GapMind for catabolism of small carbon sources

 

Protein CA265_RS23325 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS23325 MFS transporter

Length: 443 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-xylose catabolism xylT med D-xylose-proton symporter (characterized) 38% 97% 320.5 D-fructose transporter, sugar porter family 40% 317.4
D-fructose catabolism glcP med D-fructose transporter, sugar porter family (characterized) 40% 94% 317.4 D-xylose-proton symporter 38% 320.5
sucrose catabolism glcP med D-fructose transporter, sugar porter family (characterized) 40% 94% 317.4 D-xylose-proton symporter 38% 320.5
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 38% 96% 318.5 D-xylose-proton symporter 38% 320.5
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 38% 96% 318.5 D-xylose-proton symporter 38% 320.5
D-cellobiose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 38% 99% 285.4 D-xylose-proton symporter 38% 320.5
D-glucose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 38% 99% 285.4 D-xylose-proton symporter 38% 320.5
lactose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 38% 99% 285.4 D-xylose-proton symporter 38% 320.5
D-maltose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 38% 99% 285.4 D-xylose-proton symporter 38% 320.5
sucrose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 38% 99% 285.4 D-xylose-proton symporter 38% 320.5
trehalose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 38% 99% 285.4 D-xylose-proton symporter 38% 320.5
myo-inositol catabolism iolT lo Major myo-inositol transporter IolT (characterized) 34% 96% 276.2 D-xylose-proton symporter 38% 320.5
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 86% 238.8 D-xylose-proton symporter 38% 320.5
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 86% 238.8 D-xylose-proton symporter 38% 320.5
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 31% 86% 238.8 D-xylose-proton symporter 38% 320.5
D-sorbitol (glucitol) catabolism SOT lo polyol transporter 5 (characterized) 31% 86% 238.8 D-xylose-proton symporter 38% 320.5
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 86% 238.8 D-xylose-proton symporter 38% 320.5
D-mannose catabolism STP6 lo The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized) 30% 92% 224.9 D-xylose-proton symporter 38% 320.5
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) 33% 55% 215.3 D-xylose-proton symporter 38% 320.5
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 31% 85% 194.9 D-xylose-proton symporter 38% 320.5
D-fructose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 31% 80% 173.7 D-xylose-proton symporter 38% 320.5
sucrose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 31% 80% 173.7 D-xylose-proton symporter 38% 320.5

Sequence Analysis Tools

View CA265_RS23325 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSQSKFNTAYITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALG
AMVGCLIAGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASM
LSPMYIAELAPPKFRGRLVAINQLTIVLGILITNLINYTLRNTGEDAWRWMFGLGAIPSG
IFLIGISILPESPRWLVQKGKNEKALKVLNKIGNHEFAADALKNIEQTLQRKSNVEHESI
FNKMYFPAVMIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQDDQLLQTVFIGAVNVIFT
ISAMFLVDKIGRKPLMLIGAGGLAVLYVLISQLLASGSTMVSWFLLSAIGVYAVSLAPVT
WVLISEIFPNKVRVKATTWAILCLWGAYFVLVFTFPILFDWLKESIFYIYAAICTLGCIG
IWKFVKETKGKTLEEIEDIQIVH

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 paper from 2022 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