELHARGLSRRSLARKLSALRSFYRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   87 FLDNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLT--LPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDE 164
Cdd:TIGR02224  81 LRRGLIDANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPEEDdeDWLALRDRAILELLYSSGLRVSELVGLDLSDLDLDF 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  165 GFIKVEGKGSKQRLVPISETAIKEIKNYLYDRNHVPVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHT 244
Cdd:TIGR02224 161 GEVRVRGKGNKERIVPFGPYARDALQAYLEARRSPLLASEGQDALFLNRRGGRLTPRGVQYRLQQLRAKAGLPKHVHPHA 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 495421495  245 FRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPRSK 298
Cdd:TIGR02224 241 LRHSFATHLLNNGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHPRAK 294
XerD COG4974
Site-specific recombinase XerD [Replication, recombination and repair];
8-295 8.99e-107

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


Pssm-ID: 443999 [Multi-domain]  Cd Length: 291  Bit Score: 312.31  E-value: 8.99e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   8 VERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKY-ADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFL 86
Cdd:COG4974    7 LEAFLEELKREKGLSPNTIKAYRRDLRRFLRFLEELGKIPlAEITPEDIRAYLNYLRERGLSPSTINRYLAALRSFFRYA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  87 FLDNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGF 166
Cdd:COG4974   87 VREGLLEDNPAAKVKLPKKPRKLPRVLTEEEIEALLEALDTETPEGLRDRALLLLLYATGLRVSELLGLKWSDIDLDRGT 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 167 IKV-EGKGSKQRLVPISETAIKEIKNYLYDRNHVPvkkgfEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTF 245
Cdd:COG4974  167 IRVrRGKGGKERTVPLSPEALEALREYLEERRPRD-----SDYLFPTRRGRPLSRRAIRKILKRLAKRAGIPKRVTPHSL 241

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 495421495 246 RHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHP 295
Cdd:COG4974  242 RHTFATHLLEAGVDLRTVQELLGHSSISTTQIYTHVSDEELREAVEKLHP 291
XerC COG4973
Site-specific recombinase XerC [Replication, recombination and repair];
8-288 1.09e-88

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


Pssm-ID: 443998 [Multi-domain]  Cd Length: 287  Bit Score: 266.06  E-value: 1.09e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   8 VERYKTYLRlEKALSANSIDAYLTDLDKLTNFVESEGKKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFLF 87
Cdd:COG4973    8 LEAYLEHLR-ERRLSPKTLEAYRRDLRRLIPLLGDADLPLEELTPADVRRFLARLHRRGLSPRTLNRRLSALRSFFNWAV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  88 LDNYITTDPTELLESPKIGLKLPEVLTVNEINSILDTIDLTlPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFI 167
Cdd:COG4973   87 REGLLEANPAAGVKAPKAPRKLPRALTVDELAQLLDALADD-PLAVRDRAIVELLYSTGLRLGELVGLDWEDVDLDAGEV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 168 KVEGKGSKQRLVPISETAIKEIKNYLYDRNHVPVKKgfEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRH 247
Cdd:COG4973  166 RVRGKTGKSRTVPLGPKALAALREWLAVRPELAAPD--EGALFPSRRGTRLSPRNVQKRLRRLAKKAGLPKHVHPHDLRH 243

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 495421495 248 SFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRK 288
Cdd:COG4973  244 SFATHLLESGGDLRAVQELLGHASISTTQIYTHLDFQHLAE 284
INT_XerDC_C cd00798
XerD and XerC integrases, C-terminal catalytic domains; XerDC-like integrases are involved in ...
 115-286 2.70e-85

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: 253.20  E-value: 2.70e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 115 VNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEGKGSKQRLVPISETAIKEIKNYLY 194
Cdd:cd00798    1 VDEVERLLDAPDTDTPLGLRDRAILELLYASGLRVSELVGLDLSDVDLDEGLVRVTGKGNKERLVPFGSYAVEALEEYLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 195 DRNHVPVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITT 274
Cdd:cd00798   81 ERRPLLLKKKPPDALFLNKRGKRLSRRGVWRILKKYAERAGLPKHVSPHTLRHSFATHLLEGGADLRVVQELLGHASLST 160

                        170
                 ....*....|..
gi 495421495 275 TEIYTHIDRQFL 286
Cdd:cd00798  161 TQIYTHVSFERL 172
xerC PRK01287
site-specific tyrosine recombinase XerC; Reviewed
 69-301 4.66e-55

site-specific tyrosine recombinase XerC; Reviewed


Pssm-ID: 234935 [Multi-domain]  Cd Length: 358  Bit Score: 182.25  E-value: 4.66e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  69 PRSQARIISGIKSFYRFLFLDNYITTDPTELLESPKIGLKLP-EVLTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGL 147
Cdd:PRK01287  92 TRTQRTQLSPLRVWFRWLLKRHHILYNPAEDLELPKEEKRLPrQILSEAETEQVLASPDLTTLQGLRDRALLELLWSTGI 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 148 RVSELVSLRFTDVYFDEGFIKV-EGKGSKQRLVPISETAIKEIKNYLYD-RNHVPVKKGFEDiLFLSRRGTALSRIMVFH 225
Cdd:PRK01287 172 RRGELARLDLYDVDASRGVVTVrQGKGNKDRVVPVGERALAWLQRYLQDvRPQLAVRPDSGA-LFVAMDGDGLARNTLTN 250

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495421495 226 IIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHIDRQFLRKEILEHHPRSKPRD 301
Cdd:PRK01287 251 MVGRYIRAAGIEKAGACHLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVHASTHPAERKAD 326
INT_IntI_C cd01193
Integron integrase and similar protiens, C-terminal catalytic domain; Integron integrases ...
 108-281 6.20e-55

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: 175.93  E-value: 6.20e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 108 KLPEVLTVNEINSILDTIdltlpEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVE-GKGSKQRLVPISETAI 186
Cdd:cd01193    1 KLPVVLSPDEVRRILGAL-----TELRHRLILSLLYGAGLRISELLRLRVKDIDFERGVIRVRqGKGGKDRVVPLPEKLL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 187 KEIKNYLYDRNHVP------VKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANL 260
Cdd:cd01193   76 EPLRRYLKSARPKEeldpaeGRAGVLDPRTGVERRHHISETTVQRALKKAVEQAGITKRVTPHTLRHSFATHLLEAGTDI 155

                        170       180
                 ....*....|....*....|.
gi 495421495 261 LAIQEMLGHEKITTTEIYTHI 281
Cdd:cd01193  156 RTIQELLGHSDLSTTMIYTHV 176
Phage_integrase pfam00589
Phage integrase family; Members of this family cleave DNA substrates by a series of staggered ...
 112-282 6.54e-50

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: 162.87  E-value: 6.54e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  112 VLTVNEINSILDTIDlTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVE-GKGSKQRLVPISETAIKEIK 190
Cdd:pfam00589   1 RLTEDEVERLLDAAE-TGPLSIRDKALLELLYATGLRISELCSLRWSDIDFENGVIRVHrGKGNKERTVPLSDAALELLK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  191 NYLYDRNhvpVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHE 270
Cdd:pfam00589  80 EWLSKRL---LEAPKSDYLFASKRGKPLSRQTVRKIFKRAGKEAGLELPLHPHMLRHSFATHLLEAGVDLRVVQKLLGHS 156

                         170
                  ....*....|..
gi 495421495  271 KITTTEIYTHID 282
Cdd:pfam00589 157 SISTTQIYTHVA 168
INT_RitC_C_like cd01182
C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio; ...
 113-290 5.07e-42

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: 143.19  E-value: 5.07e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 113 LTVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEG-FIKVEGKGSKQRLVPISETAIKEIKN 191
Cdd:cd01182    1 LTREEMKALLAAPDRNTSLGRRDHALLLLLYDTGARVQELADLTIRDLRLDDPaTVRLHGKGRKERTVPLWKETVAALKA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 192 YLYDRNHVPVKKGFEdILFLSRRGTALSRIMVFHIIKQQTEMA-----GIKKNVSPHTFRHSFATHLLEGGANLLAIQEM 266
Cdd:cd01182   81 YLQEFHLTPDPKQLF-PLFPNRRGQPLTRDGVAYILNKYVALAsnrcpSLPKRITPHTLRHTKAMHLLQAGVDLTVIRDW 159

                        170       180
                 ....*....|....*....|....
gi 495421495 267 LGHEKITTTEIYTHIDRQFLRKEI 290
Cdd:cd01182  160 LGHESVETTQIYAEADLEMKREAL 183
DNA_BRE_C cd00397
DNA breaking-rejoining enzymes, C-terminal catalytic domain; The DNA breaking-rejoining enzyme ...
 117-279 2.19e-41

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: 141.08  E-value: 2.19e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 117 EINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEGKG---SKQRLVPISETAIKEIKNYL 193
Cdd:cd00397    1 ELEKLLDAIDEDKKIDLRDRAILLLLLETGLRISELLALKVKDIDLDNGTIRVRGKKtkgGKERTVPLPKELAEELKEYL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 194 ---YDRNHVPVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKknVSPHTFRHSFATHLLEGGANLLAIQEMLGHE 270
Cdd:cd00397   81 kerRDKRGPLLKSLYLNKLFGTKLGERLSRRTLRRIFKKAGIEAGRK--ITPHSLRHTFATNLLENGVDIKVVQKLLGHS 158


                 ....*....
gi 495421495 271 KITTTEIYT 279
Cdd:cd00397  159 SISTTQRYL 167
integrase_gron TIGR02249
integron integrase; Members of this family are integrases associated with integrons (and ...
 6-281 5.66e-34

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: 125.97  E-value: 5.66e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495    6 DKVERYKTYLRLEKAlsanSIDAYLtdlDKLTNFVESEGKKYADVTYD-DLQQFVARLHDIG-IHPRSQARIISGIKSFY 83
Cdd:TIGR02249   3 DQVREHMRTRHYAKR----TEEAYL---HWIKRFIRFHNKRHPSTMGDtEVEAFLSDLAVDGkVAASTQNQALNALLFLY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495   84 RfLFLDNYITTDptELLESPKIGLKLPEVLTVNEINSILDTIDltlpegQRNRAMLEVLYSCGLRVSELVSLRFTDVYFD 163
Cdd:TIGR02249  76 K-EILKTPLSLM--ERFVRAKRPRKLPVVLTREEVRRLLEHLE------GKYRLIAKLLYGSGMRLMECLRLRIQDIDFD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  164 EGFIKV-EGKGSKQRLVPISETAIKEIKNY------LYDRNHVPvkkGFEDI---------------------LFLSRRg 215
Cdd:TIGR02249 147 YGEIRIrQGKGGKDRTVTLPKELIPPLREQielaraYHEADLAE---GYGGVylphalarkypnapkewgwqyLFPSHR- 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  216 taLSR------IMVFHI--------IKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHI 281
Cdd:TIGR02249 223 --LSRdpesgvIRRHHInettiqraVRRAVERAGIEKPVTCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
INT_RitA_C_like cd01188
C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio; ...
 117-288 2.88e-31

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: 115.03  E-value: 2.88e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 117 EINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEG-KGSKQRLVPISETAIKEIKNYLYD 195
Cdd:cd01188    4 EVRRLLAAIDRLTPVGLRDYAILLLLARLGLRAGDVAGLRLDDIDWRSGTITVRQkKTGRPVELPLTEPVGEALADYLRD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 196 RNhvpvKKGFEDILFLSRR---GTALSRIMVFHIIKQQTEMAGIKKN-VSPHTFRHSFATHLLEGGANLLAIQEMLGHEK 271
Cdd:cd01188   84 GR----PRTDSREVFLRARapyRPLSSTSQISSIVRRYLRKAGIEPShRGTHSLRHSLATRMLRAGTSLKVIADLLGHRS 159

                        170
                 ....*....|....*..
gi 495421495 272 ITTTEIYTHIDRQFLRK 288
Cdd:cd01188  160 IETTAIYAKIDVDDLRE 176
xerS PRK05084
site-specific tyrosine recombinase XerS; Reviewed
 16-282 9.09e-28

site-specific tyrosine recombinase XerS; Reviewed


Pssm-ID: 235339 [Multi-domain]  Cd Length: 357  Bit Score: 110.01  E-value: 9.09e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  16 RLEKALSANSIDAYLTDLDKLTNFVESEG----KKYADVTYDDL--------QQFV----------ARLHDIGIHPRSQA 73
Cdd:PRK05084  28 KLATPYSPTTLYEYLTEYRRFFNWLISEGlsdaSKIKDIPLSTLenltkkdvEAFIlylrerpllnGHSTKKGNSQTTIN 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  74 RIISGIKSFYRFLfldnyittdpTELLESP------------KIGLKLPEV-------------LTVNEINSILDTID-- 126
Cdd:PRK05084 108 RTLSALKSLFKYL----------TEEAENEdgepyfyrnvmkKIELKKKKEtlaarahnlkqklFLGDEDYEFLDFIDne 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 127 --LTLPEGQ---------RNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEGKGSKQRLVPISETAIKEIKNYL-- 193
Cdd:PRK05084 178 yeQKLSNRAlssfkknkeRDLAIIALILGSGLRVSELVNLDLSDLNLKQMTIDVTRKGGKRDSVNIAPFALPYLEEYLki 257

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 194 -YDRNHVPVKkgfEDILFLSRRGTALSRIMVFHIIKqqteM-----AGIKKNVSPHTFRHSFATHLLEGGANLLAIQEML 267
Cdd:PRK05084 258 rASRYKAEKQ---EKALFLTKYRGKPNRISARAIEK----MvakysEAFGVRLTPHKLRHTLATRLYDATKDQVLVADQL 330

                        330
                 ....*....|....*
gi 495421495 268 GHEKITTTEIYTHID 282
Cdd:PRK05084 331 GHTSTETTDLYTHIV 345
INT_C_like_5 cd01195
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 114-280 1.84e-26

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: 102.16  E-value: 1.84e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 114 TVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEGKGSKQR-LVPISETAIKEIKNY 192
Cdd:cd01195    1 SREEARQRLDAADRHTAKGKRDEALVRLLLDNALRRSEAVALDVEDLEKEHRRLRILGKGKKQReVVTLPPTTREALAAW 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 193 LYDRNHVpvkkgfEDILFLS----RRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLA-IQEML 267
Cdd:cd01195   81 LAARGEA------EGPLFVSldraSRGRRLSPQAVYRIVRRLAERIGLGKRLSPHGLRHSAITLALDAGAGLIRkVQDFS 154

                        170
                 ....*....|...
gi 495421495 268 GHEKITTTEIYTH 280
Cdd:cd01195  155 RHADLRTLQVYDD 167
INT_RitB_C_like cd00797
C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio; ...
 113-280 2.55e-25

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: 100.07  E-value: 2.55e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 113 LTVNEINSILDTIDLTLPEGQRNRAMLE----VLYSCGLRVSELVSLRFTDVYFDEGFIKV-EGKGSKQRLVPISETAIK 187
Cdd:cd00797    1 YTDAEIRRLLAAADQLPPESPLRPLTYAtlfgLLYATGLRVGEALRLRLEDVDLDSGILTIrQTKFGKSRLVPLHPSTVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 188 EIKNYLYDRnHVPVKKGFEDILFLSRRGTALSRIMVFHIIKQQTEMAGIK-----KNVSPHTFRHSFATHLL----EGGA 258
Cdd:cd00797   81 ALRDYLARR-DRLLPSPSSSYFFVSQQGGRLTGGGVYRVFRRLLRRIGLRgagdgRGPRLHDLRHTFAVNRLtrwyREGA 159

                        170       180
                 ....*....|....*....|....*.
gi 495421495 259 N----LLAIQEMLGHEKITTTEIYTH 280
Cdd:cd00797  160 DverkLPVLSTYLGHVNVTDTYWYLT 185
INT_Rci_Hp1_C cd00796
Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal ...
 111-280 1.09e-23

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: 94.70  E-value: 1.09e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 111 EVLTVNEINSILDTIDLTlpEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFI-KVEGKGSKQRLVPISETAIKEI 189
Cdd:cd00796    3 RFLTEDEEARLLAALEES--TNPHLRLIVLLALYTGARRGEILSLRWDDIDLEVGLIvLPETKNGKPRTVPLSDEAIAIL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 190 KNY--LYDRNHVPVKKGFEDILFLSRRgtalsrimvfHIIKQQTEMAGIKkNVSPHTFRHSFATHLLEGGANLLAIQEML 267
Cdd:cd00796   81 KELkrKRGKDGFFVDGRFFGIPIASLR----------RAFKKARKRAGLE-DLRFHDLRHTFASRLVQAGVPIKTVAKIL 149

                        170
                 ....*....|...
gi 495421495 268 GHEKITTTEIYTH 280
Cdd:cd00796  150 GHSSIKMTMRYAH 162
INT_ICEBs1_C_like cd01189
C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons; ...
 116-280 1.24e-22

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: 91.47  E-value: 1.24e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 116 NEINSILDTIDLtlpEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEG-----------------KGSKqRL 178
Cdd:cd01189    2 EELKKLLEALKK---RGDRYYLLFLLALLTGLRRGELLALTWSDIDFENGTIRINRtlvrkkkggyvikppktKSSI-RT 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 179 VPISETAIKEIKNYLydrnhvpvkkgfedilflsrrgtALSRIMvfhiikqqtEMAGIKkNVSPHTFRHSFATHLLEGGA 258
Cdd:cd01189   78 IPLPDELIELLKELK-----------------------AFKKLL---------KKAGLP-RITPHDLRHTFASLLLEAGV 124

                        170       180
                 ....*....|....*....|...
gi 495421495 259 NLLAIQEMLGHEKI-TTTEIYTH 280
Cdd:cd01189  125 PLKVIAERLGHSDIsTTLDVYAH 147
INT_C_like_4 cd01194
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 113-280 3.05e-22

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: 91.28  E-value: 3.05e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 113 LTVNEINSILDTID-LTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEG--FIKVEGKG--SKQRLVPISETAIK 187
Cdd:cd01194    1 LTLEQARQLLASLPiDDSIIGLRDRAIISLMVTEGLRTVEIVRADVGDLRQEGEgtILYVQGKGktSKDDFVYLRPDVLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 188 EIKNYLYDRnhvpVKKGFEDILFLS----RRGTALSRIMVFHIIKQQTEMAGIKKN-VSPHTFRHSFATHLLEGGANLLA 262
Cdd:cd01194   81 ALQAYLKAR----GKLDFEEPLFTSlsnnSKGQRLTTRSIRRIIKKYLRKAGLDDDrLTAHSLRHTAGTLALKAGKSLRE 156

                        170
                 ....*....|....*...
gi 495421495 263 IQEMLGHEKITTTEIYTH 280
Cdd:cd01194  157 VQQLLRHSDPNTTMIYAH 174
INTN1_C_like cd01185
Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal ...
 125-282 6.66e-22

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: 89.63  E-value: 6.66e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 125 IDLTLPEGQRNRAMLEV-LYSC--GLRVSELVSLRFTDVYFDEG--FIKVE-GKGSKQRLVPISETAIKEIKNYLYDRNH 198
Cdd:cd01185    7 MALELSDTSRLELVRDMfLFSCytGLRFSDLKNLTWKNIVEASGrtWIRYRrKKTGKPVTVPLLPVAREILEKYKDDRSE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 199 VPVKKGfedilflsrrgtaLSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIY 278
Cdd:cd01185   87 GKLFPV-------------LSNQKINRYLKEIAKIAGIDKHLTFHVARHTFATLLLLKGVDIETISKLLGHSSIKTTQIY 153


                 ....
gi 495421495 279 THID 282
Cdd:cd01185  154 AKIV 157
PRK15417 PRK15417
integron integrase;
103-281 3.78e-21

integron integrase;


Pssm-ID: 185315 [Multi-domain]  Cd Length: 337  Bit Score: 91.65  E-value: 3.78e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 103 PKIGLKLPEVLTVNEINSILDTIdltlpEGQrNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKV-EGKGSKQRLVPI 181
Cdd:PRK15417 107 PRPSRRLPVVLTPDEVVRILGFL-----EGE-HRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVrEGKGSKDRALML 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 182 SET---AIKE---------IKNYLYDRNHVPVKKGFEDILflSRRGTALSRIMVF----------------HIIKQQT-- 231
Cdd:PRK15417 181 PESlapSLREqlsrarawwLKDQAEGRSGVALPDALERKY--PRAGHSWPWFWVFaqhthstdprsgvvrrHHMYDQTfq 258

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495421495 232 -------EMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTHI 281
Cdd:PRK15417 259 rafkravEQAGITKPATPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 315
PRK09870 PRK09870
tyrosine recombinase; Provisional
 104-279 3.89e-21

tyrosine recombinase; Provisional


Pssm-ID: 182125  Cd Length: 200  Bit Score: 88.84  E-value: 3.89e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 104 KIGLKLPEVLTVNEINSILDTIDlTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEG-KGSKQRLVPIS 182
Cdd:PRK09870   4 KADNKKRNFLTHSEIESLLKAAN-TGPHAARNYCLTLLCFIHGFRASEICRLRISDIDLKAKCIYIHRlKKGFSTTHPLL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 183 ETAIKEIKNYLYDRNHVPVKKgfEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLA 262
Cdd:PRK09870  83 NKEIQALKNWLSIRTSYPHAE--SEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALANMGIDTRL 160

                        170
                 ....*....|....*..
gi 495421495 263 IQEMLGHEKITTTEIYT 279
Cdd:PRK09870 161 IQDYLGHRNIRHTVWYT 177
INT_FimBE_like cd01197
FimB and FimE and related proteins, integrase/recombinases; This CD includes proteins similar ...
 113-279 7.94e-21

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: 87.56  E-value: 7.94e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 113 LTVNEINSILDTIDLTlPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEG-KGSKQRLVPISETAIKEIKN 191
Cdd:cd01197    7 LTGKEVQALLQAACRG-RTPARDYCLLLLAFRHGFRVSELCDLHLSDVDLESRRLHIRRlKNGFSTTHPLRFDEREALEA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 192 YLYDRNHVPVKKgfEDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEK 271
Cdd:cd01197   86 WLKERANWKGAD--TDWIFLSRRGGPLSRQQAYRIIRDLGKEAGTVTQTHPHMLRHACGYALADRGADTRLIQDYLGHRN 163


                 ....*...
gi 495421495 272 ITTTEIYT 279
Cdd:cd01197  164 IRHTVIYT 171
INT_C_like_3 cd01192
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 122-288 1.64e-20

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: 86.58  E-value: 1.64e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 122 LDTIDLTLPE-GQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEGKGSKQRLVPISETAIKEIKNYLYDRNHVP 200
Cdd:cd01192   12 IKEIKLYLKKaNPRNYLLFIVGINTGLRISDLLSLKVEDVTNKDKLSIKEQKTGKQKTFPLNPTLVKALKEYIDDLDLKR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 201 VKKGFEdiLFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTH 280
Cdd:cd01192   92 NDYLFK--SLKQGPEKPISRKQAYKILKKAADDLGLNYNIGTHSLRKTFGYHVYKQGKDIELLMKLLNHSSPSITLRYLG 169


                 ....*...
gi 495421495 281 IDRQFLRK 288
Cdd:cd01192  170 IDQEDVDK 177
INT_C_like_6 cd01196
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 114-290 5.25e-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: 271196  Cd Length: 183  Bit Score: 82.53  E-value: 5.25e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 114 TVNEINSILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYF--DEGFIKVEGKGSKQRLVPISETAIKEIKN 191
Cdd:cd01196    1 TAPEARRLLESIDSTHPVGLRDRALIALMVYSFARIGAVLAMRVEDVYDqgRRLWVRLAEKGGKQHEMPCHHDLEEYLRA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 192 YLydrnhvpVKKGFED-----ILFLSRRGT------ALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANL 260
Cdd:cd01196   81 YL-------EAAEIEEdpkgpLFRTTRGGTrklthnPLTQANAYRMVRRRAIAADIPTAIGNHSFRATGITAYLKNGGTL 153

                        170       180       190
                 ....*....|....*....|....*....|
gi 495421495 261 LAIQEMLGHEKITTTEIYTHIDRQFLRKEI 290
Cdd:cd01196  154 EDAQNMANHASTRTTQLYDRRSDKITLDEV 183
FimB COG0582
Integrase/recombinase, includes phage integrase [Replication, recombination and repair, ...
 48-292 2.15e-17

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


Pssm-ID: 440347 [Multi-domain]  Cd Length: 391  Bit Score: 81.62  E-value: 2.15e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  48 ADVTYDDLQQFVARLHDIGIHprSQA-RIISGIKSFYRFLFLDNYITTDPTELLespKIGLKLPEV-----LTVNEINSI 121
Cdd:COG0582  140 AEITPPDLLAVLRPIEARGAP--ETArRVRQRLRQVFRYAVARGLIERNPAADL---KGALPKPKVkhhpaLTPEELPEL 214

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 122 LDTIDlTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEG---KGSKQRLVPISETAIKEIKnylydrnH 198
Cdd:COG0582  215 LRALD-AYRGSPVTRLALRLLLLTGVRPGELRGARWSEIDLEAALWTIPAermKTRRPHIVPLSRQALEILK-------E 286

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 199 VPVKKGFEDILFLSRRG--TALSRimvfHIIKQQTEMAGIKKnVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTE 276
Cdd:COG0582  287 LKPLTGDSEYVFPSRRGpkKPMSE----NTLNKALRRMGYGR-FTPHGFRHTASTLLNEAGFPPDVIERQLAHKDGNKVR 361

                        250
                 ....*....|....*....
gi 495421495 277 -IYTHIDrqFL--RKEILE 292
Cdd:COG0582  362 aAYNRAD--YLeeRREMMQ 378
INT_tnpA_C_Tn554 cd01186
Putative Transposase A from transposon Tn554, C-terminal catalytic domain; This family ...
 112-289 5.30e-17

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: 77.07  E-value: 5.30e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 112 VLTVNEINSILDTIDLTlpegqRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEGKG----------SKQRLVPI 181
Cdd:cd01186    1 VLTPREVQELINACNNL-----RDKFLLALLYETGLRIGEALGLRIEDIDMADNQIELVPREdntnearaksMRERRIPV 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 182 SETAIKEIKNYLYDRNHVPVKKGFEDILFLSRR--GTALSRIMVFHIIKQQTEMAGIkkNVSPHTFRHSFATHLLEGGAN 259
Cdd:cd01186   76 SQDLIDLYADYLTYIYCEEAEFSITVFVNVKGGnqGKAMNYSDVYDLVRRLKKRTGI--DFTPHMFRHTHATALIRAGWS 153

                        170       180       190
                 ....*....|....*....|....*....|.
gi 495421495 260 LLAIQEMLGHEKI-TTTEIYTHIDRQFLRKE 289
Cdd:cd01186  154 IEVVARRLGHAHVqTTLNTYGHLSEEDIRRE 184
Phage_int_SAM_1 pfam02899
Phage integrase, N-terminal SAM-like domain;
8-86 1.19e-16

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 427047 [Multi-domain]  Cd Length: 83  Bit Score: 73.45  E-value: 1.19e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495421495    8 VERYKTYLRLEKALSANSIDAYLTDLDKLTNFVESEGKKYADVTYDDLQQFVARLHDIGIHPRSQARIISGIKSFYRFL 86
Cdd:pfam02899   1 IDQFLEYLSLERGLSPHTLRAYRRDLLAFLKFLSEGGSSLEQITTSDVRAFLAELRAQGLSASSLARRLSALRSFYQFL 79
PRK09871 PRK09871
tyrosine recombinase; Provisional
 130-279 1.71e-16

tyrosine recombinase; Provisional


Pssm-ID: 182126  Cd Length: 198  Bit Score: 76.17  E-value: 1.71e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 130 PEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEG-KGSKQRLVPISETAIKEIKNYLYDRNHVpvkKGFE-- 206
Cdd:PRK09871  23 ATGARDYCLILLAYRHGMRISELLDLHYQDLDLNEGRINIRRlKNGFSTVHPLRFDEREAVERWTQERANW---KGADrt 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495421495 207 DILFLSRRGTALSRIMVFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYT 279
Cdd:PRK09871 100 DAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYT 172
INT_Cre_C cd00799
C-terminal catalytic domain of Cre recombinase (also called integrase); Cre-like recombinases ...
 120-287 1.38e-15

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: 73.49  E-value: 1.38e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 120 SILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYF--DEGFI------K--VEGKGskqRLVPISET----A 185
Cdd:cd00799    3 AMLATLDDTTLRGLRDRALLLLGFAGALRRSELVALRVEDLTRfvDGGLLirlrrsKtdQDGEG---EIKALPYGpetcP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 186 IKEIKNYLYDRN--HVPVkkgFEDIlflSRRGTALSRIM----VFHIIKQQTEMAGI-KKNVSPHTFRHSFATHLLEGGA 258
Cdd:cd00799   80 VRALRAWLEAAGipSGPL---FRRI---RRGGSVGTTRLsdrsVARIVKRRAALAGLdPGDFSGHSLRRGFATEAARAGA 153

                        170       180
                 ....*....|....*....|....*....
gi 495421495 259 NLLAIQEMLGHEKITTTEIYTHIDRQFLR 287
Cdd:cd00799  154 SLPEIMAQGGHKSVATVMRYIREADRFKD 182
INT_C_like_2 cd01191
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 142-278 3.59e-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: 60.90  E-value: 3.59e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 142 LYSCGLRVSELVSLRFTDVyfDEGFIKVEGKGSKQRLVPISETAIKEIKNYLYDRNHvpvKKGFediLFLSRRGTALSRI 221
Cdd:cd01191   29 LAATGARVSELIKIKVEHV--ELGYFDIYSKGGKLRRLYIPKKLRNEALEWLKSTNR---KSGY---IFLNRFGERITTR 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495421495 222 MVFHIIKQQTEMAGIKKNV-SPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIY 278
Cdd:cd01191  101 GIAQQLKNYARKYGLNPKVvYPHSFRHRFAKNFLEKYNDIALLADLMGHESIETTRIY 158
int PHA02601
integrase; Provisional
 113-280 5.68e-11

integrase; Provisional


Pssm-ID: 222904 [Multi-domain]  Cd Length: 333  Bit Score: 62.44  E-value: 5.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 113 LTVNEINSILDTIDltlpeGQRNRAMLEVLYSC---GLRVSELVSLRFTDV-YFDEGFIKVegKGSKQRLVPISEtaike 188
Cdd:PHA02601 173 LTKEEIERLLDACD-----GSRSPDLGLIAKIClatGARWSEAETLKRSQIsPYKITFVKT--KGKKNRTVPISE----- 240

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 189 iknYLYDRnhVPVKKGFediLFlsrrGTALSRimvFH-IIKQqtemAGIK--KNVSPHTFRHSFATHLLEGGANLLAIQE 265
Cdd:PHA02601 241 ---ELYKM--LPKRRGR---LF----KDAYES---FErAVKR----AGIDlpEGQATHVLRHTFASHFMMNGGNILVLQR 301

                        170
                 ....*....|....*
gi 495421495 266 MLGHEKITTTEIYTH 280
Cdd:PHA02601 302 ILGHATIEMTMAYAH 316
INT_P4_C cd00801
Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in ...
 116-292 2.84e-10

Bacteriophage P4 integrase, C-terminal catalytic domain; P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. 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: 271182 [Multi-domain]  Cd Length: 180  Bit Score: 58.44  E-value: 2.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 116 NEINSILDTIDLTLPEGQRNRAMLEVLYScGLRVSELVSLRFTDVYFDEG--FIKVE-GKGSKQRLVPISETAIKEIKNY 192
Cdd:cd00801    3 DELPELWRALDTANLSPPTKLALRLLLLT-GQRIGELARARWSEIDLEEKtwTIPAErTKNKRPHRVPLSDQALEILEEL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 193 lydRNHVPVKkgfeDILFLSRRGTAlsRIMVFHIIKQQT-EMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGH-E 270
Cdd:cd00801   82 ---KEFTGDS----GYLFPSRRKKK--KPISENTINKALkRLGYKGKEFTPHDLRRTFSTLLNELGIDPEVIERLLNHvL 152

                        170       180
                 ....*....|....*....|....*
gi 495421495 271 KITTTEIYthiDR-QFL--RKEILE 292
Cdd:cd00801  153 GGVVRAAY---NRyDYLeeRREALQ 174
xerD PRK02436
site-specific tyrosine recombinase XerD;
18-278 4.14e-09

site-specific tyrosine recombinase XerD;


Pssm-ID: 235038 [Multi-domain]  Cd Length: 245  Bit Score: 56.15  E-value: 4.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  18 EKALSANSIDAYLTDLDKLTNFVESEgkkyadVTYDDLQQFVARLHDigIHPRSQARIISGIKSFYRFLFLDNYItTDPT 97
Cdd:PRK02436  11 SKQLSENSQKSYRYDLQQFLQLVGER------VSQEKLKLYQQSLAN--LKPSAQKRKISAVNQFLYFLYQKGEL-DSFF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495  98 ELLESPKIGLKLPEVLTVNEINSILDtiDLTLPEGQrnRAMLEVLYsCGLRVSELVSLRFTDVYFDEGFIKVEgKGSKQR 177
Cdd:PRK02436  82 KLKETAKLPESKKEKLEILDLSSFYQ--ETPFPEGQ--LIALLILE-LGLTPSEIAGLKVADIDLDFQVLTIE-KAGGKR 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 178 LVPISETAIKEIKNYLYDrnhvpvkkgfeDILFLsRRGTALSRIMVFHIIKQQTEMAGiKKNVSPHTFRHSFATHLLEGG 257
Cdd:PRK02436 156 VLTLPEALLPFLEAILNQ-----------TYLFE-HKGKPYSRQWFFNQLKSFVKSIG-YPGLSAQKLREQFILKQKEAG 222

                        250       260
                 ....*....|....*....|.
gi 495421495 258 ANLLAIQEMLGHEKITTTEIY 278
Cdd:PRK02436 223 KSIYELARLLGLKSPVTLEKY 243
INT_C_like_1 cd01184
Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain; Tyrosine ...
 142-280 1.40e-08

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: 53.46  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 142 LYScGLRVSELVSLRFTDVYFDEG--FIKV----EGKGSKQ----RLVPISETAI--------KEIKnylyDRNHVPVKK 203
Cdd:cd01184   33 LYT-GARLNEICQLRVDDIKEEDGiwCIDInddaEGRRLKTkasrRLVPIHPRLIelgfldyvEALR----ADGKLFLFP 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 204 GFEDILFlsRRGTALSRIMVFHIIKqqtemAGIK--KNVSPHTFRHSFATHLLEGGANLLAIQEMLGHE-KITTTEIYTH 280
Cdd:cd01184  108 EKRDKDG--KYSKAASKWFNRLLRK-----LGIKddERKSFHSFRHTFITALKRAGVPEELIAQIVGHSrGGVTHDTYGK 180
INT_Lambda_C cd00800
C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; ...
 136-279 1.59e-08

C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase; Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase 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: 271181 [Multi-domain]  Cd Length: 161  Bit Score: 53.12  E-value: 1.59e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 136 RAMLEVLYSCGLRVSELVSLRFTDVyfDEGFIKVE-GKGSKQRLVPISEtaikEIKNYLYDRNHVPVKKGFedILFLSRR 214
Cdd:cd00800   15 RLAMELALLTGQRQGDLLRLKWSDI--TDGGLLVEqSKTGKKLLIPWTP----SLRALVDRIRALPRKRSE--YLINSRK 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495421495 215 GTALSRIMVFHIIKQQTEMAGIKKNVSPHTF---RHSFATHLLEGGaNLLAIQEMLGHEKITTTEIYT 279
Cdd:cd00800   87 GGPLSYDTLKSAWRRARKAAGLKGETEGFTFhdlRAKAATDYAEQG-GSTDAQALLGHKSDAMTERYT 153
INT_tnpB_C_Tn554 cd01187
Putative Transposase B from transposon Tn554, C-terminal catalytic domain; This family ...
 137-280 1.33e-07

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: 49.74  E-value: 1.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 137 AMLEVLYSCGLRVSELVSLRFTDVYFDEG-------FIKVEGKGSKQRLVPISETAIKEIKNYLYDRNHvpvkkgfedil 209
Cdd:cd01187   17 PVVQAAVFTGARASELATLKFGCLHAQTSddgtflyWLKWENKGGKQLDIPISKKVAELIKTINWTLNE----------- 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495421495 210 flsrrgtalsrimvFHIIKQQTEMAGIKKNVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYTH 280
Cdd:cd01187   86 --------------LSELKNISDDHGERFRFHTHRFRHTVATRLANSGMGILVLQQLLGHSSPEMTLRYAL 142
INT_StrepXerD_C_like cd01190
Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; ...
 121-279 1.20e-04

Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain; This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. 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: 271190  Cd Length: 150  Bit Score: 41.56  E-value: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495421495 121 ILDTIDLTLPEGQRNRAMLEVLYSCGLRVSELVSLRFTDVYFDEGFIKVEgKGSKQRLVPISETAIKEIKnylydrnhvP 200
Cdd:cd01190    5 ILDLSSFYQGDFLKGQLIALLILELGLTPSEIANLKWADFDLDFQVLTIE-KGGIKRVLPLPKKLLPFLE---------Q 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495421495 201 VKKGfeDILFLSRRGTALSRIMVFHIIKQQTEMAGIKKnVSPHTFRHSFATHLLEGGANLLAIQEMLGHEKITTTEIYT 279
Cdd:cd01190   75 HIKA--DYLEFDHEGKAYSRQWLFNQLKKFLNSIGLSG-LTAQKLREQYILKQKEAGKSIYELAKLLGLKSPVTLEKYY 150
Phage_int_SAM_4 pfam13495
Phage integrase, N-terminal SAM-like domain;
9-86 1.64e-04

Phage integrase, N-terminal SAM-like domain;


Pssm-ID: 463898 [Multi-domain]  Cd Length: 83  Bit Score: 39.52  E-value: 1.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495421495    9 ERYKTYLRLEKaLSANSIDAYLTDLDKLTNFVEseGKKYADVTYDDLQQFVARL-HDIGIHPRSQARIISGIKSFYRFL 86
Cdd:pfam13495   3 ERFREALRLRG-YAERTIKAYLRWIRRFLRFHD--KKHPEELTEEDIEAYLSHLaNERNVSASTQNQALNALSFFYRWV 78
 
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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