GapMind for catabolism of small carbon sources

 

Protein WP_066326767.1 in Flavobacterium glycines Gm-149

Annotation: NCBI__GCF_900100165.1:WP_066326767.1

Length: 439 amino acids

Source: GCF_900100165.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 45% 93% 364.4 Arabinose-proton symporter; Arabinose transporter 35% 272.3
sucrose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 45% 93% 364.4 Arabinose-proton symporter; Arabinose transporter 35% 272.3
D-cellobiose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 97% 271.9 D-fructose transporter, sugar porter family 45% 364.4
D-glucose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 97% 271.9 D-fructose transporter, sugar porter family 45% 364.4
lactose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 97% 271.9 D-fructose transporter, sugar porter family 45% 364.4
D-maltose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 97% 271.9 D-fructose transporter, sugar porter family 45% 364.4
sucrose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 97% 271.9 D-fructose transporter, sugar porter family 45% 364.4
trehalose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 35% 97% 271.9 D-fructose transporter, sugar porter family 45% 364.4
myo-inositol catabolism iolT lo Major myo-inositol transporter, IolT1, of 456 aas (characterized) 34% 95% 262.3 D-fructose transporter, sugar porter family 45% 364.4
D-xylose catabolism xylT lo D-xylose transporter; D-xylose-proton symporter (characterized) 35% 95% 261.9 D-fructose transporter, sugar porter family 45% 364.4
L-arabinose catabolism araE lo Arabinose/xylose transporter, AraE (characterized) 34% 91% 243.4 D-fructose transporter, sugar porter family 45% 364.4
xylitol catabolism PLT5 lo Polyol (xylitol):H+ symporter, PLT4 (characterized) 33% 90% 233.8 D-fructose transporter, sugar porter family 45% 364.4
D-sorbitol (glucitol) catabolism SOT lo Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized) 32% 92% 232.6 D-fructose transporter, sugar porter family 45% 364.4
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) 32% 92% 224.6 D-fructose transporter, sugar porter family 45% 364.4
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) 32% 92% 224.6 D-fructose transporter, sugar porter family 45% 364.4
D-galactose catabolism galP 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) 33% 85% 219.5 D-fructose transporter, sugar porter family 45% 364.4
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) 33% 85% 219.5 D-fructose transporter, sugar porter family 45% 364.4
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 86% 211.8 D-fructose transporter, sugar porter family 45% 364.4
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 86% 211.8 D-fructose transporter, sugar porter family 45% 364.4
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 30% 86% 211.8 D-fructose transporter, sugar porter family 45% 364.4
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 36% 59% 206.1 D-fructose transporter, sugar porter family 45% 364.4

Sequence Analysis Tools

View WP_066326767.1 at NCBI

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

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Sequence

MNKKIMSWSIVASFAGFLFGFDTVVISGADKALQILWDSSDFFHGSVVMAMALWGTVIGA
IFGGIPTNKIGRKSTLLIIGILFSISALGSSLANGPWIFAFFRFIGGLGIGASTIAAPAY
ISEIAPAKDRGRLVGLYQFNIVFGILTAFLSNYLLSDIGENAWRWMLGIQVFPSVVYTVL
AFYIPESPRWLLTQSQIDEARVILNKINSKEDVQSIIDNISEDNKNTSSDENIFMKKYSF
PLILVFLIAAFNQLSGINAFLYYAPRIFEEAGLGAKTALLSSIGIGFVNLIFTLIGVYLI
DRLGRRKLMIFGSLGYIFSLSMVAISFYLSWTGMAVPIFLFVFIASHAIGQGAVIWVFIS
EIFPNHLRASGQSFGSSVHWVLAAIIPSMVPILFSNFGVGNVFSFFAIMMVFQLVFVLFM
MPETKGVSLESMNLSLNKK

This GapMind analysis is from Sep 24 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