GapMind for catabolism of small carbon sources

 

Protein WP_084931118.1 in Pantoea rwandensis LMG 26275

Annotation: NCBI__GCF_002095475.1:WP_084931118.1

Length: 506 amino acids

Source: GCF_002095475.1 in NCBI

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 43% 97% 403.7 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 42% 399.8
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 39% 100% 367.1 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 43% 403.7
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 38% 99% 363.2 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 43% 403.7
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) 40% 99% 361.3 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 43% 403.7
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 37% 97% 335.9 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 43% 403.7
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 95% 297.7 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 43% 403.7
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 36% 95% 297.7 Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter 43% 403.7

Sequence Analysis Tools

View WP_084931118.1 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

MQAQMQPLARLEGIKKSYPGVKALSGIDFDLLSGEIHCLVGENGAGKSTLMRVLTGATQP
DSGTIYIDEKPTVLDAKTRLDHGIGIVWQELDLIPAMSVAENIYIGHEPMLSLGRIDHQI
LRQNTQKLLSNFDLDVSPDTRVDRLAPAQQQLVQIAKALSHNNRILILDEPTASLTNNEV
ANLFDLLRKLRQQGLGIVYISHRLEELTAIGDRLTVLRDGHFILTAQVASLSHNDIIKAM
VGRPLAEQFPRGSRKTQAIGLEVKELGRHGEFEEISFSVNQGEVLAIAGIIGAGRSELLE
TLFGLRKADKGSISINGVAVNIRHPRDAVRLGLGLVPEERRESGLILNRAINDNLIYPII
NRLGNILHFSRSQMRAVSDRLIKQLSIKAPSGQALAGSLSGGNQQKIVIGKWLAAGVKVL
LLDEPTRGVDVNAKAEIYRLIDELAQTGVTVVVVSSELPEVLGISDRVLVIAQGRQTALL
TTANTSQEEIMAFAVASKAMPQQEEA

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