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1  structure 3712  species 0  interactions 3748  sequences 3  architectures

Family: YecM (PF06185)

Summary: YecM protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "YecM bacterial protein domain". More...

YecM bacterial protein domain Edit Wikipedia article

PDB 1k4n EBI.jpg
structural genomics, protein ec4020
Symbol YecM
Pfam PF06185
Pfam clan CL0104
InterPro IPR010393
SCOP 1k4n

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.[1]


The protein domain, YecM, is a monomer. The eight, mostly antiparallel beta-strands form around C-terminal alpha-helix. There are four alpha helices in total. [1]


  1. ^ a b Ling SH, Decker CJ, Walsh MA, She M, Parker R, Song H (2008). "Crystal structure of human Edc3 and its functional implications.". Mol Cell Biol 28 (19): 5965–76. doi:10.1128/MCB.00761-08. PMC 2547010. PMID 18678652. 

This article incorporates text from the public domain Pfam and InterPro IPR010393

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

YecM protein Provide feedback

This family consists of several bacterial YecM proteins of unknown function.

Literature references

  1. 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

This tab holds annotation information from the InterPro database.

InterPro entry IPR010393

This family consists of several bacterial YecM proteins of unknown function.

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 Glyoxalase (CL0104), which has the following description:

This clan contains the VOC metalloenzyme superfamily [1]. 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) [1].

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 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

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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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_11108 (release 9.0)
Previous IDs: DUF991;
Type: Family
Author: Moxon SJ, Bateman A
Number in seed: 50
Number in full: 3748
Average length of the domain: 176.20 aa
Average identity of full alignment: 74 %
Average coverage of the sequence by the domain: 93.61 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.8 31.1
Noise cut-off 23.1 23.4
Model length: 180
Family (HMM) version: 8
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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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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