GapMind for catabolism of small carbon sources

 

Protein WP_068215461.1 in Roseivirga spongicola UST030701-084

Annotation: NCBI__GCF_001592965.1:WP_068215461.1

Length: 553 amino acids

Source: GCF_001592965.1 in NCBI

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 hi Na+/glucose cotransporter (characterized, see rationale) 51% 100% 582.4 Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 38% 410.2
D-cellobiose catabolism SSS-glucose med Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized) 38% 97% 410.2
D-glucose catabolism SSS-glucose med Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized) 38% 97% 410.2
lactose catabolism SSS-glucose med Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized) 38% 97% 410.2
D-maltose catabolism SSS-glucose med Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized) 38% 97% 410.2
sucrose catabolism SSS-glucose med Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized) 38% 97% 410.2
trehalose catabolism SSS-glucose med Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized) 38% 97% 410.2
myo-inositol catabolism SMIT1 med 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) 41% 71% 376.3 Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 38% 410.2
D-galactose catabolism SGLT1 lo sodium/glucose cotransporter 1 (characterized) 37% 83% 392.9 Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 38% 410.2
D-galactose catabolism sglS lo Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 34% 91% 328.2 Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 38% 410.2
D-xylose catabolism Echvi_1871 lo SSS sodium solute transporter (characterized, see rationale) 36% 89% 298.1 Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 38% 410.2
L-arabinose catabolism Echvi_1880 lo SSS sodium solute transporter (characterized, see rationale) 33% 78% 288.9 Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 38% 410.2

Sequence Analysis Tools

View WP_068215461.1 at NCBI

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

MNSVLETADWVVLGLYFLALIGVAVWVIVQKNKNTEDYFLAGRNVGWFVIGASIFASNIG
SEHVVGLAGTGAESGMPMAHYELHAWIVLLLGWLFLPFYFRSNAFTMPEFLEKRYDSRSR
WFLSIFSLVGYVITKVSVTIYAGGIVVSELLGIPFWYGAIGVVLFTGLYTVIGGMKAVIY
TETLQTVVLILGSVVITVLGMQAVGGWDELQATVRATSPDHFNMWRSASDPDFPWTGLLI
GGTIVGVWYWCTDQYIVQRTLAANNIKIGRRGAIFGAYLKILPIFIFLIPGIIAYALNQK
GLIELGRADEAFPTLVKALLPVGLKGLVAGGLMAALMSSLASVFNSCSTIFTIDIYKKLK
PQESEKRLLTVGRYATGIVVVLGIVWIPIMDKIGGGVMYQYLQSVQSYIAPPIAAVFVLG
ILWKRMNSKGAIITLFAGLVVAILRIASELIYSDQIAQFKETGVHVASGMLYHYARINFA
NMAIFMFLFSAIVLIVSSLATASPNYANIQGLAFGTLSDEQKQLKKGSFTWVDILFSVLL
VIVVISILTYFTG

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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