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0  structures 53  species 0  interactions 63  sequences 3  architectures

Family: PARM (PF17061)

Summary: PARM

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.

PARM Provide feedback

Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present in most tissues, with high levels in the heart, kidney and placenta [1]. It has been shown to be induced and expressed in prostate after castration [2] and may have a role in cell proliferation and immortalisation in prostate cancer [3,1].

Literature references

  1. Fladeby C, Gupta SN, Barois N, Lorenzo PI, Simpson JC, Saatcioglu F, Bakke O;, Int J Cancer. 2008;122:1229-1235.: Human PARM-1 is a novel mucin-like, androgen-regulated gene exhibiting proliferative effects in prostate cancer cells. PUBMED:18027867 EPMC:18027867

  2. Bruyninx M, Hennuy B, Cornet A, Houssa P, Daukandt M, Reiter E, Poncin J, Closset J, Hennen G;, Endocrinology. 1999;140:4789-4799.: A novel gene overexpressed in the prostate of castrated rats: hormonal regulation, relationship to apoptosis and to acquired prostatic cell androgen independence. PUBMED:10499539 EPMC:10499539

  3. Cornet AM, Hanon E, Reiter ER, Bruyninx M, Nguyen VH, Hennuy BR, Hennen GP, Closset JL;, Prostate. 2003;56:220-230.: Prostatic androgen repressed message-1 (PARM-1) may play a role in prostatic cell immortalisation. PUBMED:12772192 EPMC:12772192


This tab holds annotation information from the InterPro database.

InterPro entry IPR031431

Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein present in most tissues, with high levels in the heart, kidney and placenta [PUBMED:18027867]. It is induced and expressed in prostate after castration [PUBMED:10499539] and may have a role in cell proliferation and immortalisation in prostate cancer [PUBMED:18027867, PUBMED:12772192]. PARM-1 also contributes to ovulation and/or luteal function by acting as a novel regulator of progesterone metabolism [PUBMED:24085821].

Domain organisation

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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, 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
(16)
Full
(63)
Representative proteomes UniProt
(73)
NCBI
(239)
Meta
(0)
RP15
(8)
RP35
(22)
RP55
(41)
RP75
(56)
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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
(16)
Full
(63)
Representative proteomes UniProt
(73)
NCBI
(239)
Meta
(0)
RP15
(8)
RP35
(22)
RP55
(41)
RP75
(56)
Alignment:
Format:
Order:
Sequence:
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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
(16)
Full
(63)
Representative proteomes UniProt
(73)
NCBI
(239)
Meta
(0)
RP15
(8)
RP35
(22)
RP55
(41)
RP75
(56)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: PHMMER:Q5RAF8
Previous IDs: none
Type: Family
Author: Llagostera M
Number in seed: 16
Number in full: 63
Average length of the domain: 237.60 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 92.24 %

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 35.0 35.0
Trusted cut-off 60.7 43.4
Noise cut-off 30.8 30.0
Model length: 297
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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