GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS28215 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS28215 D-ribose transporter ATP binding protein

Length: 509 amino acids

Source: BFirm in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism HSERO_RS03640 hi Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 48% 98% 457.6 Inositol transport system ATP-binding protein 46% 438.0
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 46% 98% 438 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 47% 428.7
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) 47% 99% 428.7 Inositol transport system ATP-binding protein 46% 438.0
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) 47% 99% 428.7 Inositol transport system ATP-binding protein 46% 438.0
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) 47% 99% 428.7 Inositol transport system ATP-binding protein 46% 438.0
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) 47% 99% 428.7 Inositol transport system ATP-binding protein 46% 438.0
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) 47% 99% 428.7 Inositol transport system ATP-binding protein 46% 438.0
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) 47% 99% 428.7 Inositol transport system ATP-binding protein 46% 438.0
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) 47% 99% 428.7 Inositol transport system ATP-binding protein 46% 438.0
myo-inositol catabolism iatA med Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 48% 96% 427.9 Inositol transport system ATP-binding protein 46% 438.0
L-rhamnose catabolism rhaT' med 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) 45% 99% 421.8 Inositol transport system ATP-binding protein 46% 438.0
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 44% 99% 392.5 Inositol transport system ATP-binding protein 46% 438.0
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 44% 99% 392.5 Inositol transport system ATP-binding protein 46% 438.0
L-arabinose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 42% 98% 365.5 Inositol transport system ATP-binding protein 46% 438.0
D-galactose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 42% 98% 365.5 Inositol transport system ATP-binding protein 46% 438.0
xylitol catabolism PS417_12065 med 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) 43% 97% 357.5 Inositol transport system ATP-binding protein 46% 438.0
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 39% 98% 362.8 Inositol transport system ATP-binding protein 46% 438.0
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 39% 97% 326.2 Inositol transport system ATP-binding protein 46% 438.0
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 39% 97% 326.2 Inositol transport system ATP-binding protein 46% 438.0

Sequence Analysis Tools

View BPHYT_RS28215 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

MQQPTSAVPRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVH
QPDTGELVVDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQ
YDAMRREVDGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSL
PEVERLFTIVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIV
AKMVGRDLETFYPKAERPPGEVRLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSE
VARAIFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASM
TVLGRLVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGP
KVLIIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRIS
ADIARADADEERIMGAALGQPMPPLGHAA

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 preprint 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