GapMind for catabolism of small carbon sources

 

Protein BWI76_RS03110 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS03110

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

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

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:

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