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Conserved domains on  [gi|488959368|ref|WP_002870410|]
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MULTISPECIES: DUF448 domain-containing protein [Campylobacter]

Protein Classification

YlxR family protein( domain architecture ID 4442)

YlxR family protein may be an RNA-binding protein, similar to Bacillus subtilis YlxR

CATH:  3.30.1230.10
Gene Ontology:  GO:0003723
PubMed:  11679764
SCOP:  4003626

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YlxR super family cl00189
Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; ...
 1-60 3.54e-09

Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation


The actual alignment was detected with superfamily member COG2740:

Pssm-ID: 469647  Cd Length: 93  Bit Score: 48.74  E-value: 3.54e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488959368  1 MKKHIPIRMCIVCKNRFEQNMLFRF-KVVLGDIVP----KAeHGRSGYLCQN--CIEKEDK--ILQKAF 60
Cdd:COG2740   3 KAKKIPLRTCIGCRERKPKKELIRIvRSPDGEVVPdptgKL-PGRGAYLCPDreCLEKAVKkrAFARAL 70
 
Name Accession Description Interval E-value
YlxR COG2740
Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function ...
 1-60 3.54e-09

Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function prediction only];


Pssm-ID: 442042  Cd Length: 93  Bit Score: 48.74  E-value: 3.54e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488959368  1 MKKHIPIRMCIVCKNRFEQNMLFRF-KVVLGDIVP----KAeHGRSGYLCQN--CIEKEDK--ILQKAF 60
Cdd:COG2740   3 KAKKIPLRTCIGCRERKPKKELIRIvRSPDGEVVPdptgKL-PGRGAYLCPDreCLEKAVKkrAFARAL 70
YlxR pfam04296
Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate ...
 8-60 4.35e-05

Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate metabolic gene expression.


Pssm-ID: 427847  Cd Length: 75  Bit Score: 37.81  E-value: 4.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488959368   8 RMCIVCKNRFEQNMLFRF-KVVLGDIVP----KAEhGRSGYLCQN--CIEK--EDKILQKAF 60
Cdd:pfam04296  1 RKCIGCREMKPKKELIRIvRTPDGEVVLdptgKLP-GRGAYICPDreCLEKakKKKALERAL 61
YlxR cd00279
Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; ...
 6-62 1.63e-03

Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation


Pssm-ID: 238173  Cd Length: 79  Bit Score: 33.84  E-value: 1.63e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488959368  6 PIRMCIVCKNRFEQNMLFRF-KVVLGDIVP----KAeHGRSGYLCQN--CIE--KEDKILQKAFSK 62
Cdd:cd00279   1 PLRKCIVTGEMKPKKELIRFvAGPEGEVVPdptgKL-PGRGAYVCADreCIEkaKKKKLFNRAFKA 65
 
Name Accession Description Interval E-value
YlxR COG2740
Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function ...
 1-60 3.54e-09

Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function prediction only];


Pssm-ID: 442042  Cd Length: 93  Bit Score: 48.74  E-value: 3.54e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488959368  1 MKKHIPIRMCIVCKNRFEQNMLFRF-KVVLGDIVP----KAeHGRSGYLCQN--CIEKEDK--ILQKAF 60
Cdd:COG2740   3 KAKKIPLRTCIGCRERKPKKELIRIvRSPDGEVVPdptgKL-PGRGAYLCPDreCLEKAVKkrAFARAL 70
YlxR pfam04296
Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate ...
 8-60 4.35e-05

Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate metabolic gene expression.


Pssm-ID: 427847  Cd Length: 75  Bit Score: 37.81  E-value: 4.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488959368   8 RMCIVCKNRFEQNMLFRF-KVVLGDIVP----KAEhGRSGYLCQN--CIEK--EDKILQKAF 60
Cdd:pfam04296  1 RKCIGCREMKPKKELIRIvRTPDGEVVLdptgKLP-GRGAYICPDreCLEKakKKKALERAL 61
YlxR cd00279
Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; ...
 6-62 1.63e-03

Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation


Pssm-ID: 238173  Cd Length: 79  Bit Score: 33.84  E-value: 1.63e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488959368  6 PIRMCIVCKNRFEQNMLFRF-KVVLGDIVP----KAeHGRSGYLCQN--CIE--KEDKILQKAFSK 62
Cdd:cd00279   1 PLRKCIVTGEMKPKKELIRFvAGPEGEVVPdptgKL-PGRGAYVCADreCIEkaKKKKLFNRAFKA 65
 
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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