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889  structures 4068  species 0  interactions 35190  sequences 69  architectures

Family: SBP_bac_1 (PF01547)

Summary: Bacterial extracellular solute-binding protein

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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Bacterial extracellular solute-binding protein Provide feedback

This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.

Literature references

  1. Spurlino JC, Lu GY, Quiocho FA; , J Biol Chem 1991;266:5202-5219.: The 2.3-A resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. PUBMED:2002054 EPMC:2002054

  2. Bruns CM, Nowalk AJ, Arvai AS, McTigue MA, Vaughan KG, Mietzner TA, McRee DE; , Nat Struct Biol 1997;4:919-924.: Structure of Haemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily. PUBMED:9360608 EPMC:9360608

  3. Vassylyev DG, Tomitori H, Kashiwagi K, Morikawa K, Igarashi K; , J Biol Chem 1998;273:17604-17609.: Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity. PUBMED:9651355 EPMC:9651355

  4. Tam R, Saier MH Jr; , Microbiol Rev 1993;57:320-346.: Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. PUBMED:8336670 EPMC:8336670

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006059

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins [ PUBMED:8003968 , PUBMED:18310026 ].

On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped into eight family clusters [ PUBMED:8336670 ], which generally correlate with the nature of the solute bound. This entry represents the family 1.

Family 1 members include:

  • Maltose/maltodextrin-binding proteins of Enterobacteriaceae (gene malE) [ PUBMED:7853407 ] and Streptococcus pneumoniae malX
  • Multiple oligosaccharide binding protein of Streptococcus mutans (gene msmE)
  • Escherichia coli glycerol-3-phosphate-binding protein
  • Serratia marcescens iron-binding protein (gene sfuA) and the homologous proteins (gene fbp) from Haemophilus influenzae and Neisseria
  • E. coli thiamine-binding protein (gene tbpA)

Interestingly, these thiamin-binding proteins share protein structural similarity with thiaminase-I. They may be evolved from a common ancestor [ PUBMED:18177053 ]. This entry also includes thiaminase-1 from Paenibacillus thiaminolyticus (Bacillus thiaminolyticus).

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 PBP (CL0177), which has the following description:

Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors [2].

The clan contains the following 27 members:

CypI DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 PDT Phosphonate-bd Porphobil_deam SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_C


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

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Representative proteomes UniProt

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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.

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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_269 (release 4.0)
Previous IDs: SBP_bacterial_1;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Griffiths-Jones SR
Number in seed: 129
Number in full: 35190
Average length of the domain: 298.40 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 65.41 %

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 26.0 26.0
Trusted cut-off 26.0 26.0
Noise cut-off 25.9 25.9
Model length: 315
Family (HMM) version: 28
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 SBP_bac_1 domain has been found. There are 889 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
A0QXD9 View 3D Structure Click here
O06989 View 3D Structure Click here
O07009 View 3D Structure Click here
O30142 View 3D Structure Click here
O32156 View 3D Structure Click here
O32208 View 3D Structure Click here
O34335 View 3D Structure Click here
O50499 View 3D Structure Click here
O51233 View 3D Structure Click here
O53485 View 3D Structure Click here
P0A0Y4 View 3D Structure Click here
P0AEX9 View 3D Structure Click here
P0AEY0 View 3D Structure Click here
P0AG78 View 3D Structure Click here
P0AG80 View 3D Structure Click here
P16700 View 3D Structure Click here
P19576 View 3D Structure Click here
P27366 View 3D Structure Click here
P35755 View 3D Structure Click here
P37966 View 3D Structure Click here
P39665 View 3D Structure Click here
P45192 View 3D Structure Click here
P45323 View 3D Structure Click here
P46338 View 3D Structure Click here
P55454 View 3D Structure Click here
P55601 View 3D Structure Click here
P71619 View 3D Structure Click here
P71894 View 3D Structure Click here
P76042 View 3D Structure Click here
P76108 View 3D Structure Click here
P94528 View 3D Structure Click here
P96062 View 3D Structure Click here
P9WGT9 View 3D Structure Click here
P9WGU1 View 3D Structure Click here
P9WGU3 View 3D Structure Click here
P9WGU9 View 3D Structure Click here
Q00749 View 3D Structure Click here
Q01903 View 3D Structure Click here
Q2YKZ9 View 3D Structure Click here
Q2YLW8 View 3D Structure Click here