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9  structures 5596  species 0  interactions 11921  sequences 18  architectures

Family: ABC-3 (PF00950)

Summary: ABC 3 transport family

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

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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.

ABC 3 transport family Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001626

This subfamily consists of integral membrane components from a number of bacterial transport systems that have similar sequences [ PUBMED:11421271 ], and include TroC and TroD, and ScaB (required for Mn2+ import in Streptococcus [ PUBMED:9440518 ]).

Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters are involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of a PBP, two transmembrane regions (TMs), and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment [ PUBMED:11421276 ]. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The TMs are bundles of alpha helices that transverse the cytoplasmic membrane multiple times. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Each TM has a prominent cytoplasmic loop which contacts an ABC and represents a conserved motif. The two TMs form either a homodimer (e.g. in the case of the BtuC subunits of the Escherichia coli BtuCD vitamin B12 transporter) [ PUBMED:12004122 , PUBMED:17673622 ], a heterodimer (e.g. the TroC and TroD subunits of the Treponema pallidum general transition metal transporter, TroBCD) [ PUBMED:17581125 , PUBMED:9332349 ], or a pseudo-heterodimer (e.g. the FhuB protein of the E. coli ferrichrome transporter, FhuBC) [ PUBMED:2823072 , PUBMED:9802017 ].

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...

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Pfam Clan

This family is a member of clan Membrane_trans (CL0142), which has the following description:

This clan contains membrane proteins involved in the transport of molecules including amino acids sugars and signalling molecules. It also includes integral membrane cell cycle proteins and some putative ammonia monooxygenases.

The clan contains the following 7 members:

ABC-3 AbrB BPD_transp_2 DUF1275 FecCD FTSW_RODA_SPOVE Pam17


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.

Representative proteomes UniProt
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PP/heatmap 1            

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

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

Format an alignment

Representative proteomes UniProt

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.

Representative proteomes UniProt
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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...


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_1591 (release 2.1)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 14
Number in full: 11921
Average length of the domain: 250.7 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 87.87 %

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 20.1 20.1
Trusted cut-off 20.1 20.1
Noise cut-off 20.0 20.0
Model length: 258
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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


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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 ABC-3 domain has been found. There are 9 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.

Protein Predicted structure External Information
A0A0H3GS06 View 3D Structure Click here
A0A0H3GUA5 View 3D Structure Click here
A0A0H3GUE0 View 3D Structure Click here
A0A0H3H1Z2 View 3D Structure Click here
H9L416 View 3D Structure Click here
H9L4A7 View 3D Structure Click here
K0EM02 View 3D Structure Click here
K0ENA9 View 3D Structure Click here
O34500 View 3D Structure Click here
O34610 View 3D Structure Click here
O35024 View 3D Structure Click here
O83079 View 3D Structure Click here
O84072 View 3D Structure Click here
O84073 View 3D Structure Click here
O84422 View 3D Structure Click here
O86339 View 3D Structure Click here
P39832 View 3D Structure Click here
P44660 View 3D Structure Click here
P44661 View 3D Structure Click here
P44691 View 3D Structure Click here
P57402 View 3D Structure Click here
P73087 View 3D Structure Click here
P96118 View 3D Structure Click here
P96119 View 3D Structure Click here
Q0PBZ6 View 3D Structure Click here
Q2FY18 View 3D Structure Click here
Q2G2D9 View 3D Structure Click here
Q32GF9 View 3D Structure Click here
Q32GG0 View 3D Structure Click here
Q32HA2 View 3D Structure Click here
Q55282 View 3D Structure Click here
Q56954 View 3D Structure Click here
Q56955 View 3D Structure Click here
Q5FA62 View 3D Structure Click here
Q89AJ1 View 3D Structure Click here
Q8CWN1 View 3D Structure Click here
Q8DNW7 View 3D Structure Click here
Q8Y652 View 3D Structure Click here
Q8ZNV6 View 3D Structure Click here
Q9CCW1 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;