GapMind for catabolism of small carbon sources

 

Protein Ac3H11_3036 in Acidovorax sp. GW101-3H11

Annotation: Fructose ABC transporter, permease component FrcC

Length: 319 amino acids

Source: acidovorax_3H11 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
D-fructose catabolism frcC hi Fructose import permease protein FrcC (characterized) 46% 85% 263.8 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 39% 228.4
D-mannose catabolism frcC hi Fructose import permease protein FrcC (characterized) 46% 85% 263.8 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 39% 228.4
D-ribose catabolism frcC hi Fructose import permease protein FrcC (characterized) 46% 85% 263.8 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 39% 228.4
sucrose catabolism frcC hi Fructose import permease protein FrcC (characterized) 46% 85% 263.8 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 39% 228.4
xylitol catabolism PS417_12060 med ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 42% 93% 233.4 Fructose import permease protein FrcC 46% 263.8
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 41% 92% 214.9 Fructose import permease protein FrcC 46% 263.8
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 40% 92% 210.3 Fructose import permease protein FrcC 46% 263.8
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) 39% 99% 228.4 Fructose import permease protein FrcC 46% 263.8
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) 39% 99% 228.4 Fructose import permease protein FrcC 46% 263.8
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) 39% 99% 228.4 Fructose import permease protein FrcC 46% 263.8
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) 39% 99% 228.4 Fructose import permease protein FrcC 46% 263.8
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) 39% 99% 228.4 Fructose import permease protein FrcC 46% 263.8
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) 39% 99% 228.4 Fructose import permease protein FrcC 46% 263.8
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) 39% 99% 228.4 Fructose import permease protein FrcC 46% 263.8
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 38% 88% 200.7 Fructose import permease protein FrcC 46% 263.8
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 35% 91% 189.1 Fructose import permease protein FrcC 46% 263.8
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) 35% 95% 188 Fructose import permease protein FrcC 46% 263.8
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 33% 95% 173.7 Fructose import permease protein FrcC 46% 263.8
L-rhamnose catabolism rhaP lo RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 34% 88% 159.1 Fructose import permease protein FrcC 46% 263.8
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 38% 82% 147.5 Fructose import permease protein FrcC 46% 263.8
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 35% 76% 143.7 Fructose import permease protein FrcC 46% 263.8
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 31% 85% 139.8 Fructose import permease protein FrcC 46% 263.8

Sequence Analysis Tools

View Ac3H11_3036 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

MSSTASKLPPLATLGPFIALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLV
ILTAGIDLSCGMVMALGGIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLP
PFIVTLGTLNIAFAATQLYSGAQTITDIPAGMTALGNTFQLGQTAIVWGAVLMLALYLVT
WFALRETAPGRHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGD
PNAGQTENLDAISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVT
GILVILAVATDQLSRKGVR

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