Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
4  structures 6385  species 0  interactions 24590  sequences 105  architectures

Family: Xan_ur_permease (PF00860)

Summary: Permease family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Nucleobase cation symporter-2". More...

Nucleobase cation symporter-2 Edit Wikipedia article

Xan_ur_permease
Identifiers
SymbolXan_ur_permease
PfamPF00860
Pfam clanCL0062
InterProIPR006043
PROSITEPDOC00860
TCDB2.A.40
OPM superfamily67
OPM protein3qe7

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

  1. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  4. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)
  5. ^ 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)
  6. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR006043

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

External database links

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.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

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_permease

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 and the UniProtKB 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
(20)
Full
(24590)
Representative proteomes UniProt
(104634)
RP15
(3099)
RP35
(11255)
RP55
(23686)
RP75
(41340)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(20)
Full
(24590)
Representative proteomes UniProt
(104634)
RP15
(3099)
RP35
(11255)
RP55
(23686)
RP75
(41340)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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)
RP15
(3099)
RP35
(11255)
RP55
(23686)
RP75
(41340)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: 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 View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 389
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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.

Loading structure mapping...

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.

Protein Predicted structure External Information
A0A044UB11 View 3D Structure Click here
A0A077Z400 View 3D Structure Click here
A0A077Z5Y8 View 3D Structure Click here
A0A077Z937 View 3D Structure Click here
A0A077ZIA8 View 3D Structure Click here
A0A096QFX2 View 3D Structure Click here
A0A0D2EV05 View 3D Structure Click here
A0A0D2GVT9 View 3D Structure Click here
A0A0H3GHN2 View 3D Structure Click here
A0A0H3GL77 View 3D Structure Click here
A0A0H3GTC4 View 3D Structure Click here
A0A0H3GWL3 View 3D Structure Click here
A0A0H3GXG8 View 3D Structure Click here
A0A0H3H0H6 View 3D Structure Click here
A0A0H3H0Q5 View 3D Structure Click here
A0A0J9XV13 View 3D Structure Click here
A0A0J9YUX7 View 3D Structure Click here
A0A0K0E064 View 3D Structure Click here
A0A0K0E8Q5 View 3D Structure Click here
A0A0N4UCP9 View 3D Structure Click here
A0A0R0E3T5 View 3D Structure Click here
A0A0R0FHH8 View 3D Structure Click here
A0A0R0IKM1 View 3D Structure Click here
A0A0R0ITE3 View 3D Structure Click here
A0A0R0KA42 View 3D Structure Click here
A0A0R0LEW4 View 3D Structure Click here
A0A140LG99 View 3D Structure Click here
A0A175W1S3 View 3D Structure Click here
A0A175WH41 View 3D Structure Click here
A0A1C1C6I0 View 3D Structure Click here
A0A1C1CL02 View 3D Structure Click here
A0A1C1CQS1 View 3D Structure Click here
A0A1C1CZE8 View 3D Structure Click here
A0A1D6EP29 View 3D Structure Click here
A0A1D6EVW8 View 3D Structure Click here
A0A1D6F3V9 View 3D Structure Click here
A0A1D6F536 View 3D Structure Click here
A0A1D6G835 View 3D Structure Click here
A0A1D6GB39 View 3D Structure Click here
A0A1D6I8M9 View 3D Structure Click here