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Conserved domains on  [gi|15599062|ref|NP_252556|]
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DNA invertase [Pseudomonas aeruginosa PAO1]

Protein Classification

recombinase family protein( domain architecture ID 18951323)

recombinase family protein is a serine recombinase that catalyzes the site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme

CATH:  3.40.50.1390
Gene Ontology:  GO:0015074|GO:0000150|GO:0003677|GO:0006310
PubMed:  11972771|16077726|9348666|21645851|26104451
SCOP:  3000065

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-121 9.25e-54

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


:

Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 167.27  E-value: 9.25e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   2 LIGYVRISTDDQLLDLQRDAMAKAG-CERVFEDTASGAKADRIGLAALLANLRRGDTVVVWRLDRLGRSIKDLIYLVEQL 80
Cdd:cd03768   1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 15599062  81 EDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRE 121
Cdd:cd03768  81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRE 121
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 138-180 4.32e-07

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


The actual alignment was detected with superfamily member cd00569:

Pssm-ID: 481199 [Multi-domain]  Cd Length: 42  Bit Score: 44.62  E-value: 4.32e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15599062 138 GRKKRLDPAKRKVALKLYHERQyTVVEICRMMGIGRSTLYNYI 180
Cdd:cd00569   1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-121 9.25e-54

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 167.27  E-value: 9.25e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   2 LIGYVRISTDDQLLDLQRDAMAKAG-CERVFEDTASGAKADRIGLAALLANLRRGDTVVVWRLDRLGRSIKDLIYLVEQL 80
Cdd:cd03768   1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 15599062  81 EDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRE 121
Cdd:cd03768  81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRE 121
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-182 1.24e-44

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 152.10  E-value: 1.24e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   1 MLIGYVRISTDDQL---LDLQRDAM----AKAGCE--RVFEDTA-SGAKADRIGLAALLANLRRG--DTVVVWRLDRLGR 68
Cdd:COG1961   3 RAAGYARVSTDDQEglsLERQREALrayaEKAGWEivRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062  69 SIKDLIYLVEQLEDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRECTHARLSAARARGRLGG---------R 139
Cdd:COG1961  83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGrppygyrdpK 162

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 15599062 140 KKRLDPAKRKV---ALKLYHERqYTVVEICRMM---GI---GRSTLYNYITE 182
Cdd:COG1961 163 KLVIDEEEAEVvrrIFELYLEG-KSLREIARELnerGIptwSRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-136 1.28e-42

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 139.71  E-value: 1.28e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062     3 IGYVRISTDDQ--LLDLQRDAMAKAGCER----VFEDT-ASGAKADRIGLAALLANLR--RGDTVVVWRLDRLGRSIKDL 73
Cdd:pfam00239   2 IGYARVSTEDQddSLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRagKGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599062    74 IYLVEQLEDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRECTHARLSAARARGRL 136
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-135 6.79e-39

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 130.44  E-value: 6.79e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062      3 IGYVRISTDDQL---LDLQRDAMAKA----GCE--RVFEDTA-SGAKADRIGLAALLANLRRGD--TVVVWRLDRLGRSI 70
Cdd:smart00857   2 AGYARVSTDDQAdgsLERQLEALRAYaernGWEvvRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599062     71 KDLIYLVEQLEDAGVGLKSLQENI-DTTSTGGRLVFHLFAALAEFERNLIRECTHARLSAARARGR 135
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-180 4.32e-18

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 77.84  E-value: 4.32e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062    1 MLIGYVRISTDDQLLDLQRDAMAKAGCERVF------EDTASGAKA--DRiGLAALLANLRRGDTVVVWRLDRLGRSIKD 72
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLtidkwiEETISGTKSykDR-KLGKLLKKMRKGDILIVSELSRLGRNLME 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   73 LIYLVEQLEDAGVGLKS------LQENIDTTStggrLVFhLFAALAEFERNLIRECTHARLSAARARGRLGGRKKRLDPA 146
Cdd:PRK13413  80 IMSILNICMEKEVIVYTikegyeLGDDINSKV----LAF-AFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKGSTPK 154

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 15599062  147 KRKVA-----LKLYHERQYTVVEICRMMGIGRSTLYNYI 180
Cdd:PRK13413 155 KYKLTgkeekIKKLLDKGTSKSEIARKLGVSRTTLARFL 193
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 138-180 4.32e-07

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 44.62  E-value: 4.32e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15599062 138 GRKKRLDPAKRKVALKLYHERQyTVVEICRMMGIGRSTLYNYI 180
Cdd:cd00569   1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
HTH_Tnp_1 pfam01527
Transposase; Transposase proteins are necessary for efficient DNA transposition. This family ...
 138-184 5.37e-04

Transposase; Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.


Pssm-ID: 426308 [Multi-domain]  Cd Length: 75  Bit Score: 37.33  E-value: 5.37e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15599062   138 GRKKRLDPAKRKVALKLYHERQYTVVEICRMMGIGRSTLYNYITEAE 184
Cdd:pfam01527   2 KKRRRFSEEFKLRAVKEVLEPGRTVKEVARRHGVSPNTLYQWRRQYE 48
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
139-187 1.65e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 36.44  E-value: 1.65e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15599062 139 RKKRLDPAKRKVALKLYHERQYTVVEICRMMGIGRSTLYNYITEAERNA 187
Cdd:COG2963   4 KRRRYSPEFKAEAVRLVLEGGASVAEVARELGISPSTLYRWVRQYREGG 52
 
Name Accession Description Interval E-value
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 2-121 9.25e-54

Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1.


Pssm-ID: 239737 [Multi-domain]  Cd Length: 126  Bit Score: 167.27  E-value: 9.25e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   2 LIGYVRISTDDQLLDLQRDAMAKAG-CERVFEDTASGAKADRIGLAALLANLRRGDTVVVWRLDRLGRSIKDLIYLVEQL 80
Cdd:cd03768   1 VIGYARVSTDDQSLERQLEALKAAGeCDKIFEEKGSGGKKERPELQKLLEDLREGDTLVVTKLDRLGRSTKDLLEIVEEL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 15599062  81 EDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRE 121
Cdd:cd03768  81 REKGVSLRSLTEGIDTSTPSGKLMLTILGAFAEFERELIRE 121
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-182 1.24e-44

Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair];


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 152.10  E-value: 1.24e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   1 MLIGYVRISTDDQL---LDLQRDAM----AKAGCE--RVFEDTA-SGAKADRIGLAALLANLRRG--DTVVVWRLDRLGR 68
Cdd:COG1961   3 RAAGYARVSTDDQEglsLERQREALrayaEKAGWEivRIYVDEGvSGTSKDRPGLQRLLADLRAGkfDTLVVWKLDRLGR 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062  69 SIKDLIYLVEQLEDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRECTHARLSAARARGRLGG---------R 139
Cdd:COG1961  83 NLADLLELVEELKERGVRLISLTEGIDTSTPMGRLLLTILAAFAEFERELISERTRAGLAAAKARGKYLGrppygyrdpK 162

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
gi 15599062 140 KKRLDPAKRKV---ALKLYHERqYTVVEICRMM---GI---GRSTLYNYITE 182
Cdd:COG1961 163 KLVIDEEEAEVvrrIFELYLEG-KSLREIARELnerGIptwSRSTVYRILKN 213
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 3-136 1.28e-42

Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796.


Pssm-ID: 425548 [Multi-domain]  Cd Length: 144  Bit Score: 139.71  E-value: 1.28e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062     3 IGYVRISTDDQ--LLDLQRDAMAKAGCER----VFEDT-ASGAKADRIGLAALLANLR--RGDTVVVWRLDRLGRSIKDL 73
Cdd:pfam00239   2 IGYARVSTEDQddSLERQLEALRAYAACNgkivEFEDKgVSGRKLDRPGLQRLLALLRagKGDVLVVYKLDRLGRSLRDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599062    74 IYLVEQLEDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRECTHARLSAARARGRL 136
Cdd:pfam00239  82 LTLVEELREKGVDLVSLDEGIDTSTPMGRLLLTILAALAEFERALIRERTRAGLAAAAARGKL 144
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 3-135 6.79e-39

Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.


Pssm-ID: 214861 [Multi-domain]  Cd Length: 148  Bit Score: 130.44  E-value: 6.79e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062      3 IGYVRISTDDQL---LDLQRDAMAKA----GCE--RVFEDTA-SGAKADRIGLAALLANLRRGD--TVVVWRLDRLGRSI 70
Cdd:smart00857   2 AGYARVSTDDQAdgsLERQLEALRAYaernGWEvvRIYEDEGvSGKKADRPGLQRLLADLRAGDidVLVVYKLDRLGRSL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599062     71 KDLIYLVEQLEDAGVGLKSLQENI-DTTSTGGRLVFHLFAALAEFERNLIRECTHARLSAARARGR 135
Cdd:smart00857  82 RDLLALLELLEEKGVRLVSLKEGIlDTSTPAGRLLLDILAALAEFERELISERTKAGLARAAARGR 147
Ser_Recombinase cd00338
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 5-121 1.13e-24

Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are proteins with N-terminal DNA binding domains similar to IS607- and IS1535-transposases from Helicobacter and Mycobacterium.


Pssm-ID: 238206 [Multi-domain]  Cd Length: 137  Bit Score: 93.48  E-value: 1.13e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   5 YVRISTDDQL----LDLQRDAMAKAgCER-------VFEDTASGAKA--DRIGLAALLANLRRG--DTVVVWRLDRLGRS 69
Cdd:cd00338   2 YARVSTDKQEqgdsLERQREALREY-AARnglevvgEYEDAGSSATSlvDRPGLQRLLADVKAGkiDVVLVEKLDRLSRN 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 15599062  70 IKDLIYLVEQLEDAGVGLKSLQENIDTTSTGGRLVFHLFAALAEFERNLIRE 121
Cdd:cd00338  81 LVDLLELLELLEAHGVRVVTADGEIDLDSEDGRLMLGILAAMAEEESKLISE 132
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
1-180 4.32e-18

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 77.84  E-value: 4.32e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062    1 MLIGYVRISTDDQLLDLQRDAMAKAGCERVF------EDTASGAKA--DRiGLAALLANLRRGDTVVVWRLDRLGRSIKD 72
Cdd:PRK13413   1 MIYAYIRVSTDKQTVENQRFEITNFAEKNNLtidkwiEETISGTKSykDR-KLGKLLKKMRKGDILIVSELSRLGRNLME 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   73 LIYLVEQLEDAGVGLKS------LQENIDTTStggrLVFhLFAALAEFERNLIRECTHARLSAARARGRLGGRKKRLDPA 146
Cdd:PRK13413  80 IMSILNICMEKEVIVYTikegyeLGDDINSKV----LAF-AFGLSAEIERNLISQRTKEALARKKAEGVTLGRPKGSTPK 154

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 15599062  147 KRKVA-----LKLYHERQYTVVEICRMMGIGRSTLYNYI 180
Cdd:PRK13413 155 KYKLTgkeekIKKLLDKGTSKSEIARKLGVSRTTLARFL 193
SR_Res_par cd03767
Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; ...
 4-90 1.08e-07

Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subgroup is composed of proteins similar to the E. coli resolvase found in the par region of the RP4 plasmid, which encodes a highly efficient partitioning system. This protein is part of a complex stabilization system involved in the resolution of plasmid dimers during cell division. Similar to Tn3 and other resolvases, members of this family may contain a C-terminal DNA binding domain.


Pssm-ID: 239736 [Multi-domain]  Cd Length: 146  Bit Score: 48.86  E-value: 1.08e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   4 GYVRISTDDQLLDLQRDAMAKAGCER------VFEDTASGAKADRIGLAALLANLRRGDTVVVWRLDRLGR-SIKDLIYL 76
Cdd:cd03767   3 AYLRASTDEQDATRAKESLEAFATERgfyiagFYVENASGAKLDRPELFRLLDDAQSGDVLLVEQIDRLSRlPLDDWETL 82

                        90
                ....*....|....
gi 15599062  77 VEQLEDAGVGLKSL 90
Cdd:cd03767  83 KASIAAKGLRVVSL 96
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 138-180 4.32e-07

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 44.62  E-value: 4.32e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15599062 138 GRKKRLDPAKRKVALKLYHERQyTVVEICRMMGIGRSTLYNYI 180
Cdd:cd00569   1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
SR_TndX_transposase cd03770
Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of ...
 4-96 3.61e-05

Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.


Pssm-ID: 239739 [Multi-domain]  Cd Length: 140  Bit Score: 41.97  E-value: 3.61e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599062   4 GYVRISTDDqllDLQRDAMA----KAGCE-----------RVFEDTA-SGAKADRIGLAALLANLRRG--DTVVVWRLDR 65
Cdd:cd03770   3 LYCRLSRDD---DLDGESNSienqKAILEeyakengleniRHYIDDGfSGTTFDRPGFNRMIEDIEAGkiDIVIVKDMSR 79

                        90       100       110
                ....*....|....*....|....*....|..
gi 15599062  66 LGRS-IKDLIYLVEQLEDAGVGLKSLQENIDT 96
Cdd:cd03770  80 LGRNyLKVGLYMEILFPKKGVRFIAINDGVDS 111
SR_IS607_transposase_like cd03769
Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members ...
 3-68 4.80e-05

Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements.


Pssm-ID: 239738  Cd Length: 134  Bit Score: 41.48  E-value: 4.80e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15599062   3 IGYVRISTDDQLLDLQRD-------AMAKAGCERVFEDTASGAKADRIGLAALLANLRRG--DTVVVWRLDRLGR 68
Cdd:cd03769   2 VLYARVSSHDQKDDLERQierleayATAQGWIVEVIKDIGSGLNEKRKGLLKLLEDVLAGkvERVVITYKDRLAR 76
HTH_Tnp_1 pfam01527
Transposase; Transposase proteins are necessary for efficient DNA transposition. This family ...
 138-184 5.37e-04

Transposase; Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.


Pssm-ID: 426308 [Multi-domain]  Cd Length: 75  Bit Score: 37.33  E-value: 5.37e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15599062   138 GRKKRLDPAKRKVALKLYHERQYTVVEICRMMGIGRSTLYNYITEAE 184
Cdd:pfam01527   2 KKRRRFSEEFKLRAVKEVLEPGRTVKEVARRHGVSPNTLYQWRRQYE 48
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
139-187 1.65e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 36.44  E-value: 1.65e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15599062 139 RKKRLDPAKRKVALKLYHERQYTVVEICRMMGIGRSTLYNYITEAERNA 187
Cdd:COG2963   4 KRRRYSPEFKAEAVRLVLEGGASVAEVARELGISPSTLYRWVRQYREGG 52
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
138-179 1.68e-03

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 35.02  E-value: 1.68e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 15599062   138 GRKKRLDPAKRKVALKLYhERQYTVVEICRMMGIGRSTLYNY 179
Cdd:pfam02796   1 GRPPKLNEEDINEVITLL-EEGISIKQIAKIFGISRSTVYRY 41
 
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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