Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
12  structures 1335  species 0  interactions 8918  sequences 152  architectures

Family: PHM7_cyt (PF14703)

Summary: Cytosolic domain of 10TM putative phosphate transporter

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

Cytosolic domain of 10TM putative phosphate transporter Provide feedback

PHM7_cyt is the predicted cytosolic domain of integral membrane proteins, such as yeast PHM7 and TM63A_HUMAN TRANSMEMBRANE PROTEIN 63A, SwissProt:O94886. This domain usually precedes the 7TM region, PF02714 and follows a RSN1_TM, PF13967. Fold recognition programs consistently and with high significance predict this domain to be distantly homologous to RNA binding proteins from the RRM clan.

Literature references

  1. Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE;, Nat Genet. 2008;40:854-861.: Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. PUBMED:18552845 EPMC:18552845


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR027815

This is the predicted cytosolic domain of integral membrane proteins, such as yeast PHM7 and TM63A_HUMAN TRANSMEMBRANE PROTEIN 63A, SWISSPROT . This domain usually preceeds the 7TM region and follows a RSN1_TM. Fold recognition programs consistenly and with high significance predict this domain to be distantly homologous to RNA binding proteins from the RRM clan [ PUBMED:18552845 ].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan RRM (CL0221), which has the following description:

This clan contains families that are related to the RNA recognition motif domains. However, not all these families are RNA binding.

The clan contains the following 32 members:

BRAP2 Calcipressin DbpA DUF1743 DUF1866 DUF4523 GlcNAc-1_reg GUCT Limkain-b1 Nup35_RRM Nup35_RRM_2 PHM7_cyt RL RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_7 RRM_8 RRM_9 RRM_occluded RRM_Rrp7 SET_assoc Smg4_UPF3 Spo7_2_N Tap-RNA_bind Transposase_22 U1snRNP70_N xRRM XS YlmH_RBD

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
(182)
Full
(8918)
Representative proteomes UniProt
(15497)
RP15
(1311)
RP35
(3983)
RP55
(6816)
RP75
(9390)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(182)
Full
(8918)
Representative proteomes UniProt
(15497)
RP15
(1311)
RP35
(3983)
RP55
(6816)
RP75
(9390)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(182)
Full
(8918)
Representative proteomes UniProt
(15497)
RP15
(1311)
RP35
(3983)
RP55
(6816)
RP75
(9390)
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: Jackhammer:Q9P1W3
Previous IDs: DUF4463;
Type: Domain
Sequence Ontology: SO:0000417
Author: Godzik A
Number in seed: 182
Number in full: 8918
Average length of the domain: 171.10 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 21.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 176
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 PHM7_cyt domain has been found. There are 12 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.

Loading structure mapping...

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
A0A096TML4 View 3D Structure Click here
A0A0G2JVY4 View 3D Structure Click here
A0A0R0HHK2 View 3D Structure Click here
A0A0R0L4V8 View 3D Structure Click here
A0A0R4IKF9 View 3D Structure Click here
A0A1D6DQ14 View 3D Structure Click here
A0A1D6F9C8 View 3D Structure Click here
A0A1D6FLX9 View 3D Structure Click here
A0A1D6G4L0 View 3D Structure Click here
A0A1D6GIF5 View 3D Structure Click here
A0A1D6GUN5 View 3D Structure Click here
A0A1D6KA79 View 3D Structure Click here
A0A1D6KEP3 View 3D Structure Click here
A0A1D6M4Q2 View 3D Structure Click here
A0A1D6MV54 View 3D Structure Click here
A0A1D6NN98 View 3D Structure Click here
A0A1D8PDS7 View 3D Structure Click here
A0A1D8PEK8 View 3D Structure Click here
A0A1D8PI19 View 3D Structure Click here
A0A367GJQ4 View 3D Structure Click here
A0A368UIL5 View 3D Structure Click here
B5TYT3 View 3D Structure Click here
D3ZNF5 View 3D Structure Click here
D4A105 View 3D Structure Click here
F1R745 View 3D Structure Click here
F4HYR3 View 3D Structure Click here
F4I248 View 3D Structure Click here
F4IBD7 View 3D Structure Click here
F4JCY2 View 3D Structure Click here
I1JIM3 View 3D Structure Click here
I1JNS0 View 3D Structure Click here
I1JTT9 View 3D Structure Click here
I1KNG9 View 3D Structure Click here
I1LXJ1 View 3D Structure Click here
I1M1I9 View 3D Structure Click here
I1M8X6 View 3D Structure Click here
I1MF04 View 3D Structure Click here
I1N9F1 View 3D Structure Click here
K7K7Q0 View 3D Structure Click here
K7LF61 View 3D Structure Click here
K7MGW7 View 3D Structure Click here
K7MJC9 View 3D Structure Click here
K7MUV4 View 3D Structure Click here
K7MW51 View 3D Structure Click here
K7N1Y1 View 3D Structure Click here
K7WH29 View 3D Structure Click here
O43022 View 3D Structure Click here
O94886 View 3D Structure Click here
Q03516 View 3D Structure Click here
Q06538 View 3D Structure Click here
Q09766 View 3D Structure Click here
Q09809 View 3D Structure Click here
Q10S28 View 3D Structure Click here
Q12252 View 3D Structure Click here
Q2QLP9 View 3D Structure Click here
Q2QN15 View 3D Structure Click here
Q3TWI9 View 3D Structure Click here
Q54RR3 View 3D Structure Click here
Q59TM5 View 3D Structure Click here
Q5ANH1 View 3D Structure Click here
Q5JKX1 View 3D Structure Click here
Q5JLH8 View 3D Structure Click here
Q5T3F8 View 3D Structure Click here
Q5TKG1 View 3D Structure Click here
Q5XEZ5 View 3D Structure Click here
Q6AU79 View 3D Structure Click here
Q6NP91 View 3D Structure Click here
Q6ZLQ0 View 3D Structure Click here
Q75GI5 View 3D Structure Click here
Q75JR4 View 3D Structure Click here
Q75JX3 View 3D Structure Click here
Q7XBT3 View 3D Structure Click here
Q8CBX0 View 3D Structure Click here
Q8GUH7 View 3D Structure Click here
Q8I4T2 View 3D Structure Click here
Q8VZM5 View 3D Structure Click here
Q91YT8 View 3D Structure Click here
Q94A87 View 3D Structure Click here
Q9C8G5 View 3D Structure Click here
Q9FVQ5 View 3D Structure Click here
Q9LVE4 View 3D Structure Click here
Q9P1W3 View 3D Structure Click here
Q9SY14 View 3D Structure Click here
Q9SZT4 View 3D Structure Click here
Q9XEA1 View 3D Structure Click here
X1WEM4 View 3D Structure Click here