GapMind for catabolism of small carbon sources

 

Protein WP_108358600.1 in Limnohabitans curvus MWH-C5

Annotation: NCBI__GCF_003063475.1:WP_108358600.1

Length: 264 amino acids

Source: GCF_003063475.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism frcA hi Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 65% 98% 326.6 Probable ABC-transport system ATP binding protein, component of XylFGH downstream of characterized transcriptional regulator, ROK7B7 (Sco6008); XylF (Sco6009); XylG (Sco6010); XylH (Sco6011)) 43% 204.1
D-mannose catabolism frcA hi Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 65% 98% 326.6 Probable ABC-transport system ATP binding protein, component of XylFGH downstream of characterized transcriptional regulator, ROK7B7 (Sco6008); XylF (Sco6009); XylG (Sco6010); XylH (Sco6011)) 43% 204.1
D-ribose catabolism frcA hi Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 65% 98% 326.6 Probable ABC-transport system ATP binding protein, component of XylFGH downstream of characterized transcriptional regulator, ROK7B7 (Sco6008); XylF (Sco6009); XylG (Sco6010); XylH (Sco6011)) 43% 204.1
sucrose catabolism frcA hi Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 65% 98% 326.6 Probable ABC-transport system ATP binding protein, component of XylFGH downstream of characterized transcriptional regulator, ROK7B7 (Sco6008); XylF (Sco6009); XylG (Sco6010); XylH (Sco6011)) 43% 204.1
L-arabinose catabolism xylGsa med Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 44% 94% 202.6 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
myo-inositol catabolism PGA1_c07320 med Inositol transport system ATP-binding protein (characterized) 41% 95% 180.6 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 95% 168.7 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 95% 168.7 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 95% 168.7 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 95% 168.7 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 95% 168.7 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 37% 95% 168.7 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6
D-ribose catabolism rbsA lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 51% 134.4 Fructose import ATP-binding protein FrcA; EC 7.5.2.- 65% 326.6

Sequence Analysis Tools

View WP_108358600.1 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

MSGTQHNIVMSAKGLVKRYGQVTALDGADFELRAGEILAVIGDNGAGKSSLIKCLSGATV
PDEGMISLDGNPIYFKSPIDARRAGIETVYQDLAVAPAMSIAENLFLGREIRRPGFAGNV
LRMLDKKRMLQESIERMNDLKVGIRSMTQAVETLSGGQRQCVAVSRAAAFAQHVVIMDEP
TAALGVKEGNMVLELIRRVRDKGLPVVLISHNMPHVFEIADRIHVARLGKRAAVLNPKNI
SMSDTVAVMTGAMKPEDIPAECLA

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