GapMind for catabolism of small carbon sources

 

Protein BWI76_RS27035 in Klebsiella michiganensis M5al

Annotation: BWI76_RS27035 xylose ABC transporter ATP-binding protein

Length: 513 amino acids

Source: Koxy 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-xylose catabolism xylG hi Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized) 88% 100% 894 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 45% 444.9
L-arabinose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
D-cellobiose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
D-galactose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
D-glucose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
lactose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
D-maltose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
sucrose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
trehalose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 49% 98% 449.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
D-ribose catabolism rbsA med Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 45% 97% 444.9 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 44% 94% 396.4 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 42% 97% 391 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0
2'-deoxyinosine catabolism nupA lo RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 35% 96% 293.1 Xylose import ATP-binding protein XylG; EC 7.5.2.10 88% 894.0

Sequence Analysis Tools

View BWI76_RS27035 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

MSWLLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYE
GEIIFSGETLQPGHIRDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMT
LRCEKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAI
LLNIIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVG
RELTALYPSEAHSCGDEILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAGLVGAGR
TEAVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPVMAVGKN
ITLAALNQFTGPLSSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQKAILARCL
LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE
GKLKANLINQGLTQEQVMEAALRSERHVEEHVV

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