GapMind for catabolism of small carbon sources

 

Protein Ga0059261_1891 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_1891 MFS transporter, sugar porter (SP) family

Length: 466 amino acids

Source: Korea in FitnessBrowser

Candidate for 17 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 hi Glucose/fructose transport protein (characterized, see rationale) 63% 96% 588.6 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
D-cellobiose catabolism MFS-glucose hi Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 47% 91% 416.4 D-xylose-proton symporter 38% 323.6
D-glucose catabolism MFS-glucose hi Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 47% 91% 416.4 D-xylose-proton symporter 38% 323.6
lactose catabolism MFS-glucose hi Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 47% 91% 416.4 D-xylose-proton symporter 38% 323.6
D-maltose catabolism MFS-glucose hi Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 47% 91% 416.4 D-xylose-proton symporter 38% 323.6
sucrose catabolism MFS-glucose hi Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 47% 91% 416.4 D-xylose-proton symporter 38% 323.6
trehalose catabolism MFS-glucose hi Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 47% 91% 416.4 D-xylose-proton symporter 38% 323.6
D-fructose catabolism glcP med Glucose/fructose:H+ symporter, GlcP (characterized) 45% 99% 407.1 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
sucrose catabolism glcP med Glucose/fructose:H+ symporter, GlcP (characterized) 45% 99% 407.1 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 33% 95% 286.6 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 33% 95% 286.6 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
myo-inositol catabolism iolT lo Major myo-inositol transporter IolT (characterized) 35% 96% 283.9 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 31% 90% 212.6 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 91% 210.7 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
D-mannose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 91% 210.7 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 91% 210.7 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4
myo-inositol catabolism HMIT lo inositol transporter 4 (characterized) 32% 59% 191 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 47% 416.4

Sequence Analysis Tools

View Ga0059261_1891 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

MNGESRANMGLIMAIVAVATIGGLLFGYDSGAVNGTQDGLKSAFALSEGGLGFTVGSLLI
GCFIGAFLAGRLADLIGRRNVMILTAVLFLIGALIQGFSHEQWIFVAARIAGGMAVGAAS
VLSPAYISEVAPANIRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLFWGGYEAWR
WMYWMQAIPATVFLIALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNKLTEIQASF
SDHRPTLRDILDPVKGGVRPIVWAGLLLAVFQQLVGINVIFYYGATLWQLAGFTENDALL
INIVSGFVSIAACFVTVALVDRIGRKPLLLIGSAGMAVALFAMVFAFSRGSLDAQGKLVL
SQQLGIIAVIAANLYVVFFNVSWGPVMWVMLGEMFPNQIRGSALAVCGFAQWFSNYLIAQ
SFPIMAAGLGLAVSYSFYAVCAVISFFLVSKFIHETKGVELEDMQG

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