Summary: Permease family
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This is the Wikipedia entry entitled "Nucleobase cation symporter-2". More...
Nucleobase cation symporter-2 Edit Wikipedia article
Xan_ur_permease | |||||||||
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Identifiers | |||||||||
Symbol | Xan_ur_permease | ||||||||
Pfam | PF00860 | ||||||||
Pfam clan | CL0062 | ||||||||
InterPro | IPR006043 | ||||||||
PROSITE | PDOC00860 | ||||||||
TCDB | 2.A.40 | ||||||||
OPM superfamily | 67 | ||||||||
OPM protein | 3qe7 | ||||||||
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Nucleobase cation symporter-2 protein family represents a susbset of the wider Amino acid-Polyamine-organoCation superfamily of transporters.[1] Characterised proteins from this family include:
- Uric acid permeases which promotes uptake of uric acid into the cell in limiting-nitrogen conditions [3]
- Sodium-dependent vitamin C transporter, a sodium/ascorbate cotransporter mediating electrogenic uptake of Vitamin C [5] These proteins generally contain 12 transmembrane regions. Many members of this family are uncharacterised and may transport other substrates eg. RutG is likely to transport pyrimidines into the cell.[6]
References
- ^ Jack DL, Paulsen IT, Saier MH (2000). "The amino acid/polyamine/organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations". Microbiology (Reading, Engl.). 146 ( Pt 8): 1797–814. PMID 10931886.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Christiansen LC, Schou S, Nygaard P, Saxild HH (1997). "Xanthine metabolism in Bacillus subtilis: characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism". J. Bacteriol. 179 (8): 2540–50. PMC 179002. PMID 9098051.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Schultz AC, Nygaard P, Saxild HH (2001). "Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator". J. Bacteriol. 183 (11): 3293–302. doi:10.1128/JB.183.11.3293-3302.2001. PMC 99626. PMID 11344136.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Ghim SY, Neuhard J (1994). "The pyrimidine biosynthesis operon of the thermophile Bacillus caldolyticus includes genes for uracil phosphoribosyltransferase and uracil permease". J. Bacteriol. 176 (12): 3698–707. PMC 205559. PMID 8206848.
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ignored (help) - ^ Liang WJ, Johnson D, Jarvis SM (2001). "Vitamin C transport systems of mammalian cells". Mol. Membr. Biol. 18 (1): 87–95. PMID 11396616.
{{cite journal}}
: CS1 maint: multiple names: authors list (link) - ^ Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, Kustu S (2006). "A previously undescribed pathway for pyrimidine catabolism". Proc. Natl. Acad. Sci. U.S.A. 103 (13): 5114–9. doi:10.1073/pnas.0600521103. PMC 1458803. PMID 16540542.
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ignored (help)CS1 maint: multiple names: authors list (link)
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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.
Permease family Provide feedback
This family includes permeases for diverse substrates such as xanthine P42086 uracil P39766 and vitamin C Q9UGH3. However many members of this family are functionally uncharacterised and may transport other substrates. Members of this family have ten predicted transmembrane helices.
Internal database links
SCOOP: | BenE Colicin_V DUF6069 MFS_MOT1 Sulfate_transp |
Similarity to PfamA using HHSearch: | Sulfate_transp |
External database links
PROSITE: | PDOC00860 |
Transporter classification: | 2.A.40 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006043
The nucleobase cation symporter 2 (NCS2) family, also known as the nucleobase ascorbate transporter(NAT) family, are a large family found in bacteria, fungi (except Saccharomyces cerevisiae), plants and mammals. Nucleobase transporter families have solute transport preferences among purines and pyrimidines. Members of this family often have overlapping but unique solute transport and binding profiles [ PUBMED:29385571 ].Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
Molecular function | transmembrane transporter activity (GO:0022857) |
Biological process | transmembrane transport (GO:0055085) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan APC (CL0062), which has the following description:
This large superfamily contains a variety of transporters including amino acid permeases that according to TCDB belong to the APC (Amino acid-Polyamine-organoCation) superfamily.
The clan contains the following 21 members:
AA_permease AA_permease_2 AA_permease_C Aa_trans BCCT BenE Branch_AA_trans CstA DUF3360 HCO3_cotransp K_trans MFS_MOT1 Na_Ala_symp Nramp SNF Spore_permease SSF Sulfate_transp Transp_cyt_pur Trp_Tyr_perm Xan_ur_permeaseAlignments
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...
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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 (20) |
Full (24590) |
Representative proteomes | UniProt (104634) |
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RP15 (3099) |
RP35 (11255) |
RP55 (23686) |
RP75 (41340) |
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Jalview | |||||||
HTML | |||||||
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 (20) |
Full (24590) |
Representative proteomes | UniProt (104634) |
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RP15 (3099) |
RP35 (11255) |
RP55 (23686) |
RP75 (41340) |
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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_1593 (release 2.1) |
Previous IDs: | xan_ur_permease; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 20 |
Number in full: | 24590 |
Average length of the domain: | 361.6 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 79.39 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 389 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 Xan_ur_permease domain has been found. There are 4 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.
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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.