GapMind for catabolism of small carbon sources

 

Protein WP_012049213.1 in Rhizorhabdus wittichii RW1

Annotation: NCBI__GCF_000016765.1:WP_012049213.1

Length: 235 amino acids

Source: GCF_000016765.1 in NCBI

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 66% 148.7 cell division ATP-binding protein ftsE 44% 181.8
L-glutamate catabolism gltL lo Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 35% 88% 130.6 cell division ATP-binding protein ftsE 44% 181.8
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 84% 130.2 cell division ATP-binding protein ftsE 44% 181.8
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 84% 130.2 cell division ATP-binding protein ftsE 44% 181.8
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 54% 104 cell division ATP-binding protein ftsE 44% 181.8

Sequence Analysis Tools

View WP_012049213.1 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

MRPGAANIVQFENVGLRYGSGAETLSDLSFGLAAGAFYFLTGPSGAGKSSLLRLIYLAQR
PSRGLIRMFGEDVVTLPRARMPGFRRRIGTVFQDFRLIPHLSAYENIALPLRVNGVAEAD
IDTPVREMLEWVGLSGRAYARPATLSGGEQQRVAIARAVIGRPEILVADEPTGNVDPDMA
GRLLYLFEALNKLGTTILVATHDLHLIPRVHHAQTIRLDSGRLDNGKLEAPGGAR

This GapMind analysis is from Apr 09 2024. 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