GapMind for Amino acid biosynthesis

 

Protein Synpcc7942_1410 in Synechococcus elongatus PCC 7942

Annotation: FitnessBrowser__SynE:Synpcc7942_1410

Length: 540 amino acids

Source: SynE in FitnessBrowser

Candidate for 3 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-leucine biosynthesis leuA hi 2-isopropylmalate synthase (EC 2.3.3.13) (characterized) 52% 87% 503.8 homocitrate synthase (EC 2.3.3.14) 49% 459.9
L-leucine biosynthesis leuA med leuA: 2-isopropylmalate synthase (EC 2.3.3.13) (TIGR00973) 100% 779.3 homocitrate synthase (EC 2.3.3.14) 49% 459.9
L-lysine biosynthesis hcs med homocitrate synthase (EC 2.3.3.14) (characterized) 49% 95% 459.9 2-isopropylmalate synthase (EC 2.3.3.13) 52% 503.8
L-isoleucine biosynthesis cimA med Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized) 44% 100% 364.8 2-isopropylmalate synthase (EC 2.3.3.13) 52% 503.8

Sequence Analysis Tools

View Synpcc7942_1410 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

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Sequence

MASASSNDRILIFDTTLRDGEQSPGASLNLEEKLAIARQLARLNVDIIEAGFAFASPGDF
EAVQRIAAEVGTPDGPTICSLARATRQDIKAAAEALAPAAKGRIHTFIATSDIHLEYKLK
KTRAEVLAVIPEMVGYAASLVDDVEFSPEDAGRSDPEFLYECLEAAIAAGAKTINIPDTV
GYTTPSEFGALIGGIKQNVCNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTINGI
GERAGNAALEELVMALHVRRQYFNPFLGRAADSEAPLTQVNTREIYKTSRLVSNLTGMLV
QPNKAIVGANAFAHESGIHQDGVLKNKLTYEIVDAETIGLSTNRITLGKLSGRNAFRTRL
QELGYDLGEDDLNRAFLRFKELADKKREVTDRDLEAIVNDETQQAPELFKLELVQVSAGD
HARPTATVTLRTPEGEELTDAAIGTGPVDAIYRAINRVVNIPNELIEFSVKSVTAGIDAI
GEVTIRLRHEDRIFSGHSANTDILVASAQAYIHALNRLAEALQKDKPLHPQEPIVAGMGR

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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