Summary: HipA-like C-terminal domain
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HipA-like C-terminal domain Provide feedback
The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species (for example P23874). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis [1]. When expressed alone, it is toxic to bacterial cells [1] but it is usually tightly associated with HipB [2] and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products [2].
Literature references
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Black DS, Kelly AJ, Mardis MJ, Moyed HS; , J Bacteriol 1991;173:5732-5739.: Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. PUBMED:1715862 EPMC:1715862
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Black DS, Irwin B, Moyed HS; , J Bacteriol 1994;176:4081-4091.: Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. PUBMED:8021189 EPMC:8021189
Internal database links
SCOOP: | CotH PI3_PI4_kinase |
Similarity to PfamA using HHSearch: | CotH |
This tab holds annotation information from the InterPro database.
InterPro entry IPR012893
The members of this entry are similar to a region close to the C terminus of the HipA protein expressed by various bacterial species (for example SWISSPROT). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis [PUBMED:1715862]. When expressed alone, it is toxic to bacterial cells [PUBMED:1715862], but it is usually tightly associated with HipB [PUBMED:8021189], and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products [PUBMED:8021189]. The domain is also found in the serine/threonine-protein kinase CtkA from Helicobacter pylori which is important in induction of host inflammation by inducing release of cytokines such as TNF-alpha and IL-8 by phosphorylation of NF-kappa-B [PUBMED:21098302].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan PKinase (CL0016), which has the following description:
This superfamily includes the Serine/Threonine- and Tyrosine- protein kinases as well as related kinases that act on non-protein substrates.
The clan contains the following 38 members:
ABC1 AceK Act-Frag_cataly Alpha_kinase APH APH_6_hur Choline_kinase CotH DUF1679 DUF2252 DUF4135 EcKinase Fam20C Fructosamin_kin FTA2 Haspin_kinase HipA_C Ins_P5_2-kin IPK IucA_IucC Kdo Kinase-like Kinase-PolyVal KIND Pan3_PK PI3_PI4_kinase PIP49_C PIP5K PK_Tyr_Ser-Thr Pkinase Pkinase_fungal Pox_ser-thr_kin RIO1 Seadorna_VP7 UL97 WaaY YrbL-PhoP_reg YukCAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (352) |
Full (4216) |
Representative proteomes | UniProt (21730) |
NCBI (34166) |
Meta (301) |
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RP15 (454) |
RP35 (1834) |
RP55 (4172) |
RP75 (8105) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (352) |
Full (4216) |
Representative proteomes | UniProt (21730) |
NCBI (34166) |
Meta (301) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (454) |
RP35 (1834) |
RP55 (4172) |
RP75 (8105) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_8632 (release 14.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Fenech M |
Number in seed: | 352 |
Number in full: | 4216 |
Average length of the domain: | 227.70 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 57.04 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 212 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
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 HipA_C domain has been found. There are 33 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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