Summary: HAP1 N-terminal conserved region
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HAP1 N-terminal conserved region Provide feedback
This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear [1-3]. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [4].
Literature references
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Li XJ, Li SH, Sharp AH, Nucifora FC Jr, Schilling G, Lanahan A, Worley P, Snyder SH, Ross CA; , Nature 1995;378:398-402.: A huntingtin-associated protein enriched in brain with implications for pathology. PUBMED:7477378 EPMC:7477378
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Bertaux F, Sharp AH, Ross CA, Lehrach H, Bates GP, Wanker E; , FEBS Lett 1998;426:229-232.: HAP1-huntingtin interactions do not contribute to the molecular pathology in Huntington's disease transgenic mice. PUBMED:9599014 EPMC:9599014
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Colomer V, Engelender S, Sharp AH, Duan K, Cooper JK, Lanahan A, Lyford G, Worley P, Ross CA; , Hum Mol Genet 1997;6:1519-1525.: Huntingtin-associated protein 1 (HAP1) binds to a Trio-like polypeptide, with a rac1 guanine nucleotide exchange factor domain. PUBMED:9285789 EPMC:9285789
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Hadano S, Yanagisawa Y, Skaug J, Fichter K, Nasir J, Martindale D, Koop BF, Scherer SW, Nicholson DW, Rouleau GA, Ikeda J, Hayden MR; , Genomics 2001;71:200-213.: Cloning and characterization of three novel genes, ALS2CR1, ALS2CR2, and ALS2CR3, in the juvenile amyotrophic lateral sclerosis (ALS2) critical region at chromosome 2q33-q34: candidate genes for ALS2. PUBMED:11161814 EPMC:11161814
Internal database links
SCOOP: | AAA_13 ADIP APG6_N Atg14 ATG16 Baculo_PEP_C bZIP_1 bZIP_2 bZIP_Maf CALCOCO1 CENP-F_leu_zip Crescentin DUF4201 EzrA Fez1 Filament FPP GAS KASH_CCD Spc7 TPR_MLP1_2 WEMBL ZapB |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006933
This entry represents a N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear [PUBMED:7477378, PUBMED:9599014, PUBMED:9285789]. This domain also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [PUBMED:11161814].
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 (25) |
Full (1432) |
Representative proteomes | UniProt (2238) |
NCBI (4476) |
Meta (0) |
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RP15 (204) |
RP35 (433) |
RP55 (927) |
RP75 (1453) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (25) |
Full (1432) |
Representative proteomes | UniProt (2238) |
NCBI (4476) |
Meta (0) |
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RP15 (204) |
RP35 (433) |
RP55 (927) |
RP75 (1453) |
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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_4571 (release 7.6) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Mifsud W |
Number in seed: | 25 |
Number in full: | 1432 |
Average length of the domain: | 248.20 aa |
Average identity of full alignment: | 45 % |
Average coverage of the sequence by the domain: | 34.13 % |
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: | 309 | ||||||||||||
Family (HMM) version: | 14 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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