GapMind for catabolism of small carbon sources

 

Protein CA265_RS04220 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS04220 sodium:solute symporter

Length: 550 amino acids

Source: Pedo557 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
L-arabinose catabolism BT0355 med Na+/glucose cotransporter (characterized, see rationale) 33% 100% 337.4 Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 33% 332.0
D-cellobiose catabolism SSS-glucose med Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized) 33% 81% 324.7
D-glucose catabolism SSS-glucose med Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized) 33% 81% 324.7
lactose catabolism SSS-glucose med Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized) 33% 81% 324.7
D-maltose catabolism SSS-glucose med Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized) 33% 81% 324.7
sucrose catabolism SSS-glucose med Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized) 33% 81% 324.7
trehalose catabolism SSS-glucose med Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized) 33% 81% 324.7
D-galactose catabolism SGLT1 lo sodium/glucose cotransporter 1 (characterized) 33% 78% 328.6 Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 33% 332.0
D-galactose catabolism sglS lo Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 32% 99% 297 Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 33% 332.0
myo-inositol catabolism SMIT1 lo Myoinositol:Na+ symporter, SMIT1 (characterized) 32% 76% 296.6 Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 33% 332.0
L-arabinose catabolism Echvi_1880 lo SSS sodium solute transporter (characterized, see rationale) 33% 81% 281.6 Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 33% 332.0
D-xylose catabolism Echvi_1871 lo SSS sodium solute transporter (characterized, see rationale) 31% 99% 278.1 Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 33% 332.0

Sequence Analysis Tools

View CA265_RS04220 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

MISTTDIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNI
SCLHLVSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRYNRA
CRDWLAFISILSAIIIHIAFSFLAGGIVLETLFGIDMYVSIVVIALLTGLYTIIGGLRAV
VVTETIQSLVLITGAIIITYFAWNKVGGWDHMTAILQKENAMDKLSMIRPIGDKSGMSWI
AVFLGYPVLGIWYWCADQTIVQRVLGAKDENHARVGSLFCGFIKILPVFIFVLPGLFAYI
LYKSGTMDLSSLQTVGSNGETVLNTKGIYTLMITQLLPKGLVGILVAALLSGLMSQIAGA
LNSIATLSSYDLYKRFKPETSDKKLVSVGRWSAGIALTVSIGLLPLLNSYESLFNGINDV
IAHIAPPITCVFLLGVFWKKASAKGAQYTLLLGSIIGAGVFVVNKVYGTETIIGQIPFMM
MAFYLFCICVLIQVVFSHIYPVKHTAQSETLYWTSIWEPLKSKGWSGIGNYKFLSVLLLA
IMGVLYVYFK

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