GapMind for catabolism of small carbon sources

 

Protein 7024901 in Shewanella sp. ANA-3

Annotation: Shewana3_2075 inner-membrane translocator (RefSeq)

Length: 405 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araWsh hi Inner-membrane translocator (characterized, see rationale) 100% 100% 762.3 Galactofuranose transporter permease protein YtfT 56% 337.4
D-galactose catabolism ytfT hi Galactofuranose transporter permease protein YtfT (characterized) 56% 97% 337.4 Fructose import permease protein FruF 41% 223.4
D-fructose catabolism fruF med Fructose import permease protein FruF (characterized) 42% 94% 223.4 Galactofuranose transporter permease protein YtfT 56% 337.4
sucrose catabolism fruF med Fructose import permease protein FruF (characterized) 42% 94% 223.4 Galactofuranose transporter permease protein YtfT 56% 337.4
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 37% 93% 189.5 Galactofuranose transporter permease protein YtfT 56% 337.4
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 37% 93% 189.5 Galactofuranose transporter permease protein YtfT 56% 337.4
D-ribose catabolism rbsC lo ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 36% 98% 188.3 Galactofuranose transporter permease protein YtfT 56% 337.4
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 32% 97% 169.9 Galactofuranose transporter permease protein YtfT 56% 337.4
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 81% 169.1 Galactofuranose transporter permease protein YtfT 56% 337.4
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 35% 92% 167.9 Galactofuranose transporter permease protein YtfT 56% 337.4
D-xylose catabolism xylF_Tm lo ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 32% 97% 142.5 Galactofuranose transporter permease protein YtfT 56% 337.4
D-cellobiose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 87% 141.7 Galactofuranose transporter permease protein YtfT 56% 337.4
D-glucose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 87% 141.7 Galactofuranose transporter permease protein YtfT 56% 337.4
lactose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 87% 141.7 Galactofuranose transporter permease protein YtfT 56% 337.4
D-maltose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 87% 141.7 Galactofuranose transporter permease protein YtfT 56% 337.4
sucrose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 87% 141.7 Galactofuranose transporter permease protein YtfT 56% 337.4
trehalose catabolism mglC lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 87% 141.7 Galactofuranose transporter permease protein YtfT 56% 337.4
D-xylose catabolism xylH lo Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 87% 141.7 Galactofuranose transporter permease protein YtfT 56% 337.4
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 30% 89% 137.9 Galactofuranose transporter permease protein YtfT 56% 337.4
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 31% 94% 136.3 Galactofuranose transporter permease protein YtfT 56% 337.4
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 31% 94% 136.3 Galactofuranose transporter permease protein YtfT 56% 337.4
myo-inositol catabolism iatP lo Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 31% 82% 129.4 Galactofuranose transporter permease protein YtfT 56% 337.4

Sequence Analysis Tools

View 7024901 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

MKSSAETLSSTRMSADLISPQMNASEAHSSERQPRMQESHKTMVQEKNARYQAGKSTSMG
RYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIAT
GGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIV
ATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRK
TALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGL
WLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVIL
TVLLLQSAKFRRQLSALFKSKRHADAKPAEKATSAKASAATGEKL

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