GapMind for catabolism of small carbon sources

 

Protein WP_067906114.1 in Novosphingobium fuchskuhlense FNE08-7

Annotation: NCBI__GCF_001519075.1:WP_067906114.1

Length: 249 amino acids

Source: GCF_001519075.1 in NCBI

Candidate for 15 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) 38% 66% 145.2 cell division ATP-binding protein ftsE 46% 184.1
L-arginine catabolism artP lo AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 35% 93% 136.7 cell division ATP-binding protein ftsE 46% 184.1
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 89% 135.2 cell division ATP-binding protein ftsE 46% 184.1
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 89% 135.2 cell division ATP-binding protein ftsE 46% 184.1
L-glutamate catabolism gltL lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 89% 135.2 cell division ATP-binding protein ftsE 46% 184.1
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 33% 99% 125.9 cell division ATP-binding protein ftsE 46% 184.1
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 36% 51% 118.2 cell division ATP-binding protein ftsE 46% 184.1
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 33% 53% 108.6 cell division ATP-binding protein ftsE 46% 184.1
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 96.3 cell division ATP-binding protein ftsE 46% 184.1
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 96.3 cell division ATP-binding protein ftsE 46% 184.1
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 96.3 cell division ATP-binding protein ftsE 46% 184.1
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 96.3 cell division ATP-binding protein ftsE 46% 184.1
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 96.3 cell division ATP-binding protein ftsE 46% 184.1
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 96.3 cell division ATP-binding protein ftsE 46% 184.1
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 30% 60% 93.2 cell division ATP-binding protein ftsE 46% 184.1

Sequence Analysis Tools

View WP_067906114.1 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

MSQPDAEIVQFDNVGLRYGTDKEILTDVSFTLYPGCFYFLTGASGAGKTSLLKLLYLSQR
PSRGLIRLFGTDAITLPRERLPGFRRRIGVVFQDFRLVDHLSAFDNVALPLRVAGVSERD
IARPVGEMLDWVGLGDRQHARPATLSGGEQQRVAIARAVIARPDMLVADEPTGNVDPEMA
LKLLRLFESLNRLGTTVVVATHDVHLIRKVPESLIMRLDKGRLSDPTGALRYPPRRPGMA
PGAGTQSTL

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