GapMind for catabolism of small carbon sources

 

Protein YP_001328611.1 in Sinorhizobium medicae WSM419

Annotation: NCBI__GCF_000017145.1:YP_001328611.1

Length: 356 amino acids

Source: GCF_000017145.1 in NCBI

Candidate for 6 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 56% 99% 374.4 ABC transporter for Lactose, ATPase component 56% 370.2
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 56% 98% 370.2 ABC transporter for L-Fucose, ATPase component 56% 374.4
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 50% 89% 346.7 ABC transporter for L-Fucose, ATPase component 56% 374.4
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 49% 99% 327 ABC transporter for L-Fucose, ATPase component 56% 374.4
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 49% 100% 322.8 ABC transporter for L-Fucose, ATPase component 56% 374.4
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 96% 318.5 ABC transporter for L-Fucose, ATPase component 56% 374.4

Sequence Analysis Tools

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

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Sequence

MASVDLRDIRKSYAALEVIHGVSLSIAEGEFIALVGPSGCGKSTLLRMIAGLEEISDGEV
FIGGKVVNPLTPRERNIAMVFQSYALYPHMTVAENMGFNLKLSGLPRPEIDRRVGDAARM
LALTELLGRKPSQLSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRTEIKALH
QKVATTSIYVTHDQIEAMTLADRIVVLNGGRIEQVGTPLELYRTPANLFVAGFIGSPAMN
VLDGTVDAEDGEPAVRLGDGSAIRIAAERKVRPGQAVRIGLRPEHFVAGGKGNAIAGTTL
LVEPTGAQTHVLFEFAGEQITAVVDGDHPARHGSIFTAAMDRSQVYVFDRQTGAAL

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