GapMind for catabolism of small carbon sources

 

Protein WP_068011228.1 in Pseudovibrio axinellae Ad2

Annotation: NCBI__GCF_001623255.1:WP_068011228.1

Length: 382 amino acids

Source: GCF_001623255.1 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
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 52% 95% 371.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 255.4
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 45% 73% 162.9 PotG aka B0855, component of Putrescine porter 52% 371.3
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 211.8 PotG aka B0855, component of Putrescine porter 52% 371.3
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 35% 95% 191 PotG aka B0855, component of Putrescine porter 52% 371.3

Sequence Analysis Tools

View WP_068011228.1 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

METLVSTQPVSDFAPWNNPGEVPLVHFDGVTKKFGDFTAIENLSLNIYEREFFALLGPSG
CGKTTMMRMLAGFEHPTKGNILLGQGNLQEAPPHKRPVNMMFQSYALFPHMNVEQNIGFG
LKQDKTPKAEIKRRVEEMLSLVQLEPFAKRKPHQLSGGQKQRVALARSLAKKPKLLLLDE
PLGALDRKLREQTQFELMNIQEQLGLTFVIVTHDQEEAMTVASRIAVMDHGKIVQVATPA
EIYEYPNSRYSADFLGDVNIIEGRTDISTGETASLYWSDEEAPLTVSTSLRLPAQTTAWL
AVRPEKLRISKDKPPTSDNCIQGKVWDIGYTGNISTYHVKVSNGSILKAQVSNQERLADR
PITWEDTVFVHWDKGAGVFLET

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