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Conserved domains on  [gi|1169091928|ref|WP_080447080|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Legionella]

Protein Classification

recombinase family protein( domain architecture ID 10252564)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 35-77 7.41e-11

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: 51.56  E-value: 7.41e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 1169091928 35 GRPEKLTDEQKELVKTLYANKKhSIQSICKMVGVGKTTLYKYI 77
Cdd:cd00569    1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
Ser_Recombinase super family cl02788
Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or ...
 1-32 9.55e-09

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.


The actual alignment was detected with superfamily member pfam00239:

Pssm-ID: 445923 [Multi-domain]  Cd Length: 144  Bit Score: 48.42  E-value: 9.55e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1169091928   1 MFHVFGAISEFERNLIKERTLDGLEAARAIGR 32
Cdd:pfam00239 112 LLTILAALAEFERALIRERTRAGLAAAAARGK 143
 
Name Accession Description Interval E-value
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 35-77 7.41e-11

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: 51.56  E-value: 7.41e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 1169091928 35 GRPEKLTDEQKELVKTLYANKKhSIQSICKMVGVGKTTLYKYI 77
Cdd:cd00569    1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-79 1.73e-10

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 55.03  E-value: 1.73e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169091928   1 MFHVFGAISEFERNLIKERTLDGLEAARAIGRQGGRPE---------KLTDEQKELVKTLYA--NKKHSIQSICKM---- 65
Cdd:COG1961   118 LLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPygyrdpkklVIDEEEAEVVRRIFElyLEGKSLREIARElner 197

                          90
                  ....*....|....*.
gi 1169091928  66 --VGVGKTTLYKYINR 79
Cdd:COG1961   198 giPTWSRSTVYRILKN 213
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
5-79 3.63e-09

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 50.49  E-value: 3.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169091928   5 FGAISEFERNLIKERTLDGLEAARAIGRQGGRPE-------KLTDEQKELVKTLyaNKKHSIQSICKMVGVGKTTLYKYI 77
Cdd:PRK13413  116 FGLSAEIERNLISQRTKEALARKKAEGVTLGRPKgstpkkyKLTGKEEKIKKLL--DKGTSKSEIARKLGVSRTTLARFL 193


                  ..
gi 1169091928  78 NR 79
Cdd:PRK13413  194 KT 195
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 1-32 9.55e-09

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: 48.42  E-value: 9.55e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1169091928   1 MFHVFGAISEFERNLIKERTLDGLEAARAIGR 32
Cdd:pfam00239 112 LLTILAALAEFERALIRERTRAGLAAAAARGK 143
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
35-78 1.29e-08

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 45.81  E-value: 1.29e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 1169091928 35 GRPEKLTDEQKELVKTLYaNKKHSIQSICKMVGVGKTTLYKYIN 78
Cdd:pfam02796  1 GRPPKLNEEDINEVITLL-EEGISIKQIAKIFGISRSTVYRYLA 43
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 1-32 5.34e-07

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: 43.77  E-value: 5.34e-07
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1169091928    1 MFHVFGAISEFERNLIKERTLDGLEAARAIGR 32
Cdd:smart00857 116 LLDILAALAEFERELISERTKAGLARAAARGR 147
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 1-23 9.45e-07

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: 42.85  E-value: 9.45e-07
                          10        20
                  ....*....|....*....|...
gi 1169091928   1 MFHVFGAISEFERNLIKERTLDG 23
Cdd:cd03768   104 MLTILGAFAEFERELIRERTKEG 126
 
Name Accession Description Interval E-value
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 35-77 7.41e-11

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: 51.56  E-value: 7.41e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 1169091928 35 GRPEKLTDEQKELVKTLYANKKhSIQSICKMVGVGKTTLYKYI 77
Cdd:cd00569    1 GRPPKLTPEQIAEARRLLAAGE-SVAEIARELGVSRSTLYRYL 42
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-79 1.73e-10

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 55.03  E-value: 1.73e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169091928   1 MFHVFGAISEFERNLIKERTLDGLEAARAIGRQGGRPE---------KLTDEQKELVKTLYA--NKKHSIQSICKM---- 65
Cdd:COG1961   118 LLTILAAFAEFERELISERTRAGLAAAKARGKYLGRPPygyrdpkklVIDEEEAEVVRRIFElyLEGKSLREIARElner 197

                          90
                  ....*....|....*.
gi 1169091928  66 --VGVGKTTLYKYINR 79
Cdd:COG1961   198 giPTWSRSTVYRILKN 213
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
5-79 3.63e-09

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 50.49  E-value: 3.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1169091928   5 FGAISEFERNLIKERTLDGLEAARAIGRQGGRPE-------KLTDEQKELVKTLyaNKKHSIQSICKMVGVGKTTLYKYI 77
Cdd:PRK13413  116 FGLSAEIERNLISQRTKEALARKKAEGVTLGRPKgstpkkyKLTGKEEKIKKLL--DKGTSKSEIARKLGVSRTTLARFL 193


                  ..
gi 1169091928  78 NR 79
Cdd:PRK13413  194 KT 195
Resolvase pfam00239
Resolvase, N terminal domain; The N-terminal domain of the resolvase family (this family) ...
 1-32 9.55e-09

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: 48.42  E-value: 9.55e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1169091928   1 MFHVFGAISEFERNLIKERTLDGLEAARAIGR 32
Cdd:pfam00239 112 LLTILAALAEFERALIRERTRAGLAAAAARGK 143
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
35-78 1.29e-08

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 45.81  E-value: 1.29e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 1169091928 35 GRPEKLTDEQKELVKTLYaNKKHSIQSICKMVGVGKTTLYKYIN 78
Cdd:pfam02796  1 GRPPKLNEEDINEVITLL-EEGISIKQIAKIFGISRSTVYRYLA 43
Resolvase smart00857
Resolvase, N terminal domain; The N-terminal domain of the resolvase family contains the ...
 1-32 5.34e-07

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: 43.77  E-value: 5.34e-07
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1169091928    1 MFHVFGAISEFERNLIKERTLDGLEAARAIGR 32
Cdd:smart00857 116 LLDILAALAEFERELISERTKAGLARAAARGR 147
SR_ResInv cd03768
Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members ...
 1-23 9.45e-07

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: 42.85  E-value: 9.45e-07
                          10        20
                  ....*....|....*....|...
gi 1169091928   1 MFHVFGAISEFERNLIKERTLDG 23
Cdd:cd03768   104 MLTILGAFAEFERELIRERTKEG 126
HTH_22 pfam13309
HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding ...
 28-78 2.94e-04

HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.


Pssm-ID: 463841 [Multi-domain]  Cd Length: 63  Bit Score: 35.13  E-value: 2.94e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1169091928 28 RAIGRQGGRPEKLT-DEQKELVKTLYANK----KHSIQSICKMVGVGKTTLYKYIN 78
Cdd:pfam13309  8 EVLADVGKPPARLTkEEKREIVRALDEKGafllKGAVEKVAKRLGVSRATVYNYLR 63
 
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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