GapMind for Amino acid biosynthesis

 

Protein WP_011868345.1 in Methanococcus maripaludis C5

Annotation: NCBI__GCF_000016125.1:WP_011868345.1

Length: 468 amino acids

Source: GCF_000016125.1 in NCBI

Candidate for 7 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
chorismate biosynthesis asp-kinase hi aspartate kinase (EC 2.7.2.4) (characterized) 67% 99% 618.2
chorismate biosynthesis asp-kinase hi aspartate kinase, monofunctional class (EC 2.7.2.4) (TIGR00656) 100% 474
L-lysine biosynthesis asp-kinase hi aspartate kinase (EC 2.7.2.4) (characterized) 67% 99% 618.2
L-lysine biosynthesis asp-kinase hi aspartate kinase, monofunctional class (EC 2.7.2.4) (TIGR00656) 100% 474
L-methionine biosynthesis asp-kinase hi aspartate kinase (EC 2.7.2.4) (characterized) 67% 99% 618.2
L-methionine biosynthesis asp-kinase hi aspartate kinase, monofunctional class (EC 2.7.2.4) (TIGR00656) 100% 474
L-threonine biosynthesis asp-kinase hi aspartate kinase (EC 2.7.2.4) (characterized) 67% 99% 618.2
L-threonine biosynthesis asp-kinase hi aspartate kinase, monofunctional class (EC 2.7.2.4) (TIGR00656) 100% 474
L-methionine biosynthesis hom lo aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized) 39% 56% 312 aspartate kinase (EC 2.7.2.4) 67% 618.2
L-threonine biosynthesis hom lo aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized) 39% 56% 312 aspartate kinase (EC 2.7.2.4) 67% 618.2
L-lysine biosynthesis lysA lo aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized) 31% 53% 199.9 aspartate kinase (EC 2.7.2.4) 67% 618.2

Sequence Analysis Tools

View WP_011868345.1 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

MVTVMKFGGTSVGNGERIRNVAKIVVNKTNEDKDVVVVTSAMTQVTNSLVEISAQALDVR
DIAKINNFIEDLRRKHEIAIEQAIENHDIRVEVSKTIQSSINDLEKVLVGVSYLGELTPK
SKDFILSFGERLSAPILSGAIRDMGKHSLFLAGRDAGIITDDTFTCAKILRLDVADKIEP
LLKDGFIPVVTGFVAGTEEGHITTLGRGGSDYSAALVGRGLMANMVEIWTDVSGVLSADP
RMVENVKKIPKMSYIEAMELAYFGAKVLHPRTMEPVMEKKIPLRIKNTFEPENEGTLITD
SSETSNGVIKAITTIKDVILINIFGGGMVGVSGTAARIFNVLGKSNANVILITQGSSETN
ISIVIYDGELEAKKCVRELRSEFGECHLIKDISFDKDVCVVSVVGSGMKGAKGIAGKLFD
AVAESGANIKMIAQGSSETNISFVINEDKLEPCLKNLHKTFVEDDINF

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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