GapMind for catabolism of small carbon sources

 

Protein WP_085218047.1 in Sphingomonas indica Dd16

Annotation: NCBI__GCF_900177405.1:WP_085218047.1

Length: 240 amino acids

Source: GCF_900177405.1 in NCBI

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism badH lo BadH (characterized) 39% 99% 162.2 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6
phenylacetate catabolism badH lo BadH (characterized) 39% 99% 162.2 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6
L-phenylalanine catabolism badH lo BadH (characterized) 39% 99% 162.2 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 37% 97% 141.7 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 35% 96% 137.1 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized) 36% 91% 136.3 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6
L-rhamnose catabolism LRA1 lo L-rhamnose 1-dehydrogenase (NADP(+)); RHAD; EC 1.1.1.377 (characterized) 33% 95% 116.3 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 33% 94% 103.2 (R)-3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.36) 65% 321.6

Sequence Analysis Tools

View WP_085218047.1 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

MARVAIVTGGTRGIGEAISLALRDKGLTVAANYAGNEEKAKAFTEKTGIKAYKWDVADFE
GCVAAVKQIEADLGAVDVLVNNAGITRDGTMKRMDRNAWDDVIDVNLGGCFNMAKAVWEG
MSERKYGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGARAGITVNAIAPGYI
DTDMVAAVPADVLQKIVAKIPVGRLGQASEIARGVTFLCAEDGGFITGSTLSINGGQHMY

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