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Conserved domains on  [gi|489661466|ref|WP_003565786|]
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RNase P modulator RnpM [Lacticaseibacillus paracasei]

Protein Classification

YlxR family protein( domain architecture ID 10006581)

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 COG2740
Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function ...
 1-92 1.61e-26

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


:

Pssm-ID: 442042  Cd Length: 93  Bit Score: 93.42  E-value: 1.61e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489661466  1 MKKRKIPMRKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALDPAAVKAAKGKKLIDAAFGITIEPTFYDD 80
Cdd:COG2740   2 MKAKKIPLRTCIGCRERKPKKELIRIVRSPDGEVVPDPTGKLPGRGAYLCPDRECLEKAVKKRAFARALKAKVPEDLYDE 81

                        90
                ....*....|..
gi 489661466 81 LFAYVDHQKARQ 92
Cdd:COG2740  82 LEELLERRALRR 93
 
Name Accession Description Interval E-value
YlxR COG2740
Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function ...
 1-92 1.61e-26

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


Pssm-ID: 442042  Cd Length: 93  Bit Score: 93.42  E-value: 1.61e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489661466  1 MKKRKIPMRKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALDPAAVKAAKGKKLIDAAFGITIEPTFYDD 80
Cdd:COG2740   2 MKAKKIPLRTCIGCRERKPKKELIRIVRSPDGEVVPDPTGKLPGRGAYLCPDRECLEKAVKKRAFARALKAKVPEDLYDE 81

                        90
                ....*....|..
gi 489661466 81 LFAYVDHQKARQ 92
Cdd:COG2740  82 LEELLERRALRR 93
YlxR cd00279
Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; ...
 7-85 1.88e-21

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: 80.07  E-value: 1.88e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489661466  7 PMRKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALDPAAVKAAKGKKLIDAAFGITIEPTFYDDLFAYV 85
Cdd:cd00279   1 PLRKCIVTGEMKPKKELIRFVAGPEGEVVPDPTGKLPGRGAYVCADRECIEKAKKKKLFNRAFKAKVSDSVYDELIEYV 79
YlxR pfam04296
Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate ...
 9-81 9.54e-21

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


Pssm-ID: 427847  Cd Length: 75  Bit Score: 78.26  E-value: 9.54e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489661466   9 RKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALDPAAVKAAKGKKLIDAAFGITIEPTFYDDL 81
Cdd:pfam04296  1 RKCIGCREMKPKKELIRIVRTPDGEVVLDPTGKLPGRGAYICPDRECLEKAKKKKALERALKTKVPDEVYEEL 73
PRK09190 PRK09190
RNA-binding protein;
2-52 3.27e-04

RNA-binding protein;


Pssm-ID: 236401 [Multi-domain]  Cd Length: 220  Bit Score: 37.63  E-value: 3.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489661466   2 KKRKIPMRKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALD 52
Cdd:PRK09190  10 RDRRGNERRCIVTREVGPPDELIRFVVGPDGQVVPDLKRKLPGRGCWVSAD 60
 
Name Accession Description Interval E-value
YlxR COG2740
Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function ...
 1-92 1.61e-26

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


Pssm-ID: 442042  Cd Length: 93  Bit Score: 93.42  E-value: 1.61e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489661466  1 MKKRKIPMRKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALDPAAVKAAKGKKLIDAAFGITIEPTFYDD 80
Cdd:COG2740   2 MKAKKIPLRTCIGCRERKPKKELIRIVRSPDGEVVPDPTGKLPGRGAYLCPDRECLEKAVKKRAFARALKAKVPEDLYDE 81

                        90
                ....*....|..
gi 489661466 81 LFAYVDHQKARQ 92
Cdd:COG2740  82 LEELLERRALRR 93
YlxR cd00279
Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; ...
 7-85 1.88e-21

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: 80.07  E-value: 1.88e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489661466  7 PMRKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALDPAAVKAAKGKKLIDAAFGITIEPTFYDDLFAYV 85
Cdd:cd00279   1 PLRKCIVTGEMKPKKELIRFVAGPEGEVVPDPTGKLPGRGAYVCADRECIEKAKKKKLFNRAFKAKVSDSVYDELIEYV 79
YlxR pfam04296
Protein of unknown function (DUF448); The YlxR family has been demonstrated to regulate ...
 9-81 9.54e-21

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


Pssm-ID: 427847  Cd Length: 75  Bit Score: 78.26  E-value: 9.54e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489661466   9 RKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALDPAAVKAAKGKKLIDAAFGITIEPTFYDDL 81
Cdd:pfam04296  1 RKCIGCREMKPKKELIRIVRTPDGEVVLDPTGKLPGRGAYICPDRECLEKAKKKKALERALKTKVPDEVYEEL 73
PRK09190 PRK09190
RNA-binding protein;
2-52 3.27e-04

RNA-binding protein;


Pssm-ID: 236401 [Multi-domain]  Cd Length: 220  Bit Score: 37.63  E-value: 3.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489661466   2 KKRKIPMRKDLLSNQMMPKKELVRIVKNKENVVAIDPTGKAAGRGAYVALD 52
Cdd:PRK09190  10 RDRRGNERRCIVTREVGPPDELIRFVVGPDGQVVPDLKRKLPGRGCWVSAD 60
 
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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