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Conserved domains on  [gi|489186239|ref|WP_003095657|]
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MULTISPECIES: RNA chaperone Hfq [Gammaproteobacteria]

Protein Classification

RNA chaperone Hfq( domain architecture ID 10791943)

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

Gene Ontology:  GO:0003723

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
hfq PRK00395
RNA-binding protein Hfq; Provisional
 1-78 1.89e-49

RNA-binding protein Hfq; Provisional


:

Pssm-ID: 179001  Cd Length: 79  Bit Score: 150.07  E-value: 1.89e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489186239  1 MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTV-SQMVYKHAISTVVPSRPVRLPSGDQPAE 78
Cdd:PRK00395  1 MAKGQNLQDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGkSQLVYKHAISTVVPARPVSLHEDEEEEE 79
 
Name Accession Description Interval E-value
hfq PRK00395
RNA-binding protein Hfq; Provisional
 1-78 1.89e-49

RNA-binding protein Hfq; Provisional


Pssm-ID: 179001  Cd Length: 79  Bit Score: 150.07  E-value: 1.89e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489186239  1 MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTV-SQMVYKHAISTVVPSRPVRLPSGDQPAE 78
Cdd:PRK00395  1 MAKGQNLQDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGkSQLVYKHAISTVVPARPVSLHEDEEEEE 79
Hfq COG1923
sRNA-binding regulator protein Hfq [Signal transduction mechanisms];
1-66 1.24e-39

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


Pssm-ID: 441526  Cd Length: 67  Bit Score: 124.90  E-value: 1.24e-39
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489186239  1 MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK-NTVSQMVYKHAISTVVPSR 66
Cdd:COG1923   1 MKKPINLQDQFLNQLRKERIPVTIFLVNGVKLQGKIKSFDNFTVLLErDGKQQLVYKHAISTIVPAR 67
Hfq pfam17209
Hfq protein;
7-68 2.88e-35

Hfq protein;


Pssm-ID: 435788  Cd Length: 64  Bit Score: 114.06  E-value: 2.88e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489186239   7 LQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNT-VSQMVYKHAISTVVPSRPV 68
Cdd:pfam17209  1 LQDQFLNQLRKEKIPVTVFLVNGFQLKGVIKGFDNFTVLLESDgKQQLVYKHAISTIVPARPV 63
Hfq TIGR02383
RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, ...
 6-64 1.89e-30

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: 101.64  E-value: 1.89e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489186239   6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQ-MVYKHAISTVVP 64
Cdd:TIGR02383  2 NLQDQFLNQLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQGKQqLIYKHAISTISP 61
Hfq cd01716
bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a ...
 6-64 2.43e-28

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: 96.44  E-value: 2.43e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489186239  6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK-NTVSQMVYKHAISTVVP 64
Cdd:cd01716   1 NLQDQFLNTLRKEKKPVTIYLVNGVRLKGKIKSFDNFTVLLEsDGKQQLIYKHAISTIVP 60
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 10-50 7.09e-03

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 31.70  E-value: 7.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 489186239   10 PYLNTLRKERVpvSIYLVNGIKLQGQIESFDQFV-ILLKNTV 50
Cdd:smart00651  1 KFLKKLIGKRV--LVELKNGREYRGTLKGFDQFMnLVLEDVE 40
 
Name Accession Description Interval E-value
hfq PRK00395
RNA-binding protein Hfq; Provisional
 1-78 1.89e-49

RNA-binding protein Hfq; Provisional


Pssm-ID: 179001  Cd Length: 79  Bit Score: 150.07  E-value: 1.89e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489186239  1 MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTV-SQMVYKHAISTVVPSRPVRLPSGDQPAE 78
Cdd:PRK00395  1 MAKGQNLQDPFLNALRKERVPVTIYLVNGIKLQGQIESFDNFVVLLRNTGkSQLVYKHAISTVVPARPVSLHEDEEEEE 79
Hfq COG1923
sRNA-binding regulator protein Hfq [Signal transduction mechanisms];
1-66 1.24e-39

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


Pssm-ID: 441526  Cd Length: 67  Bit Score: 124.90  E-value: 1.24e-39
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489186239  1 MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK-NTVSQMVYKHAISTVVPSR 66
Cdd:COG1923   1 MKKPINLQDQFLNQLRKERIPVTIFLVNGVKLQGKIKSFDNFTVLLErDGKQQLVYKHAISTIVPAR 67
Hfq pfam17209
Hfq protein;
7-68 2.88e-35

Hfq protein;


Pssm-ID: 435788  Cd Length: 64  Bit Score: 114.06  E-value: 2.88e-35
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489186239   7 LQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNT-VSQMVYKHAISTVVPSRPV 68
Cdd:pfam17209  1 LQDQFLNQLRKEKIPVTVFLVNGFQLKGVIKGFDNFTVLLESDgKQQLVYKHAISTIVPARPV 63
Hfq TIGR02383
RNA chaperone Hfq; This model represents the RNA-binding pleiotropic regulator Hfq, a small, ...
 6-64 1.89e-30

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: 101.64  E-value: 1.89e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489186239   6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQ-MVYKHAISTVVP 64
Cdd:TIGR02383  2 NLQDQFLNQLRKERIPVTVFLVNGVQLKGVIESFDNFTVLLESQGKQqLIYKHAISTISP 61
Hfq cd01716
bacterial Hfq-like; Hfq, an abundant, ubiquitous RNA-binding protein, functions as a ...
 6-64 2.43e-28

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: 96.44  E-value: 2.43e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489186239  6 SLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLK-NTVSQMVYKHAISTVVP 64
Cdd:cd01716   1 NLQDQFLNTLRKEKKPVTIYLVNGVRLKGKIKSFDNFTVLLEsDGKQQLIYKHAISTIVP 60
PRK14091 PRK14091
RNA chaperone Hfq;
3-70 5.86e-24

RNA chaperone Hfq;


Pssm-ID: 237607 [Multi-domain]  Cd Length: 165  Bit Score: 88.33  E-value: 5.86e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489186239   3 KGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILL-KNTVSQMVYKHAISTVVPSRPVRL 70
Cdd:PRK14091   8 KVNNLQDIFLNSLRKTKTPVTMFLVKGVKLQGIITWFDNFSILLrRDGQSQLVYKHAISTIMPAHPLDL 76
PRK14091 PRK14091
RNA chaperone Hfq;
2-70 3.12e-22

RNA chaperone Hfq;


Pssm-ID: 237607 [Multi-domain]  Cd Length: 165  Bit Score: 84.10  E-value: 3.12e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489186239   2 SKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILL-KNTVSQMVYKHAISTVVPSRPVRL 70
Cdd:PRK14091  87 KKSRLLQDVFLSAVRDSGEPVTMFLVNGVMLQGEIAAFDLFCMLLeRDGYVQLVYKHAVSTVQPAGPVDL 156
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 10-50 7.09e-03

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 31.70  E-value: 7.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 489186239   10 PYLNTLRKERVpvSIYLVNGIKLQGQIESFDQFV-ILLKNTV 50
Cdd:smart00651  1 KFLKKLIGKRV--LVELKNGREYRGTLKGFDQFMnLVLEDVE 40
CuRO_3_FVIII_like cd04227
The third cupredoxin domain of coagulation factor VIII and similar proteins; Factor VIII ...
 40-80 8.77e-03

The third cupredoxin domain of coagulation factor VIII and similar proteins; Factor VIII functions in the factor X-activating complex of the intrinsic coagulation pathway. It facilitates blood clotting by acting as a cofactor for factor IXa. In the presence of Ca2+ and phospholipids, Factor VIII and IXa form a complex that converts factor X to the activated form Xa. A variety of mutations in the Factor VIII gene can cause hemophilia A, which typically requires replacement therapy with purified protein. Factor VIII is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor VIII is initially processed through proteolysis to generate a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2), which circulates in a tight complex with von Willebrand factor (VWF). Further processing of the heavy chain produces activated factor VIIIa, a heterotrimer composed of polypeptides (1-2), (3-4), and the light chain. This model represents the cupredoxin domain 3 of unprocessed Factor VIII or the heavy chain of circulating Factor VIII, and similar proteins.


Pssm-ID: 259889 [Multi-domain]  Cd Length: 177  Bit Score: 32.98  E-value: 8.77e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 489186239  40 DQFVILLKNTVSQ--MVYKHAISTVVPSRPVRLPSG-----DQPAEPG 80
Cdd:cd04227   80 DQIHIMFKNTASRpyNIYPHGLTSVRPMYRSRNPAGekdlkTMPIGPG 127
 
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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