GapMind for catabolism of small carbon sources

 

Protein WP_022529984.1 in Lactobacillus shenzhenensis LY-73

Annotation: NCBI__GCF_000469325.1:WP_022529984.1

Length: 274 amino acids

Source: GCF_000469325.1 in NCBI

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism peb1A lo major cell-binding factor (characterized) 35% 91% 132.5 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-aspartate catabolism peb1A lo major cell-binding factor (characterized) 35% 91% 132.5 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-glutamate catabolism peb1A lo major cell-binding factor (characterized) 35% 91% 132.5 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-glutamate catabolism gltI lo Probable binding protein component of ABC transporter, 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) 34% 87% 128.6 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-glutamate catabolism gtrC lo GtrC aka GLNH aka SLL1104, component of Tripartite glutamate:Na+ symporter (characterized) 31% 87% 126.3 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-asparagine catabolism aatJ lo ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized) 31% 88% 114 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-aspartate catabolism aatJ lo ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized) 31% 88% 114 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-glutamate catabolism gluB lo GluB aka CGL1951, component of Glutamate porter (characterized) 33% 87% 114 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-arginine catabolism artJ lo ABC transporter for L-Arginine, substrate-binding component (characterized) 35% 80% 105.1 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-citrulline catabolism AO353_03055 lo ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 33% 81% 103.2 ABC transporter glutamine-binding protein GlnH 55% 281.6
L-lysine catabolism argT lo Putative amino-acid binding periplasmic protein (characterized, see rationale) 32% 80% 97.1 ABC transporter glutamine-binding protein GlnH 55% 281.6

Sequence Analysis Tools

View WP_022529984.1 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

MRKFKSWLWLLPLLAFAVLLSSCGTKSVADEDILSRAKATNSITWGVKNDTRLFGLMDIS
DGQIKGFDIDIAKEVSHRIIGQNVQINFVPVTSQTRIPLLKNGNVDAIIATMTNTPDRRK
VVDFSDTYFNAGQALLVKKGSPIKSVKDLKKGTKVIGVQGSNSVQNIKKVAPDAQVLQLS
DYAQAFTALQSGQGDALTTDNGILYGMSADNPNYVVVGGTFTKEPYAIAVNKGQKAFLDD
VNLALTSMRQDGTYKQIEDKWFGNIAGFSDGGLK

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