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33  structures 1287  species 4  interactions 2296  sequences 11  architectures

Family: HipA_C (PF07804)

Summary: HipA-like C-terminal domain

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

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

  1. 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

  2. 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

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].

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 35 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 KIND PI3_PI4_kinase PIP49_C PIP5K Pkinase Pkinase_Tyr Pox_ser-thr_kin RIO1 Seadorna_VP7 UL97 WaaY YrbL-PhoP_reg YukC

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(391)
Full
(2296)
Representative proteomes UniProt
(7559)
NCBI
(14888)
Meta
(302)
RP15
(356)
RP35
(1256)
RP55
(2391)
RP75
(4054)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(391)
Full
(2296)
Representative proteomes UniProt
(7559)
NCBI
(14888)
Meta
(302)
RP15
(356)
RP35
(1256)
RP55
(2391)
RP75
(4054)
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
(391)
Full
(2296)
Representative proteomes UniProt
(7559)
NCBI
(14888)
Meta
(302)
RP15
(356)
RP35
(1256)
RP55
(2391)
RP75
(4054)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Pfam-B_8632 (release 14.0)
Previous IDs: none
Type: Domain
Author: Fenech M, Eberhardt R
Number in seed: 391
Number in full: 2296
Average length of the domain: 227.00 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 57.32 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.5 30.5
Trusted cut-off 30.5 30.5
Noise cut-off 30.3 30.2
Model length: 212
Family (HMM) version: 11
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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Interactions

There are 4 interactions for this family. More...

HTH_3 Couple_hipA HTH_3 HipA_C

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 seqence.

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