GapMind for catabolism of small carbon sources

 

Protein PP_0214 in Pseudomonas putida KT2440

Annotation: PP_0214 4-aminobutyrate aminotransferase

Length: 425 amino acids

Source: Putida in FitnessBrowser

Candidate for 13 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) 100% 100% 831.2
L-citrulline catabolism davT hi 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 100% 100% 831.2
L-lysine catabolism davT hi 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 100% 100% 831.2
L-proline catabolism davT hi 5-aminovalerate transaminase (EC 2.6.1.48) (characterized) 100% 100% 831.2
L-arginine catabolism gabT med 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized) 87% 100% 739.2 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-arginine catabolism gabT med gabT: 4-aminobutyrate transaminase (EC 2.6.1.19) (TIGR00700) 100% 548.2 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-citrulline catabolism gabT med 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized) 87% 100% 739.2 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-citrulline catabolism gabT med gabT: 4-aminobutyrate transaminase (EC 2.6.1.19) (TIGR00700) 100% 548.2 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
putrescine catabolism gabT med 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized) 87% 100% 739.2 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
putrescine catabolism gabT med gabT: 4-aminobutyrate transaminase (EC 2.6.1.19) (TIGR00700) 100% 548.2 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-lysine catabolism lysN med 2-aminoadipate transaminase (EC 2.6.1.39) (characterized) 42% 99% 347.4 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-arginine catabolism rocD lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 38% 91% 264.6 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-citrulline catabolism rocD lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 38% 91% 264.6 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-lysine catabolism lat lo Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized) 38% 91% 264.6 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-arginine catabolism astC lo Succinylornithine transaminase (EC 2.6.1.81) (characterized) 36% 92% 224.9 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2
L-citrulline catabolism astC lo Succinylornithine transaminase (EC 2.6.1.81) (characterized) 36% 92% 224.9 5-aminovalerate transaminase (EC 2.6.1.48) 100% 831.2

Sequence Analysis Tools

View PP_0214 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSKTNESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLH
PKVVAAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAV
KIARAATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGIS
VDDAIASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIAD
EVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA
GSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEV
FEKGTHTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEEC
FAEIA

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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