GapMind for catabolism of small carbon sources

 

Protein CA265_RS06755 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: FitnessBrowser__Pedo557:CA265_RS06755

Length: 542 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism sglS hi Sodium transporter (characterized, see rationale) 59% 99% 661.8 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 33% 272.3
D-xylose catabolism Echvi_1871 hi SSS sodium solute transporter (characterized, see rationale) 55% 100% 605.1 Sodium/glucose cotransporter; Na(+)/glucose symporter 48% 521.2
D-cellobiose catabolism SSS-glucose hi Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 48% 99% 521.2 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 31% 253.4
D-glucose catabolism SSS-glucose hi Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 48% 99% 521.2 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 31% 253.4
lactose catabolism SSS-glucose hi Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 48% 99% 521.2 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 31% 253.4
D-maltose catabolism SSS-glucose hi Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 48% 99% 521.2 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 31% 253.4
sucrose catabolism SSS-glucose hi Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 48% 99% 521.2 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 31% 253.4
trehalose catabolism SSS-glucose hi Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 48% 99% 521.2 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 31% 253.4
L-arabinose catabolism Echvi_1880 med SSS sodium solute transporter (characterized, see rationale) 48% 88% 499.2 Sodium/glucose cotransporter; Na(+)/glucose symporter 48% 521.2
L-arabinose catabolism BT0355 lo Na+/glucose cotransporter (characterized, see rationale) 34% 100% 288.9 Sodium/glucose cotransporter; Na(+)/glucose symporter 48% 521.2

Sequence Analysis Tools

View CA265_RS06755 at FitnessBrowser

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

Fitness BLAST: loading...

Sequence

MNHLSAFDYAVFLMYFVIVSAYGYWVYRSKKKKRTDTKDYFLAEGSLTWWAIGASIIASN
ISAEHFIGMSGSGFAMGLAIASYEWMAAATLIIVAIFFLPIYIKNKIYTMPQFLSNRYNN
TVSTLMAVFWLLVYVFVNLTSIFFLGAIAIETITGVPFNICIIFLAIFSAIITLGGMKVI
GYTDVIQVFVLVAGGLITCYMALKLVSEKLDAPSVLASLPLLRSEASDHFHMIFSKGDKF
YNELPGIAVLVGGLWINNLNYWGCNQYIVQRALGADLKTGRNGLIFAAFLKLLIPVIVVI
PGIAAYVLYQRGYFHSEMLDAAGVVKPDHAYPVLMNLLPAGIKGLAFAALTAAIVASLAG
KCNSIATIFTLDIYKKFIKPEASETRLVSVGRWSVVIASLIAIIIAPALRSFDQVYQFIQ
EYVGFISPGVFAIFLLGFFWKKTTSRAALTAALLTIPLSTLFKFLPAVTNGAIAPIPFLN
RMSWVFMIIIGLMIVVTLTDPKSKDNPQGLEIDSSMFKVTPAFTIASVMICGILAALYTV
FW

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:

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