GapMind for catabolism of small carbon sources

 

Protein 3610525 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)

Length: 533 amino acids

Source: Dino in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism SSS-glucose med sodium/glucose cotransporter 1 (characterized) 34% 81% 302.8
D-galactose catabolism SGLT1 med sodium/glucose cotransporter 1 (characterized) 34% 81% 302.8 Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs 32% 297.4
D-glucose catabolism SSS-glucose med sodium/glucose cotransporter 1 (characterized) 34% 81% 302.8
lactose catabolism SSS-glucose med sodium/glucose cotransporter 1 (characterized) 34% 81% 302.8
D-maltose catabolism SSS-glucose med sodium/glucose cotransporter 1 (characterized) 34% 81% 302.8
sucrose catabolism SSS-glucose med sodium/glucose cotransporter 1 (characterized) 34% 81% 302.8
trehalose catabolism SSS-glucose med sodium/glucose cotransporter 1 (characterized) 34% 81% 302.8
L-arabinose catabolism BT0355 lo Na+/glucose cotransporter (characterized, see rationale) 32% 99% 290.4 sodium/glucose cotransporter 1 34% 302.8
D-galactose catabolism sglS lo Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 34% 91% 289.7 sodium/glucose cotransporter 1 34% 302.8
myo-inositol catabolism SMIT1 lo Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; rKST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized) 33% 78% 284.6 sodium/glucose cotransporter 1 34% 302.8
D-xylose catabolism Echvi_1871 lo SSS sodium solute transporter (characterized, see rationale) 34% 91% 272.7 sodium/glucose cotransporter 1 34% 302.8
L-arabinose catabolism Echvi_1880 lo SSS sodium solute transporter (characterized, see rationale) 35% 76% 272.3 sodium/glucose cotransporter 1 34% 302.8

Sequence Analysis Tools

View 3610525 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

MGDAKFDLHWIDYAIVVIYFIGVIAHGVYVSRKNEEGADGYFLAGRSLPWYLIGFSLFAS
NMSGSSFVGLMGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQRYD
VRSRRAFSIFTILAILFIDTAGALYAGGLVISNVTGYLNLWTAVAVLALVAGIYTILGGL
SAVVVTDTVQAILLIIGAAILFWLGLDEIGGWEQLFVDIPEGHDQLILPADDDFLPWTGL
WGVVLLGFYYWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPNIFLMIIPGVIALKLYP
ELETPDLAFPTLAFELMPIGVRGLIMAALIAAIMSSLDSAMNSASTLVVKDFVEPIWEVD
EGKQVWIGRLVTGAVMVFGAIYAPSIAGFESLFSYFQSSLSYIIPTIVVVYIVGLFVPWL
NGNGAFWTIILGLVVGIPLFIMKEVTGVWAGMGLPEIHYTIMSTLMMCLGLATHFGISAL
TRKADKENIEDLVWSAADTKAIFTQWEEPLWQDRTIWAGLLILSTIGFVAWFW

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