Summary: Citrate transporter
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Citrate transporter Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | ABG_transport ArsB CitMHS_2 DctM DcuA_DcuB DcuC DUF1646 DUF401 DUF969 FtsX GntP_permease Lactate_perm MatC_N Na_H_antiport_2 Na_H_antiporter Na_sulph_symp NhaB SCFA_trans TrkA_C |
Similarity to PfamA using HHSearch: | Na_sulph_symp Na_sulph_symp ArsB GntP_permease DctM MatC_N CitMHS_2 |
External database links
Transporter classification: | 2.A.11 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004680
This domain is found in proteins belonging to the CitM transporter, NhaD Na+/H+ antiporter and Na+/sulfate symporter families, such as CitM from Bacillus subtilis [PUBMED:11891560], NhaD from Halomonas elongata [PUBMED:16872527] and SLT1 from Chlamydomonas reinhardtii [PUBMED:20498339].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | integral component of membrane (GO:0016021) |
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 IT (CL0182), which has the following description:
This superfamily of secondary carriers specific for cationic and anionic compounds, has been termed the ion transporter (IT) superfamily [1].
The clan contains the following 19 members:
ABG_transport ArsB CitMHS CitMHS_2 DctM DcuA_DcuB DcuC DUF1646 DUF401 EXS GntP_permease Lactate_perm MatC_N Na_H_antiport_2 Na_H_antiport_3 Na_H_antiporter Na_sulph_symp NhaB SCFA_transAlignments
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 (564) |
Full (12690) |
Representative proteomes | UniProt (55811) |
NCBI (188587) |
Meta (2980) |
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RP15 (1651) |
RP35 (5977) |
RP55 (12396) |
RP75 (21080) |
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HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (564) |
Full (12690) |
Representative proteomes | UniProt (55811) |
NCBI (188587) |
Meta (2980) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1651) |
RP35 (5977) |
RP55 (12396) |
RP75 (21080) |
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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: | TIGRFAMs |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
TIGRFAMs, Griffiths-Jones SR |
Number in seed: | 564 |
Number in full: | 12690 |
Average length of the domain: | 364.30 aa |
Average identity of full alignment: | 14 % |
Average coverage of the sequence by the domain: | 84.93 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null --hand 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: | 295 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
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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