GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS16930 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS16930 arabinose ABC transporter ATP-binding protein

Length: 512 amino acids

Source: BFirm in FitnessBrowser

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-galactose catabolism BPHYT_RS16930 hi Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 100% 100% 994.6 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
L-arabinose catabolism araG hi L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 53% 98% 517.3 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 45% 424.1
D-cellobiose catabolism mglA med 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) 45% 99% 424.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
D-glucose catabolism mglA med 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) 45% 99% 424.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
lactose catabolism mglA med 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) 45% 99% 424.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
D-maltose catabolism mglA med 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) 45% 99% 424.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
sucrose catabolism mglA med 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) 45% 99% 424.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
trehalose catabolism mglA med 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) 45% 99% 424.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
D-xylose catabolism xylG med 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) 45% 99% 424.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 44% 95% 409.8 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
myo-inositol catabolism PS417_11890 med m-Inositol ABC transporter, ATPase component (itaA) (characterized) 43% 94% 403.7 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 43% 96% 401 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3
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% 394 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 53% 517.3

Sequence Analysis Tools

View BPHYT_RS16930 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR
VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF
VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF
KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR
EISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY
GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY
LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI
LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT
RKDATEQSVLSLALPQSSTALPGTQAAAQQAA

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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