GapMind for catabolism of small carbon sources

 

Protein WP_043917998.1 in Jannaschia aquimarina GSW-M26

Annotation: NCBI__GCF_000877395.1:WP_043917998.1

Length: 430 amino acids

Source: GCF_000877395.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism davT hi 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 52% 98% 427.9
L-citrulline catabolism davT hi 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 52% 98% 427.9
L-lysine catabolism davT hi 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 52% 98% 427.9
L-proline catabolism davT hi 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 52% 98% 427.9
L-arginine catabolism gabT med 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized) 55% 98% 433.3 5-aminovalerate transaminase (EC 2.6.1.48) 52% 427.9
L-citrulline catabolism gabT med 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized) 55% 98% 433.3 5-aminovalerate transaminase (EC 2.6.1.48) 52% 427.9
putrescine catabolism gabT med 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized) 55% 98% 433.3 5-aminovalerate transaminase (EC 2.6.1.48) 52% 427.9
L-lysine catabolism lysN med 2-aminoadipate transaminase (EC 2.6.1.39) (characterized) 45% 93% 327.8 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 55% 433.3
L-arginine catabolism rocD lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 34% 91% 231.9 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 55% 433.3
L-citrulline catabolism rocD lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 34% 91% 231.9 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 55% 433.3
L-lysine catabolism lat lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 34% 91% 231.9 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 55% 433.3
L-arginine catabolism astC lo Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized) 39% 90% 231.1 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 55% 433.3
L-citrulline catabolism astC lo Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized) 39% 90% 231.1 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 55% 433.3
L-arginine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 83% 189.5 5-aminovalerate transaminase (EC 2.6.1.48) 52% 427.9
L-citrulline catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 83% 189.5 5-aminovalerate transaminase (EC 2.6.1.48) 52% 427.9
L-lysine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 83% 189.5 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) 55% 433.3
putrescine catabolism patA lo putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized) 34% 83% 189.5 5-aminovalerate transaminase (EC 2.6.1.48) 52% 427.9

Sequence Analysis Tools

View WP_043917998.1 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

MDGQQNIGDALDLRREAAVPRGVATRGLWADAAQGAILTLADGREMIDFAAGIAVVNTGH
RHPAVMEAAGAQMARFTHTCFHVAPYEGYVALAERLNAAAPGAFAKRTMLVTTGAEAVEN
AIKMARAFTGRSGVVAFGGSFHGRTLMGMALTGKQVPYKAGFGAMPPEIHHAPFPDPLGG
IDEAEALAALDRLFAGAIDPARVAAMIVEPVQGEGGFNPASPDFLRALRERCDRHGIVMI
ADEVQTGIARTGALFAMERAGVAADITTLAKGLAGGFPLSAVVARAEIADAAPAGGLGGT
YAGNPVAAAAALAVLDTVEAEGLCAAARRIGEAMTARLSALAAEGHGIAEVRGPGAMVAV
EFGEGEGSAYRPDPARAGRVIAGCEARGLIVLPCGTRGNAVRLLPPLVVDDATLARAMDI
FEAATREAGA

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