Summary: Periplasmic binding proteins and sugar binding domain of LacI family
Periplasmic binding proteins and sugar binding domain of LacI family Provide feedback
This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (PF00356).
Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Lu P; , Science 1996;271:1247-1254.: Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. PUBMED:8638105 EPMC:8638105
Internal database links
|Similarity to PfamA using HHSearch:||Peripla_BP_3 Peripla_BP_4 Peripla_BP_6|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001761
This family includes some periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (lacI) [PUBMED:1583688, PUBMED:8638105].
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This clan includes proteins involved in chemotaxis, membrane transport of sugars and allocrites, and the LacI family transcriptional regulators. It also includes some antigenic basic membrane lipoproteins.
The clan contains the following 9 members:ABC_sub_bind ANF_receptor Bmp LppC Peripla_BP_1 Peripla_BP_3 Peripla_BP_4 Peripla_BP_5 Peripla_BP_6
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||MRC-LMB Genome group|
|Author:||Bateman A, Griffiths-Jones SR|
|Number in seed:||6|
|Number in full:||5137|
|Average length of the domain:||255.60 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||79.54 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Peripla_BP_1 domain has been found. There are 27 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 seqence.
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