GapMind for catabolism of small carbon sources

 

Protein BWI76_RS14860 in Klebsiella michiganensis M5al

Annotation: BWI76_RS14860 ABC transporter

Length: 510 amino acids

Source: Koxy in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism HSERO_RS05250 hi Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 49% 95% 460.3 Inositol transport system ATP-binding protein 45% 432.2
D-mannose catabolism HSERO_RS03640 hi Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 47% 96% 442.6 Inositol transport system ATP-binding protein 45% 432.2
myo-inositol catabolism PS417_11890 hi Inositol transport system ATP-binding protein (characterized) 45% 96% 432.2 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 43% 414.8
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 48% 95% 417.9 Inositol transport system ATP-binding protein 45% 432.2
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 48% 95% 417.9 Inositol transport system ATP-binding protein 45% 432.2
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 44% 97% 394 Inositol transport system ATP-binding protein 45% 432.2
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 40% 98% 392.5 Inositol transport system ATP-binding protein 45% 432.2
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 44% 94% 387.9 Inositol transport system ATP-binding protein 45% 432.2
myo-inositol catabolism iatA med Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 43% 97% 382.5 Inositol transport system ATP-binding protein 45% 432.2
D-galactose catabolism ytfR med galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 40% 97% 363.2 Inositol transport system ATP-binding protein 45% 432.2
xylitol catabolism PS417_12065 lo D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 99% 353.2 Inositol transport system ATP-binding protein 45% 432.2
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 99% 302.4 Inositol transport system ATP-binding protein 45% 432.2
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 99% 302.4 Inositol transport system ATP-binding protein 45% 432.2
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 40% 94% 182.6 Inositol transport system ATP-binding protein 45% 432.2
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 37% 97% 161.8 Inositol transport system ATP-binding protein 45% 432.2
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 37% 97% 161.8 Inositol transport system ATP-binding protein 45% 432.2

Sequence Analysis Tools

View BWI76_RS14860 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MADISSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQ
RDSGVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDR
KRMHREAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRA
ETLQLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVSTTDIVR
MMVGRQIVDLYQHEPRTPGDVLLEVRDLAGSATGPVSFEVSAGEVVSMSGLVGSGRTEVA
RLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISS
LDNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSRL
LILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQ
LPSCSATEEEVMLHATGTFTSQSGECHGQQ

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

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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