GapMind for catabolism of small carbon sources

 

Protein BWI76_RS14860 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS14860

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

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

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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 (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