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0  structures 4851  species 0  interactions 66028  sequences 83  architectures

Family: EamA (PF00892)

Summary: EamA-like transporter family

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 "EamA". More...

EamA Edit Wikipedia article

EamA
Identifiers
Symbol EamA
Pfam PF00892
Pfam clan CL0184
InterPro IPR000620
TCDB 2.A.7
cysteine and O-acetyl-L-serine efflux system
Identifiers
Organism Escherichia coli
(strain K12 substrain MG1655)
Symbol eamA
Alt. symbols ydeD
RefSeq (Prot) NP_416050.4
UniProt P31125
Other data
Chromosome genome: 1.62 - 1.62 Mb

EamA (named after the O-acetyl-serine/cysteine export gene in E. coli) is a protein domain found in a wide range of proteins including the Erwinia chrysanthemi PecM protein, which is involved in pectinase, cellulase and blue pigment regulation, the Salmonella typhimurium PagO protein (function unknown), and some members of the solute carrier family group 35 (SLC35) nucleoside-sugar transporters. Many members of this family have no known function and are predicted to be integral membrane proteins and many of the proteins contain two copies of the domain.

Domain

EamA was long called DUF6 (domain unknown function) 6, and was one of the first DUF families to appear in Pfam.[1] Maximum likelihood phylogenetic analysis indicates that this family contains four stable sub-families with high bootstrap values: SLC35C/E, SLC35F, SLC35G (acyl-malonyl condensing enzyme-like AMAC), and purine permeases.[2]

The EamA HMM domain organization shows the two domain structure of EamA. However, the entries for UAA, Nuc_sug_transp, and DUF914, which may likely have derived from EamA, the HMM covers the duplicated structure as a single HMM.

Function

AMAC (acyl-malonyl condensing enzyme) is an interchangeable, but more general biochemical term than FAE 3-ketoacyl-CoA synthase 1, which would refer only to synthase #1. However, the transmembrane structure indicates that AMACs are transporters, not enzymes. Hence TMEM20, TMEM22, AMAC1 and AMAC-like (AMAC1L1, AMAC1L2, AMAC1L3) sequences have been renamed to SLC35Gs in RefSeq for Human and Mouse (SLC35G1 – 6). Furthermore, EamA is the only drug/metabolite transporter family to cross the prokaryote/eukaryote border, even though none of the original families crossed this border.[3] The highly diverse EamA Pfam family has been created by iterative expansion of the original dataset.

Evolution

The likely evolutionary order of human 5 + 5 TM nucleotide sugar transporters is identified.[2] It was done by training HMMs on each halve of these proteins: EamA, TPT, DUF914, UAA, and NST. The first method was multidimensional scaling in IBM SPSS, where a matrix of pairwise similarity measures from HMM-HMM comparisons was used as input. The output was a graph, showing a clear bipartitioning between DMT-1 and DMT-2 domains, where EamA-1 and EamA-2 were clearly in the middle. This result could be interpreted that EamA duplicated, and that the other families represent “diverged” copies from EamA.

The distance (100-p) between domain halves was measured, and the families were sorted by the following distances: EamA (smallest distance between domain halves), TPT, DUF914, UAA, and NST (highest distance between domain halves). What was perhaps surprising was that this order also replicated the distance to EamA, so that NST had the highest “distance” to EamA, UAA the second highest, and so on. The possibility that EamA (previously DUF6) may be an “artifact”, that has formed a "multipotent" HMM through iterative expansion of a diverse seed data, should be considered.[2]

During DNA replication of circular bacterial genomes, multiple proteins are involved in synthesizing the leading strand, and the Okazaki fragments on the lagging strand. If a sequence contains an inverted repeat (a palindrome) longer than 10 bp, and a spacer/insert of less than 75-150 basepairs, the sequence could be accessible to SbcCD,[4] a protein which inhibits the propagation of replicons containing long palindromic DNA sequences. Watson-Crick basepairing of the palindrome, and a break in the sequence may occur, creating an opportunity for priming DNA synthesis in the opposite direction. This may be followed by spontaneous strand switching and continuation of normal replication. This phenomenon is referred to as Tandem Inversion Duplication (TID).[5] Then there may have been degradation of the third (inverted) copy which would be in the middle. Strand slippage deletion (illegitimate recombination) may be responsible. The presence of two palindromes in the regional duplication may increase the probability of degradation.

A concrete bioinformatic example could be a DUF606 protein, known to exist in both paired and fused copies in bacterial genomes,[6] where a DUF606 protein (Accession: ACL39356.1) from Arthrobacter chlorophenolicus A6, has a 5+5 TM structure and matches 2 x DUF606 HMM in Pfam, and thus appears to be duplicated. Interestingly, when the genomic sequence (1530600 – 1531700) of the protein from Arthrobacter is obtained, it is found that it contains a palindrome (cgtggcggcg and gcaccgccgc) in the middle of the domain halves, although it may be too short and have too long a spacer to be able to initiate a new TID.

See also

References

  1. ^ Bateman A, Coggill P, Finn RD (October 2010). "DUFs: families in search of function". Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (Pt 10): 1148–52. doi:10.1107/S1744309110001685. PMC 2954198. PMID 20944204. 
  2. ^ a b c Västermark Å, Almén MS, Simmen MW, Fredriksson R, Schiöth HB (2011). "Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae". BMC Evol. Biol. 11: 123. doi:10.1186/1471-2148-11-123. PMC 3111387. PMID 21569384. 
  3. ^ Jack DL, Yang NM, Saier MH (July 2001). "The drug/metabolite transporter superfamily". Eur. J. Biochem. 268 (13): 3620–39. doi:10.1046/j.1432-1327.2001.02265.x. PMID 11432728. 
  4. ^ Leach DR, Lloyd RG, Coulson AF (1992). "The SbcCD protein of Escherichia coli is related to two putative nucleases in the UvrA superfamily of nucleotide-binding proteins". Genetica 87 (2): 95–100. doi:10.1007/bf00120998. PMID 1490631. 
  5. ^ Kugelberg E, Kofoid E, Andersson DI, Lu Y, Mellor J, Roth FP, Roth JR (May 2010). "The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types". Genetics 185 (1): 65–80. doi:10.1534/genetics.110.114074. PMC 2870977. PMID 20215473. 
  6. ^ Lolkema JS, Dobrowolski A, Slotboom DJ (May 2008). "Evolution of antiparallel two-domain membrane proteins: tracing multiple gene duplication events in the DUF606 family". J. Mol. Biol. 378 (3): 596–606. doi:10.1016/j.jmb.2008.03.005. PMID 18384811. 

This article incorporates text from the public domain Pfam and InterPro IPR000620

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.

EamA-like transporter family Provide feedback

This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000620

This domain is found in proteins including the Erwinia chrysanthemi PecM protein, which is involved in pectinase, cellulase and blue pigment regulation; and the Salmonella typhimurium PagO protein, the function of which is unknown. Many members of this family are classed as drug/metabolite transporters and have no known function. They are predicted to be integral membrane proteins and many of the proteins contain two copies of this domain [PUBMED:11432728].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 DMT (CL0184), which has the following description:

This clan contains a variety of transporters which have 4, 5, 9 or 10 membrane spanning helices. Many of the 10 membrane spanning transporters appear to be a duplication of the 5 spanning unit [1]. Many of these families contain a characteristic glycine rich motif close to the C-terminus.

The clan contains the following 20 members:

Cation_efflux CRCB CRT-like DUF1632 DUF486 DUF606 DUF914 EamA EmrE Mg_trans_NIPA Multi_Drug_Res Nuc_sug_transp RhaT Sugar_transport TPT UAA UPF0060 UPF0546 Ureide_permease Zip

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(98)
Full
(66028)
Representative proteomes NCBI
(56174)
Meta
(36728)
RP15
(4905)
RP35
(10337)
RP55
(14119)
RP75
(17444)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(98)
Full
(66028)
Representative proteomes NCBI
(56174)
Meta
(36728)
RP15
(4905)
RP35
(10337)
RP55
(14119)
RP75
(17444)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(98)
Full
(66028)
Representative proteomes NCBI
(56174)
Meta
(36728)
RP15
(4905)
RP35
(10337)
RP55
(14119)
RP75
(17444)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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.

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...

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: Pfam-B_177 (release 3.0)
Previous IDs: DUF6;
Type: Family
Author: Bateman A
Number in seed: 98
Number in full: 66028
Average length of the domain: 125.00 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 75.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.2
Model length: 126
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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