GapMind for catabolism of small carbon sources

 

Protein WP_034269775.1 in Amycolatopsis halophila YIM 93223

Annotation: NCBI__GCF_000504245.1:WP_034269775.1

Length: 347 amino acids

Source: GCF_000504245.1 in NCBI

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism PS417_12060 hi ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 41% 97% 219.2 Ribose import permease protein RbsC 40% 202.2
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 42% 90% 205.7 Ribose import permease protein RbsC 40% 202.2
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 42% 90% 205.7 Ribose import permease protein RbsC 40% 202.2
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 40% 93% 202.2 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) 36% 194.5
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 40% 88% 193 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 193 Ribose import permease protein RbsC 40% 202.2
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 38% 87% 192.2 Ribose import permease protein RbsC 40% 202.2
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 34% 98% 191 Ribose import permease protein RbsC 40% 202.2
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 92% 182.2 Ribose import permease protein RbsC 40% 202.2
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 36% 90% 178.7 Ribose import permease protein RbsC 40% 202.2
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) 36% 97% 174.9 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 174.1 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 174.1 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 174.1 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 174.1 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 174.1 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 174.1 Ribose import permease protein RbsC 40% 202.2
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) 37% 96% 174.1 Ribose import permease protein RbsC 40% 202.2
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 88% 171 Ribose import permease protein RbsC 40% 202.2
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 88% 171 Ribose import permease protein RbsC 40% 202.2
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 34% 94% 163.3 Ribose import permease protein RbsC 40% 202.2
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 34% 96% 160.6 Ribose import permease protein RbsC 40% 202.2
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 33% 94% 154.8 Ribose import permease protein RbsC 40% 202.2
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 31% 77% 154.5 Ribose import permease protein RbsC 40% 202.2
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 32% 98% 152.9 Ribose import permease protein RbsC 40% 202.2
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 34% 92% 151.4 Ribose import permease protein RbsC 40% 202.2
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 34% 92% 151.4 Ribose import permease protein RbsC 40% 202.2
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) 31% 92% 139.4 Ribose import permease protein RbsC 40% 202.2
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 89% 137.5 Ribose import permease protein RbsC 40% 202.2
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 89% 137.5 Ribose import permease protein RbsC 40% 202.2
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 31% 89% 137.1 Ribose import permease protein RbsC 40% 202.2
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 31% 87% 134.4 Ribose import permease protein RbsC 40% 202.2
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 31% 87% 134.4 Ribose import permease protein RbsC 40% 202.2

Sequence Analysis Tools

View WP_034269775.1 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

MSVASEERAGTGGADVPSRESPLRSVTALFSGPAGRNLGLVIALALLCIVGMITAGDRFV
SFDNMMTILRLASVIGVVSVGMTFVITGGGIDLSVGAIVALSSVWASTIATQTLAENTHW
IVMVSTALLVGAVCGLVNGLLIAYGRMAAFIVTLAMLAGARGLAEIIAQKRTQVVTISEF
IDVVGGRVLGIPVLVLIFAIVAVAGWILLNRTTFGRRTLAVGGNPEAARLAGINVKRHTT
LLYVLVGVACGLAAVMLLARTTAGTSTHGMLMELDAIAAVVIGGTLLSGGRGTIVGTVFG
VLIFTTLTNVFTLNNLDTSTQAVAKGVIIVVAVLLQQRVAARNGSPP

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