GapMind for catabolism of small carbon sources

 

Protein WP_007727336.1 in Rhodococcus qingshengii djl-6-2

Annotation: NCBI__GCF_002893965.1:WP_007727336.1

Length: 270 amino acids

Source: GCF_002893965.1 in NCBI

Candidate for 17 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) 51% 97% 247.7 Probable ABC-transport system ATP binding protein, component of XylFGH downstream of characterized transcriptional regulator, ROK7B7 (Sco6008); XylF (Sco6009); XylG (Sco6010); XylH (Sco6011)) 43% 183.7
L-arabinose catabolism xylGsa med Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 41% 94% 198.4 Inositol transport system ATP-binding protein 51% 247.7
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 40% 95% 183 Inositol transport system ATP-binding protein 51% 247.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 40% 95% 183 Inositol transport system ATP-binding protein 51% 247.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 40% 95% 183 Inositol transport system ATP-binding protein 51% 247.7
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 40% 95% 183 Inositol transport system ATP-binding protein 51% 247.7
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 94% 172.2 Inositol transport system ATP-binding protein 51% 247.7
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 94% 172.2 Inositol transport system ATP-binding protein 51% 247.7
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 94% 172.2 Inositol transport system ATP-binding protein 51% 247.7
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 94% 172.2 Inositol transport system ATP-binding protein 51% 247.7
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 94% 172.2 Inositol transport system ATP-binding protein 51% 247.7
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 94% 172.2 Inositol transport system ATP-binding protein 51% 247.7
myo-inositol catabolism PS417_11890 lo m-Inositol ABC transporter, ATPase component (itaA) (characterized) 34% 51% 155.2 Inositol transport system ATP-binding protein 51% 247.7
L-rhamnose catabolism rhaT' lo RhaT, 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) 33% 50% 154.5 Inositol transport system ATP-binding protein 51% 247.7
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 31% 51% 148.3 Inositol transport system ATP-binding protein 51% 247.7
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) 32% 50% 141.7 Inositol transport system ATP-binding protein 51% 247.7
D-xylose catabolism xylG lo Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized) 32% 51% 137.5 Inositol transport system ATP-binding protein 51% 247.7

Sequence Analysis Tools

View WP_007727336.1 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

MSTTAEVPALSNSGGNVPLIELKDVGKQYGNIIALKGINLRVGAGEVTGVLGDNGAGKST
LIKIIAGLHQQSEGELLVDGEPTTFHSPKEALGKGIATVYQDLAVVALMPVWRNFFLGQE
LRKGGLIKSLDANAMRATTLSELSKMGIELPDVDAPIGSLSGGQRQCVAIARAIFFGARV
LILDEPTAALGVKQSGMVLRYITAAKEQGFGVIFITHNPHHAYMVGDHFVLLNRGRQKLD
AKYDDISLEELTKEMAGGDELETLTHELRR

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