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293  structures 6540  species 0  interactions 50641  sequences 755  architectures

Family: SBP_bac_3 (PF00497)

Summary: Bacterial extracellular solute-binding proteins, family 3

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Bacterial extracellular solute-binding proteins, family 3 Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001638

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 [ PUBMED:8336670 ] into eight families or clusters, which generally correlate with the nature of the solute bound.

This entry represents a domain found in the solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. This domain can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. MltF is a murein-degrading enzyme that degrades murein glycan strands and insoluble, high-molecular weight murein sacculi, with the concomitant formation of a 1,6-anhydromuramoyl product [ PUBMED:18234673 ].

Familiy 3 members include:

  • Histidine-binding protein (gene hisJ) of Escherichia coli and related bacteria. An homologous lipoprotein exists in Neisseria gonorrhoeae.
  • Lysine/arginine/ornithine-binding proteins (LAO) (gene argT) of Escherichia coli and related bacteria are involved in the same transport system than hisJ. Both solute-binding proteins interact with a common membrane-bound receptor hisP of the binding protein dependent transport system HisQMP.
  • Glutamine-binding proteins (gene glnH) of Escherichia coli and Bacillus stearothermophilus.
  • Glutamate-binding protein (gene gluB) of Corynebacterium glutamicum.
  • Arginine-binding proteins artI and artJ of Escherichia coli.
  • Nopaline-binding protein (gene nocT) from Agrobacterium tumefaciens.
  • Octopine-binding protein (gene occT) from Agrobacterium tumefaciens.
  • Major cell-binding factor (CBF1) (gene: peb1A) from Campylobacter jejuni.
  • Bacteroides nodosus protein aabA.
  • Cyclohexadienyl/arogenate dehydratase of Pseudomonas aeruginosa, a periplasmic enzyme which forms an alternative pathway for phenylalanine biosynthesis.
  • Escherichia coli protein fliY.
  • Vibrio harveyi protein patH.
  • Escherichia coli hypothetical protein ydhW.
  • Bacillus subtilis hypothetical protein yckB.
  • Bacillus subtilis hypothetical protein yckK.

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:

DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate Mycoplasma_p37 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

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
(241)
Full
(50641)
Representative proteomes UniProt
(266578)
RP15
(5753)
RP35
(22994)
RP55
(51125)
RP75
(99451)
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
(241)
Full
(50641)
Representative proteomes UniProt
(266578)
RP15
(5753)
RP35
(22994)
RP55
(51125)
RP75
(99451)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(241)
Full
(50641)
Representative proteomes UniProt
(266578)
RP15
(5753)
RP35
(22994)
RP55
(51125)
RP75
(99451)
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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 241
Number in full: 50641
Average length of the domain: 225.90 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 61.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.2 25.2
Trusted cut-off 25.2 25.2
Noise cut-off 25.1 25.1
Model length: 225
Family (HMM) version: 22
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

Selections

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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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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 SBP_bac_3 domain has been found. There are 293 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
A0A0N7KLP1 View 3D Structure Click here
A0A0P0WTE6 View 3D Structure Click here
A0A0P0WTQ8 View 3D Structure Click here
A0A0P0WTV5 View 3D Structure Click here
A0A0P0WU14 View 3D Structure Click here
A0A0P0XLY5 View 3D Structure Click here
A0A0P0XNE5 View 3D Structure Click here
A0A0R0FUT0 View 3D Structure Click here
A0A0R0FUX9 View 3D Structure Click here
A0A0R0GJI9 View 3D Structure Click here
A0A0R0GSR6 View 3D Structure Click here
A0A0R0H0I1 View 3D Structure Click here
A0A0R0IAP1 View 3D Structure Click here
A0A0R0JFH4 View 3D Structure Click here
A0A0R0JKV3 View 3D Structure Click here
A0A0R0JKV3 View 3D Structure Click here
A0A0R0JSN9 View 3D Structure Click here
A0A0R0JT57 View 3D Structure Click here
A0A1D6E1R2 View 3D Structure Click here
A0A1D6EQP7 View 3D Structure Click here
A0A1D6EQP9 View 3D Structure Click here
A0A1D6EXB6 View 3D Structure Click here
A0A1D6GTI6 View 3D Structure Click here
A0A1D6GTI9 View 3D Structure Click here
A0A1D6GTJ2 View 3D Structure Click here
A0A1D6GYP5 View 3D Structure Click here
A0A1D6HMT5 View 3D Structure Click here
A0A1D6HMU4 View 3D Structure Click here
A0A1D6HQP8 View 3D Structure Click here
A0A1D6HQP9 View 3D Structure Click here
A0A1D6I4R9 View 3D Structure Click here
A0A1D6I4S0 View 3D Structure Click here
A0A1D6IXA3 View 3D Structure Click here
A0A1D6QCK5 View 3D Structure Click here
B9G3Q7 View 3D Structure Click here
G5EGQ9 View 3D Structure Click here
I1J8B7 View 3D Structure Click here
I1JST3 View 3D Structure Click here
I1K7B0 View 3D Structure Click here
I1KDN7 View 3D Structure Click here
I1KFC6 View 3D Structure Click here
I1KMD9 View 3D Structure Click here
I1L4P7 View 3D Structure Click here
I1LU56 View 3D Structure Click here
I1LU57 View 3D Structure Click here
I1M440 View 3D Structure Click here
I1M634 View 3D Structure Click here
I1MMT0 View 3D Structure Click here
K7KBT8 View 3D Structure Click here
K7L2U8 View 3D Structure Click here
K7LEX1 View 3D Structure Click here
K7LNQ4 View 3D Structure Click here
K7LTZ4 View 3D Structure Click here
K7LWX1 View 3D Structure Click here
K7M0A1 View 3D Structure Click here
K7M1F5 View 3D Structure Click here
K7M291 View 3D Structure Click here
K7M2W3 View 3D Structure Click here
K7MFG6 View 3D Structure Click here
K7MK91 View 3D Structure Click here
K7MNP8 View 3D Structure Click here
K7UT49 View 3D Structure Click here
O04660 View 3D Structure Click here
O81078 View 3D Structure Click here
O81776 View 3D Structure Click here
P09551 View 3D Structure Click here
P0AEM9 View 3D Structure Click here
P0AEQ3 View 3D Structure Click here
P0AEU0 View 3D Structure Click here
P0AGC5 View 3D Structure Click here
P30855 View 3D Structure Click here
P30855 View 3D Structure Click here
P30859 View 3D Structure Click here
P30860 View 3D Structure Click here
P37902 View 3D Structure Click here
P96257 View 3D Structure Click here
Q0D972 View 3D Structure Click here
Q0DA37 View 3D Structure Click here
Q2FVL2 View 3D Structure Click here
Q2FX86 View 3D Structure Click here
Q3S1M4 View 3D Structure Click here
Q5QLP6 View 3D Structure Click here
Q69KK7 View 3D Structure Click here
Q69KL0 View 3D Structure Click here
Q69KL2 View 3D Structure Click here
Q69L07 View 3D Structure Click here
Q69L11 View 3D Structure Click here
Q69NA4 View 3D Structure Click here
Q69NA5 View 3D Structure Click here
Q6K4P7 View 3D Structure Click here
Q6ZGL7 View 3D Structure Click here
Q7XJL2 View 3D Structure Click here
Q7XP59 View 3D Structure Click here
Q84W41 View 3D Structure Click here
Q8GXJ4 View 3D Structure Click here
Q8LGN0 View 3D Structure Click here
Q8LGN1 View 3D Structure Click here
Q93YT1 View 3D Structure Click here
Q9C5V5 View 3D Structure Click here
Q9C8E7 View 3D Structure Click here
Q9FH75 View 3D Structure Click here
Q9LFN5 View 3D Structure Click here
Q9LFN8 View 3D Structure Click here
Q9LV72 View 3D Structure Click here
Q9M8W7 View 3D Structure Click here
Q9SDQ4 View 3D Structure Click here
Q9SHV1 View 3D Structure Click here
Q9SHV2 View 3D Structure Click here
Q9SW97 View 3D Structure Click here
Q9VFV0 View 3D Structure Click here
Q9VYN4 View 3D Structure Click here
Q9XUB4 View 3D Structure Click here