GapMind for catabolism of small carbon sources

 

Protein SM_b20855 in Sinorhizobium meliloti 1021

Annotation: SM_b20855 sugar uptake ABC transporter ATP-binding protein

Length: 504 amino acids

Source: Smeli in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism HSERO_RS05250 hi Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 46% 94% 426 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0
D-mannose catabolism HSERO_RS03640 hi Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 46% 95% 425.6 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 45% 95% 391.3 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 42% 94% 384.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 42% 94% 384.4 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0
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% 100% 382.5 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0
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% 100% 382.5 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0
D-galactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 40% 97% 379 ATP binding protein of ABC transporter for pentoses, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 45% 401.0

Sequence Analysis Tools

View SM_b20855 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MVTELANLKSISKSFGGIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPSQG
EVVINGKRTELRDPRDARALGIVVIHQELALAPDLSVAENIFLGELPTLISRFSLRRRAK
QLIDRLGFDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDAMKLHQI
IRGLRDRGVGIVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKIDDIIRMMVGRPIA
NMFPERSQRTIGAELLNVKKLNAGRMVRDVSFSVRAGEIVGLGGLIGSGRTEVARAIFGA
DPLDSGTISLKGKALKLKSPRDAVKAGIGLVPEDRKEHGVVIDKPIRVNATMARMSSVVN
ALGFLKPALERTDVTALGKSLRLKASSIDAPVSSLSGGNQQKVVLAKWFHAGGDVIILDE
PTRGVDVGAKAEIYALINKLAEDGKAVLVISSEHQELFGLCDRVLAMGQGQIRGELTPSN
YSEENLLGLSMMGGARASNQGSQV

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