GapMind for catabolism of small carbon sources

 

Protein WP_044621445.1 in Photobacterium gaetbulicola Gung47

Annotation: NCBI__GCF_000940995.1:WP_044621445.1

Length: 327 amino acids

Source: GCF_000940995.1 in NCBI

Candidate for 38 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 73% 100% 464.2 RbsC, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) 76% 461.5
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) 50% 89% 286.6 Ribose import permease protein RbsC 73% 464.2
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 42% 96% 255 Ribose import permease protein RbsC 73% 464.2
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 43% 90% 248.4 Ribose import permease protein RbsC 73% 464.2
myo-inositol catabolism iatP med 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) 45% 91% 247.3 Ribose import permease protein RbsC 73% 464.2
D-xylose catabolism xylF_Tm med ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 43% 97% 237.7 Ribose import permease protein RbsC 73% 464.2
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 44% 92% 233.4 Ribose import permease protein RbsC 73% 464.2
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 44% 92% 233.4 Ribose import permease protein RbsC 73% 464.2
D-cellobiose catabolism mglC med 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) 40% 97% 223.8 Ribose import permease protein RbsC 73% 464.2
D-glucose catabolism mglC med 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) 40% 97% 223.8 Ribose import permease protein RbsC 73% 464.2
lactose catabolism mglC med 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) 40% 97% 223.8 Ribose import permease protein RbsC 73% 464.2
D-maltose catabolism mglC med 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) 40% 97% 223.8 Ribose import permease protein RbsC 73% 464.2
sucrose catabolism mglC med 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) 40% 97% 223.8 Ribose import permease protein RbsC 73% 464.2
trehalose catabolism mglC med 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) 40% 97% 223.8 Ribose import permease protein RbsC 73% 464.2
D-xylose catabolism xylH med 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) 40% 97% 223.8 Ribose import permease protein RbsC 73% 464.2
myo-inositol catabolism PS417_11895 med Inositol transport system permease protein (characterized) 46% 83% 223.4 Ribose import permease protein RbsC 73% 464.2
D-galactose catabolism BPHYT_RS16925 lo Arabinose ABC transporter permease (characterized, see rationale) 37% 98% 229.2 Ribose import permease protein RbsC 73% 464.2
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 39% 98% 221.5 Ribose import permease protein RbsC 73% 464.2
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 37% 95% 199.9 Ribose import permease protein RbsC 73% 464.2
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 35% 91% 191 Ribose import permease protein RbsC 73% 464.2
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 34% 87% 187.6 Ribose import permease protein RbsC 73% 464.2
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 34% 87% 187.6 Ribose import permease protein RbsC 73% 464.2
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 34% 87% 186 Ribose import permease protein RbsC 73% 464.2
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 34% 87% 186 Ribose import permease protein RbsC 73% 464.2
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 39% 90% 185.3 Ribose import permease protein RbsC 73% 464.2
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 34% 75% 183.3 Ribose import permease protein RbsC 73% 464.2
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% 92% 182.6 Ribose import permease protein RbsC 73% 464.2
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 32% 92% 175.6 Ribose import permease protein RbsC 73% 464.2
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 32% 92% 175.6 Ribose import permease protein RbsC 73% 464.2
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 37% 96% 174.5 Ribose import permease protein RbsC 73% 464.2
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 34% 89% 171.8 Ribose import permease protein RbsC 73% 464.2
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 34% 89% 171.8 Ribose import permease protein RbsC 73% 464.2
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 31% 84% 158.3 Ribose import permease protein RbsC 73% 464.2
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 31% 90% 156 Ribose import permease protein RbsC 73% 464.2
2'-deoxyinosine catabolism H281DRAFT_01115 lo deoxynucleoside transporter, permease component 1 (characterized) 30% 89% 140.2 Ribose import permease protein RbsC 73% 464.2
L-arabinose catabolism xylHsa lo Xylose/arabinose import permease protein XylH (characterized, see rationale) 32% 81% 136.3 Ribose import permease protein RbsC 73% 464.2
L-arabinose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 32% 50% 87.8 Ribose import permease protein RbsC 73% 464.2
D-galactose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 32% 50% 87.8 Ribose import permease protein RbsC 73% 464.2

Sequence Analysis Tools

View WP_044621445.1 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

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Sequence

MSSNAMTKQQNSGSAKLFSKEWLIEQKSLIALIFLIVVVSFLNPNFFTVDNILNILRQTS
VNAIIAVGMTLVILTAGIDLSVGSVLALCGAFAASLIAMEVPVMIAVPTALLAGAALGAI
SGVIIAKGKVQAFIATLVTMTLLRGVTMVYTDGRPISTGFTDVADSFAWFGTGYAMGIPV
PIWLMVIVFAAVWYLLNHTRFGRYIYALGGNESAARLSGINVDRVKIGVYAICGLLAALA
GIIVTSRLSSAQPTAGMGYELDAIAAVVLGGTSLAGGKGRIMGTLIGALIIGFLNNALNL
LDVSSYYQMIAKAVVILLAVLVDNKNK

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