GapMind for catabolism of small carbon sources

 

Protein WP_106714139.1 in Phyllobacterium brassicacearum STM 196

Annotation: NCBI__GCF_003010955.1:WP_106714139.1

Length: 661 amino acids

Source: GCF_003010955.1 in NCBI

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruI lo Fructose-specific PTS system, I, HPr, and IIA components (characterized) 37% 68% 379.8 phosphoenolpyruvate-protein phosphotransferase (EC 2.7.3.9) 38% 365.5
sucrose catabolism fruI lo Fructose-specific PTS system, I, HPr, and IIA components (characterized) 37% 68% 379.8 phosphoenolpyruvate-protein phosphotransferase (EC 2.7.3.9) 38% 365.5
trehalose catabolism treEIIA lo D-trehalose PTS system, I, HPr, and IIA components (characterized) 37% 74% 355.1 Fructose-specific PTS system, I, HPr, and IIA components 37% 379.8
N-acetyl-D-glucosamine catabolism nagF lo N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 36% 76% 334.7 Fructose-specific PTS system, I, HPr, and IIA components 37% 379.8
D-glucosamine (chitosamine) catabolism nagF lo N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 36% 76% 334.7 Fructose-specific PTS system, I, HPr, and IIA components 37% 379.8

Sequence Analysis Tools

View WP_106714139.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MERSTIVRVHDGLHARPATRFVKLAKSFESDIELVKADRSVNAKSSVKLMLLGVKENDEI
TVRATGADAIEAVEALIGYLENPNSGILEDGAAEAAKPAEKKVPLGPESSSVGPGSAGKL
RGVPASEGVAIGLAFGFFPAEIKHENRLLNGDEIPGEVARLKQAFAAVQDRMDKSLAATN
LAESDRGIIAALKDIAGDDELTGAVAALVDGGIDAVSAVIGATSKIAADFASMDDPYLNA
RADDVNAVGRQICLALLGQDDANLDAIPAGAILIAEDIGAWDLARAPLKRIAGVICGHGG
ATSHVAIIARAHGIPAVLGVGRSVQDLQHVNTVALDGNSGDIFPEPDQATADRFHKQIGK
AESDKQALKAYRDVTPKRADGTVIEIAANLGSLEEIEAAQDAGAMGVGLFRTELLFMRHI
HLPSEDLQAETYATLAKAFAPYPVIVRTLDIGGDKPISGIDFPAEENPFLGWRGIRMCLD
RPDVFKPQLRALLRAATHGNIKVMLPMVSGLDEVRAARVLIEECADELKREGKAYAAFDL
GVMVETPAAVMIAPMLAREVAFFSIGTNDLTQYIMAADRLNPTVAKLNDVTHPAVMAAIE
LTAKAGVEAGIMVGMCGEAAGRPDLIPSFVKMGLTELSMSPSSIPRAKKCVLDLETASQG
R

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory