Summary: YecM protein
This is the Wikipedia entry entitled "YecM bacterial protein domain". More...
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YecM bacterial protein domain Edit Wikipedia article
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structural genomics, protein ec4020
In molecular biology, YecM refers to a protein domain found in Escherichia coli. It is a conserved, hypothetical protein with sequence homologues found exclusively in bacteria. Several bacterial YecM proteins in this particular family are of unknown function.
The precise function of the YecM domain remains to be elucidated. However, YecM structural homologues reveal that all the proteins bind a divalent metal cation. This comparison suggests that YecM may be a metal-binding protein and therefore may function as an enzyme.
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This family consists of several bacterial YecM proteins of unknown function.
Zhang RG, Duke N, Laskowski R, Evdokimova E, Skarina T, Edwards A, Joachimiak A, Savchenko A; , Proteins 2003;51:311-314.: Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases. PUBMED:12660999 EPMC:12660999
External database links
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This clan contains the VOC metalloenzyme superfamily . The known types of reactions that are catalysed include isomerizations (glyoxalase I), epimerizations (methylmalonyl-CoA epimerase), oxidative cleavage of C-C bonds (extradiol dioxygenase), and nucleophilic substitutions (fosfomycin resistance proteins) .
The clan contains the following 8 members:3-dmu-9_3-mt CppA_N Glyoxalase Glyoxalase_2 Glyoxalase_3 Glyoxalase_4 Glyoxalase_5 YecM
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
You can see the alignments as HTML or in three different sequence viewers:
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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:||Pfam-B_11108 (release 9.0)|
|Author:||Moxon SJ, Bateman A|
|Number in seed:||6|
|Number in full:||775|
|Average length of the domain:||181.20 aa|
|Average identity of full alignment:||59 %|
|Average coverage of the sequence by the domain:||95.31 %|
|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:||7|
|Download:||download the raw HMM for this family|
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How the sunburst is generated
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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 YecM domain has been found. There are 1 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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