GapMind for catabolism of small carbon sources

 

Protein WP_147050628.1 in Kocuria flava HO-9041

Annotation: NCBI__GCF_001482365.1:WP_147050628.1

Length: 303 amino acids

Source: GCF_001482365.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism PGA1_c07320 hi Inositol transport system ATP-binding protein (characterized) 52% 97% 250.8 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 41% 183.7
L-arabinose catabolism xylGsa med Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 42% 96% 187.6 Inositol transport system ATP-binding protein 52% 250.8
D-fructose catabolism frcA med Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 41% 95% 183.7 Inositol transport system ATP-binding protein 52% 250.8
D-mannose catabolism frcA med Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 41% 95% 183.7 Inositol transport system ATP-binding protein 52% 250.8
D-ribose catabolism frcA med Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 41% 95% 183.7 Inositol transport system ATP-binding protein 52% 250.8
sucrose catabolism frcA med Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 41% 95% 183.7 Inositol transport system ATP-binding protein 52% 250.8
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 93% 164.9 Inositol transport system ATP-binding protein 52% 250.8
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 93% 164.9 Inositol transport system ATP-binding protein 52% 250.8
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 93% 164.9 Inositol transport system ATP-binding protein 52% 250.8
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 93% 164.9 Inositol transport system ATP-binding protein 52% 250.8
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 93% 164.9 Inositol transport system ATP-binding protein 52% 250.8
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 93% 164.9 Inositol transport system ATP-binding protein 52% 250.8
myo-inositol catabolism PS417_11890 lo Inositol transport system ATP-binding protein (characterized) 34% 50% 152.9 Inositol transport system ATP-binding protein 52% 250.8
D-ribose catabolism rbsA lo ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 33% 50% 146 Inositol transport system ATP-binding protein 52% 250.8
D-xylose catabolism xylG lo Monosaccharide-transporting ATPase, 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) 32% 56% 145.6 Inositol transport system ATP-binding protein 52% 250.8
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 32% 52% 144.1 Inositol transport system ATP-binding protein 52% 250.8
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 31% 50% 134 Inositol transport system ATP-binding protein 52% 250.8
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 31% 50% 134 Inositol transport system ATP-binding protein 52% 250.8
xylitol catabolism PS417_12065 lo D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) 31% 56% 130.6 Inositol transport system ATP-binding protein 52% 250.8
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 34% 50% 127.1 Inositol transport system ATP-binding protein 52% 250.8
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 31% 51% 125.6 Inositol transport system ATP-binding protein 52% 250.8

Sequence Analysis Tools

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTTVSTHPTTAPAGGTTAERGPAHLVSLENVGKRYGNVIALREVTMAVDAGKVTCVLGDN
GAGKSTLIKIIAGLHQHTDGTLYVNGEETTFGSPRQALDAGIATVYQDLAVVPLMPVWRN
FFLGSELTTGFGPFRRLDTARMKAITKQELADMGIDLRDVDQPIGTLSGGERQCVAIARA
VHFGAKVLILDEPTAALGVKQSGVVLRYILQAKERGLGVVFITHNPHHAYPVGDRFLLLK
RGRSIGYYEKSGIALGDLTAQMAGGAELEELTHELAQLGGHTTQMQQVRADMAESLARPR
RQG

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