NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1080263731|gb|OFK56807|]
View 

RNA-binding protein [Globicatella sp. HMSC072A10]

Protein Classification

KH domain-containing protein( domain architecture ID 10004768)

uncharacterized KH domain-containing similar to Bacillus subtilis YlqC; KH (K homology RNA-binding domain) binds single-stranded RNA or DNA

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
YlqC COG1837
Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function ...
 6-79 4.59e-25

Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only];


:

Pssm-ID: 441442  Cd Length: 76  Bit Score: 88.95  E-value: 4.59e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIVD 79
Cdd:COG1837    3 ELVEFLVKPLVDHPDDVSVTEEEGERTVVLELRVAPEDLGKVIGKQGRTAKAIRTVLSAAAAKEGKRVRLEIVD 76
 
Name Accession Description Interval E-value
YlqC COG1837
Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function ...
 6-79 4.59e-25

Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only];


Pssm-ID: 441442  Cd Length: 76  Bit Score: 88.95  E-value: 4.59e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIVD 79
Cdd:COG1837    3 ELVEFLVKPLVDHPDDVSVTEEEGERTVVLELRVAPEDLGKVIGKQGRTAKAIRTVLSAAAAKEGKRVRLEIVD 76
KH-II_YlqC-like cd22533
type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and ...
 6-78 1.77e-23

type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and similar proteins; The family includes a group of uncharacterized proteins which show sequence similarity to Bacillus subtilis UPF0109 protein YlqC. They are mainly found in bacteria and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411790  Cd Length: 75  Bit Score: 84.83  E-value: 1.77e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIV 78
Cdd:cd22533    3 ELIEYIAKSLVDHPESVRVSEIEGEKTTVYELRVAPEDVGRVIGKQGRTAKAIRTLVSAAAAKDGKRVRLEIL 75
KH_4 pfam13083
KH domain;
6-77 1.42e-19

KH domain;


Pssm-ID: 463779  Cd Length: 73  Bit Score: 75.21  E-value: 1.42e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVI 77
Cdd:pfam13083  2 ELVEDILKALVDDPEEVSVTEEEEEKTVVLELNVAGEDMGKVIGKQGRTLDALRTLVSAAANKDGKRVRVEI 73
PRK00468 PRK00468
KH domain-containing protein;
6-78 3.54e-12

KH domain-containing protein;


Pssm-ID: 179040  Cd Length: 75  Bit Score: 56.28  E-value: 3.54e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIV 78
Cdd:PRK00468   3 ELVETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEII 75
 
Name Accession Description Interval E-value
YlqC COG1837
Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function ...
 6-79 4.59e-25

Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only];


Pssm-ID: 441442  Cd Length: 76  Bit Score: 88.95  E-value: 4.59e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIVD 79
Cdd:COG1837    3 ELVEFLVKPLVDHPDDVSVTEEEGERTVVLELRVAPEDLGKVIGKQGRTAKAIRTVLSAAAAKEGKRVRLEIVD 76
KH-II_YlqC-like cd22533
type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and ...
 6-78 1.77e-23

type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and similar proteins; The family includes a group of uncharacterized proteins which show sequence similarity to Bacillus subtilis UPF0109 protein YlqC. They are mainly found in bacteria and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).


Pssm-ID: 411790  Cd Length: 75  Bit Score: 84.83  E-value: 1.77e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIV 78
Cdd:cd22533    3 ELIEYIAKSLVDHPESVRVSEIEGEKTTVYELRVAPEDVGRVIGKQGRTAKAIRTLVSAAAAKDGKRVRLEIL 75
KH_4 pfam13083
KH domain;
6-77 1.42e-19

KH domain;


Pssm-ID: 463779  Cd Length: 73  Bit Score: 75.21  E-value: 1.42e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVI 77
Cdd:pfam13083  2 ELVEDILKALVDDPEEVSVTEEEEEKTVVLELNVAGEDMGKVIGKQGRTLDALRTLVSAAANKDGKRVRVEI 73
PRK00468 PRK00468
KH domain-containing protein;
6-78 3.54e-12

KH domain-containing protein;


Pssm-ID: 179040  Cd Length: 75  Bit Score: 56.28  E-value: 3.54e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080263731  6 QLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIV 78
Cdd:PRK00468   3 ELVETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEII 75
PRK01064 PRK01064
hypothetical protein; Provisional
 4-80 2.92e-10

hypothetical protein; Provisional


Pssm-ID: 179216  Cd Length: 78  Bit Score: 51.46  E-value: 2.92e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080263731  4 INQLIRTIVEPLIEFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVRTNNRKRTRLVIVDE 80
Cdd:PRK01064   1 MKEFLAYIVKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIMEE 77
PRK02821 PRK02821
RNA-binding protein;
7-80 3.18e-07

RNA-binding protein;


Pssm-ID: 179479  Cd Length: 77  Bit Score: 43.86  E-value: 3.18e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080263731  7 LIRTIVEplieFPEELTIEEVDTDEFYEYHLYLNPEDIGRVIGKKGRVARAIRTIVYSVrTNNRKRTRLVIVDE 80
Cdd:PRK02821   9 LVRGIVD----NPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI-GGRGVRVDVVDTDR 77
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH