Summary: LMBR1-like membrane protein
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LMBR1-like membrane protein Provide feedback
Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought [1]. Vertebrate members of this family may play a role in limb development [3]. A member of this family has been shown to be a lipocalin membrane receptor [2]
Literature references
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Lettice LA, Horikoshi T, Heaney SJ, van Baren MJ, van der Linde HC, Breedveld GJ, Joosse M, Akarsu N, Oostra BA, Endo N, Shibata M, Suzuki M, Takahashi E, Shinka T, Nakahori Y, Ayusawa D, Nakabayashi K, Scherer SW, Heutink P, Hill RE, Noji S; , Proc Natl Acad Sci U S A 2002;99:7548-7553.: Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. PUBMED:12032320 EPMC:12032320
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Wojnar P, Lechner M, Merschak P, Redl B; , J Biol Chem 2001;276:20206-20212.: Molecular cloning of a novel lipocalin-1 interacting human cell membrane receptor using phage display. PUBMED:11287427 EPMC:11287427
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Ianakiev P, van Baren MJ, Daly MJ, Toledo SP, Cavalcanti MG, Neto JC, Silveira EL, Freire-Maia A, Heutink P, Kilpatrick MW, Tsipouras P; , Am J Hum Genet 2001;68:38-45.: Acheiropodia is caused by a genomic deletion in C7orf2, the human orthologue of the Lmbr1 gene. PUBMED:11090342 EPMC:11090342
Internal database links
SCOOP: | FUSC HAMP HisKA MttA_Hcf106 Tmemb_cc2 V-SNARE V-SNARE_C |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006876
This group of uncharacterised proteins have a conserved C-terminal region which is found in LMBR1 and in the lipocalin-1 receptor. LMBR1 was thought to play a role in preaxial polydactyly, but recent evidence now suggests this not to be the case [PUBMED:12032320]. Vertebrate members of this family may play a role in limb development [PUBMED:11090342]. A member of this family has been shown to be a lipocalin membrane receptor [PUBMED:11287427].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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 (82) |
Full (3217) |
Representative proteomes | UniProt (4689) |
NCBI (6586) |
Meta (7) |
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RP15 (909) |
RP35 (1702) |
RP55 (2460) |
RP75 (2943) |
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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 (82) |
Full (3217) |
Representative proteomes | UniProt (4689) |
NCBI (6586) |
Meta (7) |
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RP15 (909) |
RP35 (1702) |
RP55 (2460) |
RP75 (2943) |
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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_6189 (release 7.5) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Waterfield DI |
Number in seed: | 82 |
Number in full: | 3217 |
Average length of the domain: | 334.70 aa |
Average identity of full alignment: | 14 % |
Average coverage of the sequence by the domain: | 73.64 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 510 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
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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