GapMind for catabolism of small carbon sources

 

Protein WP_054559598.1 in Croceitalea dokdonensis DOKDO 023

Annotation: NCBI__GCF_001306415.1:WP_054559598.1

Length: 458 amino acids

Source: GCF_001306415.1 in NCBI

Candidate for 20 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% 94% 365.5 D-xylose-proton symporter 35% 275.8
sucrose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 45% 94% 365.5 D-xylose-proton symporter 35% 275.8
D-xylose catabolism xylT lo D-xylose-proton symporter (characterized) 35% 95% 275.8 D-fructose transporter, sugar porter family 45% 365.5
D-cellobiose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 34% 97% 258.1 D-fructose transporter, sugar porter family 45% 365.5
D-glucose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 34% 97% 258.1 D-fructose transporter, sugar porter family 45% 365.5
lactose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 34% 97% 258.1 D-fructose transporter, sugar porter family 45% 365.5
D-maltose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 34% 97% 258.1 D-fructose transporter, sugar porter family 45% 365.5
sucrose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 34% 97% 258.1 D-fructose transporter, sugar porter family 45% 365.5
trehalose catabolism MFS-glucose lo Glucose/fructose:H+ symporter, GlcP (characterized) 34% 97% 258.1 D-fructose transporter, sugar porter family 45% 365.5
myo-inositol catabolism iolT lo Major myo-inositol transporter, IolT1, of 456 aas (characterized) 35% 96% 255.8 D-fructose transporter, sugar porter family 45% 365.5
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 34% 94% 255.4 D-fructose transporter, sugar porter family 45% 365.5
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 34% 94% 255.4 D-fructose transporter, sugar porter family 45% 365.5
xylitol catabolism PLT5 lo Polyol (xylitol):H+ symporter, PLT4 (characterized) 30% 89% 209.9 D-fructose transporter, sugar porter family 45% 365.5
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% 89% 203 D-fructose transporter, sugar porter family 45% 365.5
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% 89% 203 D-fructose transporter, sugar porter family 45% 365.5
D-sorbitol (glucitol) catabolism SOT lo Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized) 31% 92% 199.9 D-fructose transporter, sugar porter family 45% 365.5
D-galactose catabolism MST1 lo The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) 31% 86% 183.7 D-fructose transporter, sugar porter family 45% 365.5
D-mannose catabolism MST1 lo The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) 31% 86% 183.7 D-fructose transporter, sugar porter family 45% 365.5
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 33% 60% 183 D-fructose transporter, sugar porter family 45% 365.5
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 32% 78% 178.3 D-fructose transporter, sugar porter family 45% 365.5

Sequence Analysis Tools

View WP_054559598.1 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

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MDKRILKISLTAALAGFLFGFDTVVISGANQPIKELWGTNWFLGDSIFTFHGIFIMSMAL
WGTVLGALFGGIPTDKLGRKKTLFWIGALYFISAVGSAMAPEAYSFSFFRFIGGIGVGAS
SVAAPIYISEISTADNRGRLTALYQFNIVFGILIAFISNYFIGIFLTSDISWRWMLAAEG
LPALIYTIMVLRIPNSPRWLLIKKREDSQILSALIAIGNTTESAPKELQTLKATFSTNLK
TSKGKLFSGNYRKPLVLAFLIAFFNQLSGINFVLYYAPEILERAGLATEASLFSSISIGV
INLIFTFVGIALIDKLGRKQLMYMGSVGYIVSLLMVGWCFYSGASALVLLSFVLLFIASH
AVGQGAVIWVFISEIFPNSVRAYGQSWGTSTHWVFAALITLLTPTFLDAEIGIFKDNPWP
IFVFFAGMMVLQLLWAFFFMPETKGSSLEEIEERLQSN

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