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Conserved domains on  [gi|1088576504|gb|OHD99824|]
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MAG: hypothetical protein A3E21_01045 [Sulfurimonas sp. RIFCSPHIGHO2_12_FULL_36_9]

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; ...
 1-83 3.47e-08

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: 46.42  E-value: 3.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088576504  1 MAKKFNQPLRMCISCRQRDAQNNLIRLQCL-DSQFSL-FRGT--GRSFYICK--ICLEDSKKvLKALMRQCKSGDRDKFS 74
Cdd:COG2740    1 MMKAKKIPLRTCIGCRERKPKKELIRIVRSpDGEVVPdPTGKlpGRGAYLCPdrECLEKAVK-KRAFARALKAKVPEDLY 79


                 ....*....
gi 1088576504 75 NILKEIITD 83
Cdd:COG2740   80 DELEELLER 88
 
Name Accession Description Interval E-value
YlxR COG2740
Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function ...
 1-83 3.47e-08

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


Pssm-ID: 442042  Cd Length: 93  Bit Score: 46.42  E-value: 3.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088576504  1 MAKKFNQPLRMCISCRQRDAQNNLIRLQCL-DSQFSL-FRGT--GRSFYICK--ICLEDSKKvLKALMRQCKSGDRDKFS 74
Cdd:COG2740    1 MMKAKKIPLRTCIGCRERKPKKELIRIVRSpDGEVVPdPTGKlpGRGAYLCPdrECLEKAVK-KRAFARALKAKVPEDLY 79


                 ....*....
gi 1088576504 75 NILKEIITD 83
Cdd:COG2740   80 DELEELLER 88
YlxR pfam04296
Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate ...
 10-56 6.81e-03

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


Pssm-ID: 427847  Cd Length: 75  Bit Score: 32.03  E-value: 6.81e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 1088576504 10 RMCISCRQRDAQNNLIRLQCL-DSQFSL-FRGT--GRSFYICK--ICLEDSKK 56
Cdd:pfam04296  1 RKCIGCREMKPKKELIRIVRTpDGEVVLdPTGKlpGRGAYICPdrECLEKAKK 53
 
Name Accession Description Interval E-value
YlxR COG2740
Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function ...
 1-83 3.47e-08

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


Pssm-ID: 442042  Cd Length: 93  Bit Score: 46.42  E-value: 3.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088576504  1 MAKKFNQPLRMCISCRQRDAQNNLIRLQCL-DSQFSL-FRGT--GRSFYICK--ICLEDSKKvLKALMRQCKSGDRDKFS 74
Cdd:COG2740    1 MMKAKKIPLRTCIGCRERKPKKELIRIVRSpDGEVVPdPTGKlpGRGAYLCPdrECLEKAVK-KRAFARALKAKVPEDLY 79


                 ....*....
gi 1088576504 75 NILKEIITD 83
Cdd:COG2740   80 DELEELLER 88
YlxR pfam04296
Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate ...
 10-56 6.81e-03

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


Pssm-ID: 427847  Cd Length: 75  Bit Score: 32.03  E-value: 6.81e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 1088576504 10 RMCISCRQRDAQNNLIRLQCL-DSQFSL-FRGT--GRSFYICK--ICLEDSKK 56
Cdd:pfam04296  1 RKCIGCREMKPKKELIRIVRTpDGEVVLdPTGKlpGRGAYICPdrECLEKAKK 53
 
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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