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Conserved domains on  [gi|1196994093|ref|WP_086411888|]
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MULTISPECIES: RNA chaperone Hfq [Bacillus cereus group]

Protein Classification

LSm family protein( domain architecture ID 249)

LSm family protein such as eukaryotic LSm (Sm-like proteins) and bacterial LSm-related Hfq proteins, that have an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, and are involved in processes associated with RNA processing and gene expression regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_like super family cl00259
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 1-61 1.53e-22

Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


The actual alignment was detected with superfamily member TIGR02383:

Pssm-ID: 469694  Cd Length: 61  Bit Score: 80.84  E-value: 1.53e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1196994093  1 MHTQENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVSL 61
Cdd:TIGR02383  1 QNLQDQFLNQLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQGKQQLIYKHAISTISP 61
 
Name Accession Description Interval E-value
Hfq TIGR02383
RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, ...
 1-61 1.53e-22

RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see . The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication. [Regulatory functions, Other]


Pssm-ID: 274101  Cd Length: 61  Bit Score: 80.84  E-value: 1.53e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1196994093  1 MHTQENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVSL 61
Cdd:TIGR02383  1 QNLQDQFLNQLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQGKQQLIYKHAISTISP 61
Hfq cd01716
bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a ...
 2-60 8.75e-21

bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotropic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.


Pssm-ID: 212463  Cd Length: 60  Bit Score: 76.41  E-value: 8.75e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1196994093  2 HTQENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVS 60
Cdd:cd01716    1 NLQDQFLNTLRKEKKPVTIYLVNGVRLKGKIKSFDNFTVLLESDGKQQLIYKHAISTIV 59
Hfq COG1923
sRNA-binding regulator protein Hfq [Signal transduction mechanisms];
4-60 1.21e-17

sRNA-binding regulator protein Hfq [Signal transduction mechanisms];


Pssm-ID: 441526  Cd Length: 67  Bit Score: 68.66  E-value: 1.21e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1196994093  4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVS 60
Cdd:COG1923    8 QDQFLNQLRKERIPVTIFLVNGVKLQGKIKSFDNFTVLLERDGKQQLVYKHAISTIV 64
Hfq pfam17209
Hfq protein;
4-60 2.96e-15

Hfq protein;


Pssm-ID: 435788  Cd Length: 64  Bit Score: 62.45  E-value: 2.96e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1196994093  4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVS 60
Cdd:pfam17209  2 QDQFLNQLRKEKIPVTVFLVNGFQLKGVIKGFDNFTVLLESDGKQQLVYKHAISTIV 58
hfq PRK00395
RNA-binding protein Hfq; Provisional
 4-59 4.22e-13

RNA-binding protein Hfq; Provisional


Pssm-ID: 179001  Cd Length: 79  Bit Score: 57.24  E-value: 4.22e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1196994093  4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTV 59
Cdd:PRK00395   8 QDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGKSQLVYKHAISTV 63
 
Name Accession Description Interval E-value
Hfq TIGR02383
RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, ...
 1-61 1.53e-22

RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see . The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication. [Regulatory functions, Other]


Pssm-ID: 274101  Cd Length: 61  Bit Score: 80.84  E-value: 1.53e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1196994093  1 MHTQENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVSL 61
Cdd:TIGR02383  1 QNLQDQFLNQLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQGKQQLIYKHAISTISP 61
Hfq cd01716
bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a ...
 2-60 8.75e-21

bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotropic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins.


Pssm-ID: 212463  Cd Length: 60  Bit Score: 76.41  E-value: 8.75e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1196994093  2 HTQENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVS 60
Cdd:cd01716    1 NLQDQFLNTLRKEKKPVTIYLVNGVRLKGKIKSFDNFTVLLESDGKQQLIYKHAISTIV 59
Hfq COG1923
sRNA-binding regulator protein Hfq [Signal transduction mechanisms];
4-60 1.21e-17

sRNA-binding regulator protein Hfq [Signal transduction mechanisms];


Pssm-ID: 441526  Cd Length: 67  Bit Score: 68.66  E-value: 1.21e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1196994093  4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVS 60
Cdd:COG1923    8 QDQFLNQLRKERIPVTIFLVNGVKLQGKIKSFDNFTVLLERDGKQQLVYKHAISTIV 64
Hfq pfam17209
Hfq protein;
4-60 2.96e-15

Hfq protein;


Pssm-ID: 435788  Cd Length: 64  Bit Score: 62.45  E-value: 2.96e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1196994093  4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTVS 60
Cdd:pfam17209  2 QDQFLNQLRKEKIPVTVFLVNGFQLKGVIKGFDNFTVLLESDGKQQLVYKHAISTIV 58
hfq PRK00395
RNA-binding protein Hfq; Provisional
 4-59 4.22e-13

RNA-binding protein Hfq; Provisional


Pssm-ID: 179001  Cd Length: 79  Bit Score: 57.24  E-value: 4.22e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1196994093  4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTV 59
Cdd:PRK00395   8 QDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGKSQLVYKHAISTV 63
PRK14091 PRK14091
RNA chaperone Hfq;
4-59 9.73e-11

RNA chaperone Hfq;


Pssm-ID: 237607 [Multi-domain]  Cd Length: 165  Bit Score: 53.28  E-value: 9.73e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1196994093   4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTV 59
Cdd:PRK14091   13 QDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDGQSQLVYKHAISTI 68
PRK14091 PRK14091
RNA chaperone Hfq;
4-59 6.45e-08

RNA chaperone Hfq;


Pssm-ID: 237607 [Multi-domain]  Cd Length: 165  Bit Score: 45.96  E-value: 6.45e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1196994093   4 QENFYKKLIEEKRLVTIFLLNGVRVPGIIIDVDKFSVLVSSHGKQQFIYKQAISTV 59
Cdd:PRK14091   93 QDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGYVQLVYKHAVSTV 148
 
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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