GapMind for catabolism of small carbon sources

 

Protein WP_095509043.1 in Rubrivirga marina SAORIC-28

Annotation: NCBI__GCF_002283365.1:WP_095509043.1

Length: 529 amino acids

Source: GCF_002283365.1 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 med Na+/glucose cotransporter (characterized, see rationale) 35% 100% 331.3 sodium/glucose cotransporter 1 34% 323.2
D-cellobiose catabolism SSS-glucose med Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 (characterized) 35% 82% 321.6 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 33% 307.4
D-glucose catabolism SSS-glucose med Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 (characterized) 35% 82% 321.6 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 33% 307.4
lactose catabolism SSS-glucose med Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 (characterized) 35% 82% 321.6 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 33% 307.4
D-maltose catabolism SSS-glucose med Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 (characterized) 35% 82% 321.6 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 33% 307.4
sucrose catabolism SSS-glucose med Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 (characterized) 35% 82% 321.6 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 33% 307.4
trehalose catabolism SSS-glucose med Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 (characterized) 35% 82% 321.6 Sodium/myo-inositol cotransporter; Na(+)/myo-inositol cotransporter; Sodium/myo-inositol transporter 1; SMIT1; Solute carrier family 5 member 3 33% 307.4
D-galactose catabolism sglS lo Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized) 33% 99% 297.7 sodium/glucose cotransporter 1 34% 323.2
myo-inositol catabolism SMIT1 lo Sodium/myo-inositol cotransporter (Na(+)/myo-inositol cotransporter) (Sodium/myo-inositol transporter 1) (SMIT1) (Solute carrier family 5 member 3) (characterized) 34% 75% 297.7 sodium/glucose cotransporter 1 34% 323.2
D-xylose catabolism Echvi_1871 lo SSS sodium solute transporter (characterized, see rationale) 35% 92% 296.6 sodium/glucose cotransporter 1 34% 323.2
L-arabinose catabolism Echvi_1880 lo SSS sodium solute transporter (characterized, see rationale) 32% 81% 276.2 sodium/glucose cotransporter 1 34% 323.2
pyruvate catabolism SLC5A8 lo Sodium-coupled monocarboxylate transporter 2; Electroneutral sodium monocarboxylate cotransporter; zSMCTn; Low-affinity sodium-lactate cotransporter; Solute carrier family 5 member 12; zSLC5A12 (characterized) 30% 71% 169.9 sodium/glucose cotransporter 1 34% 323.2

Sequence Analysis Tools

View WP_095509043.1 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

MPEFTLTTLDIAVVLAYGVVIFGIGLYFSRHTDDGEDYFLAGRSLTWGLIGISLVASNLS
SSSMIGMASAAYGGIGLSVYNYEWMAALVLVVFVLFFLPFYLKSGIYTMPEFLEKRFDGR
SRTYFSAISIFLSVIVDTAAALYAGALVVQLLYPDFPLWGSMTILALVAGAYTIAGGLKA
VVYTDAIQGTLLLVGAAAVSFMAWQRSGGWDAVVAVTPEEKLSLIQPLSSPDMPWLGLIT
GVFLLGFYFWTTNQFMVQRVLGAKNLDHGRWGALFGGLLKLPILFLMVMPGTFGRVLYPE
GMVANPDQIFPTLLFDLLPAGFRALVLTAMVAAIMSSVDSTLNAASTLVTMDFVKKYRPS
TSPQALARIGRIVTAICMVVAIVWSPIITRADTLWDYLQSTLAYVAPPAIALFVLGVFWK
RANGHGALAGLVAGHTASVIFLVLSITDVLRFNFLYLAPILLLISMAAMVIVSLRTAPPP
AEKTEGLMWTPAFFRAETEELKGVPAWKNYRVQSAVLVGLTAVVVGLFW

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