GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_883 in Pseudomonas fluorescens FW300-N2E2

Annotation: Major myo-inositol transporter IolT

Length: 472 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 21 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) 53% 95% 471.9 Probable metabolite transport protein CsbC 39% 333.2
D-cellobiose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 48% 96% 430.3 Major myo-inositol transporter IolT 53% 471.9
D-glucose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 48% 96% 430.3 Major myo-inositol transporter IolT 53% 471.9
lactose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 48% 96% 430.3 Major myo-inositol transporter IolT 53% 471.9
D-maltose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 48% 96% 430.3 Major myo-inositol transporter IolT 53% 471.9
sucrose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 48% 96% 430.3 Major myo-inositol transporter IolT 53% 471.9
trehalose catabolism MFS-glucose med Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 48% 96% 430.3 Major myo-inositol transporter IolT 53% 471.9
D-xylose catabolism xylT lo D-xylose transporter; D-xylose-proton symporter (characterized) 36% 95% 306.2 Major myo-inositol transporter IolT 53% 471.9
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 34% 99% 283.5 Major myo-inositol transporter IolT 53% 471.9
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 34% 99% 283.5 Major myo-inositol transporter IolT 53% 471.9
D-fructose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 34% 93% 245 Major myo-inositol transporter IolT 53% 471.9
sucrose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 34% 93% 245 Major myo-inositol transporter IolT 53% 471.9
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 241.1 Major myo-inositol transporter IolT 53% 471.9
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 241.1 Major myo-inositol transporter IolT 53% 471.9
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 241.1 Major myo-inositol transporter IolT 53% 471.9
D-sorbitol (glucitol) catabolism SOT lo polyol transporter 5 (characterized) 31% 85% 241.1 Major myo-inositol transporter IolT 53% 471.9
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 241.1 Major myo-inositol transporter IolT 53% 471.9
D-fructose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 96% 236.1 Major myo-inositol transporter IolT 53% 471.9
sucrose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 96% 236.1 Major myo-inositol transporter IolT 53% 471.9
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 35% 60% 221.1 Major myo-inositol transporter IolT 53% 471.9
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 30% 91% 194.5 Major myo-inositol transporter IolT 53% 471.9

Sequence Analysis Tools

View Pf6N2E2_883 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

MTINSYGNTADTSAAYVSPEKHQAQRYLQKITWIATFGGLLFGFDTGVINGALLYMKDDL
GLTPFTEGLVASALLIGAMMGALFSGRLSDLKGRRRIILFLAVVFFLGALACALAPTLDV
MVAARFTLGLAVGGASVVVPAYLSEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNL
FSDLDGVWRWMLALATLPAVALWLGMLYMPESPRWLATKGRFREGLEVLKLVREEYYAKA
EMEAITQQISNERFIKKGGWRDLSQKGARRIFLIGIGIAVTSQLTGVNSIMYFGTQILTE
AGLEQRSALIANVVNGIISIGATFVGIALLDRVGRRPMMLLGFTGTTLSLLLIGLVSVFV
DPSVTRAMLILGAMAMFLASMQGLIGPAFWVLLAEIFPMRIRGGCMGMAIAAFWLTNVMI
GMFFPSLVAMIGIGQTFFVFVGAGLLSLTFVAVWVPETRGSTLEEIEQRLYG

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