Summary: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
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phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | Biotin_lipoyl Biotin_lipoyl_2 Peptidase_M23 |
Similarity to PfamA using HHSearch: | Peptidase_M23 Biotin_lipoyl_2 |
External database links
HOMSTRAD: | gpr |
PROSITE: | PDOC00528 |
SCOP: | 1gla |
Transporter classification: | 4.A.1 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001127
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [PUBMED:8246840, PUBMED:2197982] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.
The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC [PUBMED:1537788]. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).
The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [PUBMED:8246840, PUBMED:1537788, PUBMED:7815935, PUBMED:11361063].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Biological process | phosphoenolpyruvate-dependent sugar phosphotransferase system (GO:0009401) |
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 Hybrid (CL0105), which has the following description:
This superfamily contains proteins with a hybrid motif [1]. This motif is embedded in structurally diverse proteins.
The clan contains the following 24 members:
Apocytochr_F_C Biotin_carb_C Biotin_lipoyl Biotin_lipoyl_2 Complex1_51K DUF2118 DUF2254 GARS_C GCV_H HlyD HlyD_2 HlyD_3 HlyD_D23 HlyD_D4 LAL_C2 NAPRTase_N NQRA OEP Peptidase_M23 PTS_EIIA_1 PurK_C PYNP_C QRPTase_N RnfC_NAlignments
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...
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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.
Seed (682) |
Full (5604) |
Representative proteomes | UniProt (32108) |
NCBI (56354) |
Meta (51) |
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RP15 (477) |
RP35 (2609) |
RP55 (5497) |
RP75 (10623) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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.
Seed (682) |
Full (5604) |
Representative proteomes | UniProt (32108) |
NCBI (56354) |
Meta (51) |
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RP15 (477) |
RP35 (2609) |
RP55 (5497) |
RP75 (10623) |
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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: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 682 |
Number in full: | 5604 |
Average length of the domain: | 126.00 aa |
Average identity of full alignment: | 39 % |
Average coverage of the sequence by the domain: | 27.20 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null 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: | 127 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 PTS_EIIA_1 domain has been found. There are 23 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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