GapMind for catabolism of small carbon sources

 

Protein CA265_RS01275 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS01275 hypothetical protein

Length: 462 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araE hi Arabinose-proton symporter; Arabinose transporter (characterized) 40% 95% 330.5 D-xylose-proton symporter 37% 302.4
D-galactose catabolism galP hi Arabinose-proton symporter; Arabinose transporter (characterized) 40% 95% 330.5 D-xylose-proton symporter 37% 302.4
D-xylose catabolism xylT hi Arabinose-proton symporter; Arabinose transporter (characterized) 40% 95% 330.5 Major myo-inositol transporter, IolT1, of 456 aas 35% 285.0
myo-inositol catabolism iolT lo Major myo-inositol transporter, IolT1, of 456 aas (characterized) 35% 96% 285 Arabinose-proton symporter; Arabinose transporter 40% 330.5
D-cellobiose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
D-fructose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
D-glucose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
lactose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
D-maltose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
sucrose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
sucrose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
trehalose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 36% 97% 272.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
xylitol catabolism PLT5 lo Polyol (xylitol):H+ symporter, PLT4 (characterized) 31% 92% 212.2 Arabinose-proton symporter; Arabinose transporter 40% 330.5
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% 91% 203 Arabinose-proton symporter; Arabinose transporter 40% 330.5
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% 91% 203 Arabinose-proton symporter; Arabinose transporter 40% 330.5
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 31% 92% 197.6 Arabinose-proton symporter; Arabinose transporter 40% 330.5
D-mannose catabolism STP6 lo sugar transport protein 6 (characterized) 31% 92% 197.6 Arabinose-proton symporter; Arabinose transporter 40% 330.5
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 31% 92% 197.6 Arabinose-proton symporter; Arabinose transporter 40% 330.5
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; AmTRET1 (characterized) 31% 82% 178.7 Arabinose-proton symporter; Arabinose transporter 40% 330.5
myo-inositol catabolism HMIT lo Probable inositol transporter 3 (characterized) 33% 58% 172.9 Arabinose-proton symporter; Arabinose transporter 40% 330.5

Sequence Analysis Tools

View CA265_RS01275 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

MRKQGANYFIFLITLIAALGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGC
IVGVSFSGYLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNV
SPLYISEVAPSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHAGAGEGILHWLFVE
NVWRGMFIVGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKINGAETGRLELDSI
KEMASQKSGGYKELMRLPLSKLLALATILTALSQFSGINGVIFYGPTILKSAGIVTSDAL
FYQVILGSANVLFTFIAISKVDTWGRRPLYIIGSLCAAGALALTGFCFLMDITGWFMLFS
IILFLLFFAFSLGPLKFVISTEIFPTHIRGTALSMCIMTMWVSDWVVNMLFPIMRDGLGI
ATTFFIFSFFCILSFLYAKKKLFETKGKSLEEIEKAWNSEVK

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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