GapMind for catabolism of small carbon sources

 

Protein BWI76_RS03110 in Klebsiella michiganensis M5al

Annotation: BWI76_RS03110 MFS transporter

Length: 499 amino acids

Source: Koxy in FitnessBrowser

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism iolT hi Major myo-inositol transporter IolT (characterized) 52% 96% 462.2 Probable metabolite transport protein CsbC 38% 340.5
D-cellobiose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 45% 94% 391.3 Major myo-inositol transporter IolT 52% 462.2
D-glucose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 45% 94% 391.3 Major myo-inositol transporter IolT 52% 462.2
lactose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 45% 94% 391.3 Major myo-inositol transporter IolT 52% 462.2
D-maltose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 45% 94% 391.3 Major myo-inositol transporter IolT 52% 462.2
sucrose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 45% 94% 391.3 Major myo-inositol transporter IolT 52% 462.2
trehalose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 45% 94% 391.3 Major myo-inositol transporter IolT 52% 462.2
D-xylose catabolism xylT lo D-xylose transporter; D-xylose-proton symporter (characterized) 40% 97% 314.3 Major myo-inositol transporter IolT 52% 462.2
D-galactose catabolism galP lo Galactose-proton symporter; Galactose transporter (characterized) 38% 94% 289.3 Major myo-inositol transporter IolT 52% 462.2
L-arabinose catabolism araE lo Arabinose/xylose transporter, AraE (characterized) 36% 92% 278.1 Major myo-inositol transporter IolT 52% 462.2
D-fructose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 100% 273.9 Major myo-inositol transporter IolT 52% 462.2
sucrose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 100% 273.9 Major myo-inositol transporter IolT 52% 462.2
xylitol catabolism PLT5 lo Polyol (xylitol):H+ symporter, PLT4 (characterized) 32% 90% 241.9 Major myo-inositol transporter IolT 52% 462.2
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 88% 237.7 Major myo-inositol transporter IolT 52% 462.2
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 88% 237.7 Major myo-inositol transporter IolT 52% 462.2
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 30% 88% 237.7 Major myo-inositol transporter IolT 52% 462.2
D-sorbitol (glucitol) catabolism SOT lo polyol transporter 5 (characterized) 30% 88% 237.7 Major myo-inositol transporter IolT 52% 462.2
myo-inositol catabolism HMIT lo Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized) 36% 55% 233.4 Major myo-inositol transporter IolT 52% 462.2
D-fructose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 32% 79% 204.5 Major myo-inositol transporter IolT 52% 462.2
sucrose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 32% 79% 204.5 Major myo-inositol transporter IolT 52% 462.2
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 30% 90% 200.7 Major myo-inositol transporter IolT 52% 462.2
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 79% 182.2 Major myo-inositol transporter IolT 52% 462.2
D-mannose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 79% 182.2 Major myo-inositol transporter IolT 52% 462.2
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 79% 182.2 Major myo-inositol transporter IolT 52% 462.2

Sequence Analysis Tools

View BWI76_RS03110 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

MSKEQYLTLNKASGPNSETPTTPFVKVVALIATLGGLLFGYDTGVISGALLFMGTELHLT
PFTTGLVTSSLLFGAAFGALLSGNLANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIF
FRLILGVAVGGAAATVPVYIAEIAPANKRGQLVTLQELMIVSGQLLAYISNATFHEVWGG
ESTWRWMLAVATLPAVLLWFGMMFMPDSPRWYAMKGRLAEARRVLERTRHKDDVEWELLE
ITETLDEQRNLGKPRFSEIMTPWLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMT
DNAALFATIANGVVSVLMTFVGIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLLPETV
NGQPDALRAYMVLAGMLLFLSFQQGALSPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANF
LISLFFPILLAWLGLSGTFFIFAGIGVFGAIFVIKCVPETRHRSLEQIEHYLRDKLDTSE
EGQAARARRIVAESQANKV

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 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