GapMind for catabolism of small carbon sources

 

Protein BWI76_RS00280 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS00280

Length: 321 amino acids

Source: Koxy in FitnessBrowser

Candidate for 30 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 hi Ribose import permease protein RbsC (characterized) 96% 100% 592.4 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) 69% 424.5
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% 93% 282.3 Ribose import permease protein RbsC 96% 592.4
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 42% 91% 242.3 Ribose import permease protein RbsC 96% 592.4
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 43% 93% 241.9 Ribose import permease protein RbsC 96% 592.4
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) 43% 95% 239.2 Ribose import permease protein RbsC 96% 592.4
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) 41% 98% 231.9 Ribose import permease protein RbsC 96% 592.4
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) 41% 98% 231.9 Ribose import permease protein RbsC 96% 592.4
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) 41% 98% 231.9 Ribose import permease protein RbsC 96% 592.4
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) 41% 98% 231.9 Ribose import permease protein RbsC 96% 592.4
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) 41% 98% 231.9 Ribose import permease protein RbsC 96% 592.4
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) 41% 98% 231.9 Ribose import permease protein RbsC 96% 592.4
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) 41% 98% 231.9 Ribose import permease protein RbsC 96% 592.4
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 45% 88% 229.2 Ribose import permease protein RbsC 96% 592.4
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 45% 88% 229.2 Ribose import permease protein RbsC 96% 592.4
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) 41% 96% 214.2 Ribose import permease protein RbsC 96% 592.4
myo-inositol catabolism PS417_11895 lo m-Inositol ABC transporter, permease component (iatP) (characterized) 39% 97% 218.8 Ribose import permease protein RbsC 96% 592.4
D-galactose catabolism BPHYT_RS16925 lo Arabinose ABC transporter permease (characterized, see rationale) 35% 99% 214.9 Ribose import permease protein RbsC 96% 592.4
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 36% 92% 196.4 Ribose import permease protein RbsC 96% 592.4
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% 184.1 Ribose import permease protein RbsC 96% 592.4
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 84% 181.8 Ribose import permease protein RbsC 96% 592.4
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 84% 181.8 Ribose import permease protein RbsC 96% 592.4
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 39% 85% 180.6 Ribose import permease protein RbsC 96% 592.4
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 35% 91% 179.5 Ribose import permease protein RbsC 96% 592.4
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 35% 91% 179.5 Ribose import permease protein RbsC 96% 592.4
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 34% 88% 179.1 Ribose import permease protein RbsC 96% 592.4
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 34% 88% 179.1 Ribose import permease protein RbsC 96% 592.4
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 34% 98% 167.5 Ribose import permease protein RbsC 96% 592.4
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 32% 82% 156.4 Ribose import permease protein RbsC 96% 592.4
L-arabinose catabolism xylHsa lo Xylose/arabinose import permease protein XylH (characterized, see rationale) 31% 83% 144.8 Ribose import permease protein RbsC 96% 592.4
2'-deoxyinosine catabolism H281DRAFT_01115 lo deoxynucleoside transporter, permease component 1 (characterized) 33% 84% 139.4 Ribose import permease protein RbsC 96% 592.4

Sequence Analysis Tools

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Sequence

MNNPAVSGRRYFTKAWLMEQKSLIALLVLIAIVSTMSPNFFTVNNLFNILQQTSVNAIMA
VGMTLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVA
KGRVQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTDNADLFGWFGIGRPLGIPTPVWIMA
IVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVA
RLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSY
YQMIVKAVVILLAVLVDNKKQ

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:

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