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Conserved domains on  [gi|150730|gb|AAA25639|]
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Bin3 protein, partial (plasmid) [Plasmid pI258]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10500321)

helix-turn-helix domain-containing protein such as the Hin-like recombinase unique to bacteria

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
17-69 4.36e-10

Helix-turn-helix domain of resolvase;


:

Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 49.28  E-value: 4.36e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 150730     17 GRPLLYSPNAkdpqkrviYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDN 69
Cdd:pfam02796  1 GRPPKLNEED--------INEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
 
Name Accession Description Interval E-value
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
17-69 4.36e-10

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 49.28  E-value: 4.36e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 150730     17 GRPLLYSPNAkdpqkrviYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDN 69
Cdd:pfam02796  1 GRPPKLNEED--------INEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-65 1.00e-06

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 43.86  E-value: 1.00e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150730     1 RQAQGIQVAKEKGVYKGRPLL-YSPNAK---DPQKRVIYHRVVEMLEEGQAISKIAKEVN------ITRQTVYRI 65
Cdd:COG1961 136 RTRAGLAAAKARGKYLGRPPYgYRDPKKlviDEEEAEVVRRIFELYLEGKSLREIARELNergiptWSRSTVYRI 210
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 38-65 9.59e-05

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: 35.76  E-value: 9.59e-05
                       10        20
               ....*....|....*....|....*...
gi 150730   38 VVEMLEEGQAISKIAKEVNITRQTVYRI 65
Cdd:cd00569 14 ARRLLAAGESVAEIARELGVSRSTLYRY 41
transpos_IS630 NF033545
IS630 family transposase;
37-68 3.52e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 33.77  E-value: 3.52e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 150730     37 RVVEMLEEGQAISKIAKEVNITRQTVYRIKHD 68
Cdd:NF033545   4 RILLLAAEGLSITEIAERLGVSRSTVYRWLKR 35
transpos_IS481 NF033577
IS481 family transposase; null
 42-66 7.74e-03

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 32.95  E-value: 7.74e-03
                         10        20
                 ....*....|....*....|....*
gi 150730     42 LEEGQAISKIAKEVNITRQTVYRIK 66
Cdd:NF033577  10 LEDGWSVREAARRFGISRKTVYKWL 34
 
Name Accession Description Interval E-value
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
17-69 4.36e-10

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 49.28  E-value: 4.36e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 150730     17 GRPLLYSPNAkdpqkrviYHRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDN 69
Cdd:pfam02796  1 GRPPKLNEED--------INEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
SpoIVCA COG1961
Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and ...
 1-65 1.00e-06

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


Pssm-ID: 441564 [Multi-domain]  Cd Length: 388  Bit Score: 43.86  E-value: 1.00e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150730     1 RQAQGIQVAKEKGVYKGRPLL-YSPNAK---DPQKRVIYHRVVEMLEEGQAISKIAKEVN------ITRQTVYRI 65
Cdd:COG1961 136 RTRAGLAAAKARGKYLGRPPYgYRDPKKlviDEEEAEVVRRIFELYLEGKSLREIARELNergiptWSRSTVYRI 210
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 38-65 9.59e-05

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: 35.76  E-value: 9.59e-05
                       10        20
               ....*....|....*....|....*...
gi 150730   38 VVEMLEEGQAISKIAKEVNITRQTVYRI 65
Cdd:cd00569 14 ARRLLAAGESVAEIARELGVSRSTLYRY 41
HTH_23 pfam13384
Homeodomain-like domain;
37-67 1.94e-04

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.32  E-value: 1.94e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 150730     37 RVVEMLEEGQAISKIAKEVNITRQTVYRIKH 67
Cdd:pfam13384  9 RALLLLAEGLSVKEIAELLGVSRRTVYRWLK 39
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 37-67 1.61e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 34.83  E-value: 1.61e-03
                        10        20        30
                ....*....|....*....|....*....|.
gi 150730    37 RVVEMLEEGQAISKIAKEVNITRQTVYRIKH 67
Cdd:COG3415  30 RAVLLLAEGLSVREIAERLGVSRSTVYRWLK 60
transpos_IS630 NF033545
IS630 family transposase;
37-68 3.52e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 33.77  E-value: 3.52e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 150730     37 RVVEMLEEGQAISKIAKEVNITRQTVYRIKHD 68
Cdd:NF033545   4 RILLLAAEGLSITEIAERLGVSRSTVYRWLKR 35
transpos_IS481 NF033577
IS481 family transposase; null
 42-66 7.74e-03

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 32.95  E-value: 7.74e-03
                         10        20
                 ....*....|....*....|....*
gi 150730     42 LEEGQAISKIAKEVNITRQTVYRIK 66
Cdd:NF033577  10 LEDGWSVREAARRFGISRKTVYKWL 34
 
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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