Annotation: FitnessBrowser__Putida:PP_0372
Length: 426 amino acids
Source: Putida in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-arginine biosynthesis | argD | hi | acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) | 41% | 99% | 240.4 | |||
L-proline biosynthesis | argD | hi | acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) | 41% | 99% | 240.4 | |||
L-arginine biosynthesis | argD'B | med | succinylornithine transaminase (EC 2.6.1.81) (characterized) | 40% | 99% | 254.2 | acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] | 41% | 240.4 |
L-lysine biosynthesis | dapC | med | acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) | 41% | 99% | 240.4 | acetylornithine transaminase (EC 2.6.1.11) | 36% | 244.2 |
L-proline biosynthesis | OAT | lo | Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized) | 36% | 94% | 221.9 | acetylornithine transaminase (EC 2.6.1.11) | 36% | 244.2 |
View PP_0372 at FitnessBrowser
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...
MNLFNLRRSAPAAAAEPKRAPVIVPHASEQSPERLMPGTERAAQVFVRGQGSWLWDNEGH AYLDFTQGGAVNSLGHSPSVLVKALGNQAQALINPGSGFHNRGLLGLVNRLCQSTGSDQA YLLNSGAEACEGAIKLARKWGQLHRNGAYHIITASQACHGRSLGALSASDPLPCNRCEPG LPGFSKVPFNDLAALHAEVDSRTVAIMLEPIQGEAGVIPATQEYLKGVETLCRELGILLI LDEVQTGIGRCGALLAEELYGVRADIITLGKGLGGGVPLAALLARGKACCAEPGELEGSH HGNALMCAAGLAVLDSVLEPGFLAQVQDNGRHLREGLSRLTGRYGQGEVRGHGLLWALQL KENLARELVAAALHEGLLLNAPQVDVVRFSPALTVSKGNIDEMLLRLARAFARLHAQQQA RREMPA
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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