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18  structures 7341  species 0  interactions 8585  sequences 29  architectures

Family: KH_dom-like (PF14714)

Summary: KH-domain-like of EngA bacterial GTPase enzymes, C-terminal

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

KH-domain-like of EngA bacterial GTPase enzymes, C-terminal Provide feedback

The KH-like domain at the C-terminus of the EngA subfamily of essential bacterial GTPases has a unique domain structure position. The two adjacent GTPase domains (GD1 and GD2), two domains of family MMR_HSR1, PF01926 pack at either side of the C-terminal domain. This C-terminal domain resembles a KH domain but is missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2. This family has not been added to the KH clan since SCOP classifies it separately due to its missing the key KH motif/fold.

Literature references

  1. Robinson VL, Hwang J, Fox E, Inouye M, Stock AM;, Structure. 2002;10:1649-1658.: Domain arrangement of Der, a switch protein containing two GTPase domains. PUBMED:12467572 EPMC:12467572


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032859

This domain can be found in the C terminus of the bacterial GTPases Der. The two adjacent GTPase domains (GD1 and GD2) pack at either side of the C-terminal domain. This C-terminal domain resembles a KH domain but is missing the distinctive RNA recognition elements [ PUBMED:12467572 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(533)
Full
(8585)
Representative proteomes UniProt
(40025)
RP15
(1302)
RP35
(4394)
RP55
(8830)
RP75
(14885)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(533)
Full
(8585)
Representative proteomes UniProt
(40025)
RP15
(1302)
RP35
(4394)
RP55
(8830)
RP75
(14885)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(533)
Full
(8585)
Representative proteomes UniProt
(40025)
RP15
(1302)
RP35
(4394)
RP55
(8830)
RP75
(14885)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: CATH:1mky_A_03
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 533
Number in full: 8585
Average length of the domain: 80.50 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 16.98 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.3 27.3
Trusted cut-off 27.6 27.6
Noise cut-off 27.1 26.9
Model length: 81
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the KH_dom-like domain has been found. There are 18 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0N7KT94 View 3D Structure Click here
A0A0R0HTV9 View 3D Structure Click here
A0A144A297 View 3D Structure Click here
A0A1D6F7R3 View 3D Structure Click here
A0A1D6MF89 View 3D Structure Click here
A0KJ48 View 3D Structure Click here
A0LJ92 View 3D Structure Click here
A0Q125 View 3D Structure Click here
A1APR9 View 3D Structure Click here
A1B4S0 View 3D Structure Click here
A1BHZ8 View 3D Structure Click here
A1K3Z3 View 3D Structure Click here
A1R5C7 View 3D Structure Click here
A1S859 View 3D Structure Click here
A1SU43 View 3D Structure Click here
A1TA72 View 3D Structure Click here
A1TM31 View 3D Structure Click here
A1URU0 View 3D Structure Click here
A1VNF8 View 3D Structure Click here
A1W581 View 3D Structure Click here
A1WE12 View 3D Structure Click here
A1WUL5 View 3D Structure Click here
A2SHB1 View 3D Structure Click here
A3CPT0 View 3D Structure Click here
A3DE77 View 3D Structure Click here
A3MZC1 View 3D Structure Click here
A3PBA9 View 3D Structure Click here
A3QCG6 View 3D Structure Click here
A4G4K6 View 3D Structure Click here
A4I1W4 View 3D Structure Click here
A4J3P1 View 3D Structure Click here
A4SDB8 View 3D Structure Click here
A4VNW7 View 3D Structure Click here
A4VX53 View 3D Structure Click here
A4X692 View 3D Structure Click here
A4XY28 View 3D Structure Click here
A4YUE1 View 3D Structure Click here
A5CDT2 View 3D Structure Click here
A5D1U6 View 3D Structure Click here
A5G692 View 3D Structure Click here