Summary: Golgin subfamily A member 5
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Golgin subfamily A member 5 Provide feedback
Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterised: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1 [1].
Literature references
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Satoh A, Wang Y, Malsam J, Beard MB, Warren G; , Traffic. 2003;4:153-161.: Golgin-84 is a rab1 binding partner involved in Golgi structure. PUBMED:12656988 EPMC:12656988
Internal database links
SCOOP: | AAA_13 ADIP Atg14 ATG16 Baculo_PEP_C CALCOCO1 CASP_C CENP-F_leu_zip Crescentin DUF1664 EzrA Fez1 Filament FPP GAS HMMR_N IFT57 KASH_CCD MscS_porin OmpH Spc7 TPR_MLP1_2 WEMBL |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019177
This entry represents a family of proteins involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterised: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1 [PUBMED:12656988].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Biological process | Golgi organization (GO:0007030) |
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...
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 (12) |
Full (767) |
Representative proteomes | UniProt (1332) |
NCBI (1757) |
Meta (0) |
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RP15 (124) |
RP35 (378) |
RP55 (594) |
RP75 (775) |
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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 (12) |
Full (767) |
Representative proteomes | UniProt (1332) |
NCBI (1757) |
Meta (0) |
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RP15 (124) |
RP35 (378) |
RP55 (594) |
RP75 (775) |
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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: | KOGs (KOG4677) |
Previous IDs: | none |
Type: | Coiled-coil |
Sequence Ontology: | SO:0001080 |
Author: |
KOGs, Finn RD |
Number in seed: | 12 |
Number in full: | 767 |
Average length of the domain: | 255.00 aa |
Average identity of full alignment: | 27 % |
Average coverage of the sequence by the domain: | 40.85 % |
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: | 306 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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