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Conserved domains on  [gi|736049918|ref|WP_034195564|]
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MULTISPECIES: RNA chaperone Hfq [Burkholderia]

Protein Classification

RNA chaperone Hfq( domain architecture ID 10109528)

RNA chaperone Hfq is an RNA-binding protein that functions as a regulator of small non-coding RNAs

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Hfq cd01716
bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a ...
 8-66 1.70e-26

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: 95.67  E-value: 1.70e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 736049918   8 HPQNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTIQ 66
Cdd:cd01716    1 NLQDQFLNTLRKEKKPVTIYLVNGVRLKGKIKSFDNFTVLLESDGKQQLIYKHAISTIV 59
 
Name Accession Description Interval E-value
Hfq cd01716
bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a ...
 8-66 1.70e-26

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: 95.67  E-value: 1.70e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 736049918   8 HPQNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTIQ 66
Cdd:cd01716    1 NLQDQFLNTLRKEKKPVTIYLVNGVRLKGKIKSFDNFTVLLESDGKQQLIYKHAISTIV 59
Hfq COG1923
sRNA-binding regulator protein Hfq [Signal transduction mechanisms];
10-66 3.47e-22

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


Pssm-ID: 441526  Cd Length: 67  Bit Score: 84.84  E-value: 3.47e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 736049918  10 QNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTIQ 66
Cdd:COG1923    8 QDQFLNQLRKERIPVTIFLVNGVKLQGKIKSFDNFTVLLERDGKQQLVYKHAISTIV 64
hfq PRK00395
RNA-binding protein Hfq; Provisional
 10-65 2.52e-21

RNA-binding protein Hfq; Provisional


Pssm-ID: 179001  Cd Length: 79  Bit Score: 83.05  E-value: 2.52e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 736049918  10 QNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTI 65
Cdd:PRK00395   8 QDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGKSQLVYKHAISTV 63
Hfq pfam17209
Hfq protein;
10-65 7.17e-19

Hfq protein;


Pssm-ID: 435788  Cd Length: 64  Bit Score: 75.93  E-value: 7.17e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 736049918   10 QNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTI 65
Cdd:pfam17209   2 QDQFLNQLRKEKIPVTVFLVNGFQLKGVIKGFDNFTVLLESDGKQQLVYKHAISTI 57
Hfq TIGR02383
RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, ...
 8-65 3.80e-18

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: 74.29  E-value: 3.80e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 736049918    8 HPQNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTI 65
Cdd:TIGR02383   2 NLQDQFLNQLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQGKQQLIYKHAISTI 59
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 12-45 6.97e-03

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 34.01  E-value: 6.97e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 736049918    12 DFINSARkeRKRVEIYLVNGIRLTGCIESFDQYL 45
Cdd:smart00651   1 KFLKKLI--GKRVLVELKNGREYRGTLKGFDQFM 32
 
Name Accession Description Interval E-value
Hfq cd01716
bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a ...
 8-66 1.70e-26

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: 95.67  E-value: 1.70e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 736049918   8 HPQNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTIQ 66
Cdd:cd01716    1 NLQDQFLNTLRKEKKPVTIYLVNGVRLKGKIKSFDNFTVLLESDGKQQLIYKHAISTIV 59
Hfq COG1923
sRNA-binding regulator protein Hfq [Signal transduction mechanisms];
10-66 3.47e-22

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


Pssm-ID: 441526  Cd Length: 67  Bit Score: 84.84  E-value: 3.47e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 736049918  10 QNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTIQ 66
Cdd:COG1923    8 QDQFLNQLRKERIPVTIFLVNGVKLQGKIKSFDNFTVLLERDGKQQLVYKHAISTIV 64
hfq PRK00395
RNA-binding protein Hfq; Provisional
 10-65 2.52e-21

RNA-binding protein Hfq; Provisional


Pssm-ID: 179001  Cd Length: 79  Bit Score: 83.05  E-value: 2.52e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 736049918  10 QNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTI 65
Cdd:PRK00395   8 QDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGKSQLVYKHAISTV 63
Hfq pfam17209
Hfq protein;
10-65 7.17e-19

Hfq protein;


Pssm-ID: 435788  Cd Length: 64  Bit Score: 75.93  E-value: 7.17e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 736049918   10 QNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTI 65
Cdd:pfam17209   2 QDQFLNQLRKEKIPVTVFLVNGFQLKGVIKGFDNFTVLLESDGKQQLVYKHAISTI 57
Hfq TIGR02383
RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, ...
 8-65 3.80e-18

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: 74.29  E-value: 3.80e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 736049918    8 HPQNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTI 65
Cdd:TIGR02383   2 NLQDQFLNQLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQGKQQLIYKHAISTI 59
PRK14091 PRK14091
RNA chaperone Hfq;
10-65 1.21e-09

RNA chaperone Hfq;


Pssm-ID: 237607 [Multi-domain]  Cd Length: 165  Bit Score: 54.44  E-value: 1.21e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 736049918  10 QNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTI 65
Cdd:PRK14091  13 QDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLRRDGQSQLVYKHAISTI 68
PRK14091 PRK14091
RNA chaperone Hfq;
1-66 2.65e-09

RNA chaperone Hfq;


Pssm-ID: 237607 [Multi-domain]  Cd Length: 165  Bit Score: 53.67  E-value: 2.65e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 736049918   1 MANPAESHPQNDFINSARKERKRVEIYLVNGIRLTGCIESFDQYLVMLRTPVGLQGIYKRAISTIQ 66
Cdd:PRK14091  84 DANKKSRLLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLERDGYVQLVYKHAVSTVQ 149
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 12-45 6.97e-03

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 34.01  E-value: 6.97e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 736049918    12 DFINSARkeRKRVEIYLVNGIRLTGCIESFDQYL 45
Cdd:smart00651   1 KFLKKLI--GKRVLVELKNGREYRGTLKGFDQFM 32
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 21-45 9.71e-03

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 33.25  E-value: 9.71e-03
                          10        20
                  ....*....|....*....|....*
gi 736049918   21 RKRVEIYLVNGIRLTGCIESFDQYL 45
Cdd:pfam01423   8 GKRVLVELKNGRELRGTLKGFDQFM 32
 
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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