GapMind for catabolism of small carbon sources

 

Protein WP_089216652.1 in Sphingopyxis indica DS15

Annotation: NCBI__GCF_900188185.1:WP_089216652.1

Length: 455 amino acids

Source: GCF_900188185.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 48% 97% 377.1 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 36% 258.8
sucrose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 48% 97% 377.1 Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) 36% 258.8
D-cellobiose catabolism MFS-glucose lo Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 36% 95% 258.8 D-fructose transporter, sugar porter family 48% 377.1
D-glucose catabolism MFS-glucose lo Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 36% 95% 258.8 D-fructose transporter, sugar porter family 48% 377.1
lactose catabolism MFS-glucose lo Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 36% 95% 258.8 D-fructose transporter, sugar porter family 48% 377.1
D-maltose catabolism MFS-glucose lo Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 36% 95% 258.8 D-fructose transporter, sugar porter family 48% 377.1
sucrose catabolism MFS-glucose lo Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 36% 95% 258.8 D-fructose transporter, sugar porter family 48% 377.1
trehalose catabolism MFS-glucose lo Glucose permease GlcP (Pimentel-Schmitt et al., 2008) (most similar to 2.A.1.1.32) (characterized) 36% 95% 258.8 D-fructose transporter, sugar porter family 48% 377.1
D-xylose catabolism xylT lo Glucose/fructose transport protein (characterized, see rationale) 34% 98% 251.5 D-fructose transporter, sugar porter family 48% 377.1
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 34% 93% 248.4 D-fructose transporter, sugar porter family 48% 377.1
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 34% 93% 248.4 D-fructose transporter, sugar porter family 48% 377.1
myo-inositol catabolism iolT lo Major myo-inositol transporter IolT (characterized) 34% 96% 243 D-fructose transporter, sugar porter family 48% 377.1
D-fructose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 92% 217.6 D-fructose transporter, sugar porter family 48% 377.1
sucrose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 92% 217.6 D-fructose transporter, sugar porter family 48% 377.1
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 34% 64% 180.6 D-fructose transporter, sugar porter family 48% 377.1
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 30% 90% 174.9 D-fructose transporter, sugar porter family 48% 377.1
D-galactose catabolism MST1 lo The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) 31% 76% 168.7 D-fructose transporter, sugar porter family 48% 377.1
D-mannose catabolism MST1 lo The monosaccharide (MST) (glucose > mannose > galactose > fructose):H+ symporter, MST1 (characterized) 31% 76% 168.7 D-fructose transporter, sugar porter family 48% 377.1

Sequence Analysis Tools

View WP_089216652.1 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

MTGELHGNQNKAGSPQGGRITLAAAIGTAALAGLLFGFDTAVIAGVTHDLTRLFALTPET
LGLTVSAALWGTLAGALFAGKPGDAFGSRDSLRVLAAFYFVAGLGCALAPSWTLFLFFRF
LCGLAIGGSSVLAPVYIAEIAPPRRRGLLVGLFQLMIVIGILTAYLSNAVIAGLVDGGAG
WRWKLGITAAPALLFFILLFAIPHSPRWLVVKGRASEAREALARIGMAPDAAAAELARVE
QALMRDPPNEKLSWRRHRRPMTLAILVAMFNQLAGINAVLYYLNDIFARAGSLSPDRQAV
LIGLANLIFTLVGMALIDRIGRKTLLLAGAAGMALCLSIAAGVLFGALGNALMLPALVGF
IAFFATSQGAVIWVYISEVFPTPVRARGSALGASTHWLMNALIAGVFPILVAWSPGAPFA
IFAAAMVLQFVVVAAIFPETRGVDLDAMAERMEAA

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