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B6db families: uncharacterized.family.yhfx
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uncharacterized family yhfx
Activity unclassified
Description unclassified activities
Notes YhfX from E. coli is a protein belonging to the Fold-type III group and distantly similar, in particular, to ornithine racemases (Family 5.1.1.12).
FTIII racemases usually contain a N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, but in this case the C-terminal domain is not recognized by pfam .
The YhfX structure (deposited in PDB, but not described in the literature) shows a covalently PLP-modified residue N6-(pyridoxal phosphate)lysine at the expected site (conserved Lys61).

NOTE: in many firmicutes (e.g., Lactobacillus rhamnosum, Jeotgalibaca dankookensis, Carnobacterium sp AT7) the yfhx gene is closely associated to a putative PLP-dependent C-S lyase (unclassified_family_yhfs).
PDB 4KDX;
PLP Fold Type III
PLP-dependent Domain
Domain alignment
Domain hmm		Fold type III
Number of sequences 24
Sequences in seed alignment
BacteriaWP_055150631 (Eubacterium contortum); WP_016370164 (Lactobacillus paracasei); WP_078697405 (Caloramator quimbayensis); WP_033573544 (Lactobacillus rhamnosus); WP_004126023 (Klebsiella michiganensis); WP_049857840 (Trabulsiella odontotermitis); YP_001705365 (Mycobacterium abscessus); WP_033059738 (Clostridium sporogenes); WP_062532506 (Jeotgalibaca dankookensis); WP_057813215 (Lactobacillus futsaii); WP_016538508 (Cedecea davisae); WP_012135487 (Citrobacter koseri); WP_013711130 (Carnobacterium sp. 17-4); WP_055669605 (Desnuesiella massiliensis); WP_039298368 (Cedecea neteri); BAG23729 (Streptomyces griseus subsp. griseus NBRC 13350); WP_062742195 (Enterobacter lignolyticus); WP_036774568 (Photorhabdus asymbiotica); NP_417840 (Escherichia coli); WP_064519313 (Buttiauxella gaviniae); WP_071877743 (Enterococcus silesiacus); WP_048283430 (Pluralibacter gergoviae); WP_072309237 (Hafnia alvei); WP_003847973 (Citrobacter freundii);

DISPLAY: Fasta format, alignment, hmm, hmm_local
Reference sequence NP_417840
Domain interval 33-264
Catalytic site 61 K
 
References Articles on uncharacterized.family.yhfx
last changed 2018/02/09 10:43

B6db families