NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1859661303|ref|YP_009849523|]
View 

RNA-dependent RNA polymerase [Gordonia phage Kenosha]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HTH_CRP super family cl46859
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 861-895 4.44e-05

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: 41.16  E-value: 4.44e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1859661303 861 KVMTTAKQQRARNLLASGRTPSEVAQILGVPVSTL 895
Cdd:cd00569     4 PKLTPEQIAEARRLLAAGESVAEIARELGVSRSTL 38
PRK07735 super family cl35608
NADH-quinone oxidoreductase subunit C;
729-861 7.95e-03

NADH-quinone oxidoreductase subunit C;


The actual alignment was detected with superfamily member PRK07735:

Pssm-ID: 236081 [Multi-domain]  Cd Length: 430  Bit Score: 39.58  E-value: 7.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859661303 729 RARKELVSTKPTPYSPSAKKVYSRE-VESLNAKLNVALKNAPRERQAQVLANAVVRQKREANPDMQSDELRKVSAKALAT 807
Cdd:PRK07735   21 EARKRLVAKHGAEISKLEEENREKEkALPKNDDMTIEEAKRRAAAAAKAKAAALAKQKREGTEEVTEEEKAKAKAKAAAA 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1859661303 808 ARARTGANKDQVVITPREWEAIQSGAVSNHKLTQILNNADIQEVKKLATPRENK 861
Cdd:PRK07735  101 AKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKAAALAKQKREGTEEVT 154
 
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 ...
 861-895 4.44e-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: 41.16  E-value: 4.44e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1859661303 861 KVMTTAKQQRARNLLASGRTPSEVAQILGVPVSTL 895
Cdd:cd00569     4 PKLTPEQIAEARRLLAAGESVAEIARELGVSRSTL 38
PRK07735 PRK07735
NADH-quinone oxidoreductase subunit C;
729-861 7.95e-03

NADH-quinone oxidoreductase subunit C;


Pssm-ID: 236081 [Multi-domain]  Cd Length: 430  Bit Score: 39.58  E-value: 7.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859661303 729 RARKELVSTKPTPYSPSAKKVYSRE-VESLNAKLNVALKNAPRERQAQVLANAVVRQKREANPDMQSDELRKVSAKALAT 807
Cdd:PRK07735   21 EARKRLVAKHGAEISKLEEENREKEkALPKNDDMTIEEAKRRAAAAAKAKAAALAKQKREGTEEVTEEEKAKAKAKAAAA 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1859661303 808 ARARTGANKDQVVITPREWEAIQSGAVSNHKLTQILNNADIQEVKKLATPRENK 861
Cdd:PRK07735  101 AKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKAAALAKQKREGTEEVT 154
 
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 ...
 861-895 4.44e-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: 41.16  E-value: 4.44e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1859661303 861 KVMTTAKQQRARNLLASGRTPSEVAQILGVPVSTL 895
Cdd:cd00569     4 PKLTPEQIAEARRLLAAGESVAEIARELGVSRSTL 38
PRK07735 PRK07735
NADH-quinone oxidoreductase subunit C;
729-861 7.95e-03

NADH-quinone oxidoreductase subunit C;


Pssm-ID: 236081 [Multi-domain]  Cd Length: 430  Bit Score: 39.58  E-value: 7.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859661303 729 RARKELVSTKPTPYSPSAKKVYSRE-VESLNAKLNVALKNAPRERQAQVLANAVVRQKREANPDMQSDELRKVSAKALAT 807
Cdd:PRK07735   21 EARKRLVAKHGAEISKLEEENREKEkALPKNDDMTIEEAKRRAAAAAKAKAAALAKQKREGTEEVTEEEKAKAKAKAAAA 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1859661303 808 ARARTGANKDQVVITPREWEAIQSGAVSNHKLTQILNNADIQEVKKLATPRENK 861
Cdd:PRK07735  101 AKAKAAALAKQKREGTEEVTEEEKAAAKAKAAAAAKAKAAALAKQKREGTEEVT 154
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH