GapMind for Amino acid biosynthesis

 

Protein WP_012709542.1 in Sinorhizobium fredii NGR234

Annotation: NCBI__GCF_000018545.1:WP_012709542.1

Length: 1256 amino acids

Source: GCF_000018545.1 in NCBI

Candidate for 3 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-methionine biosynthesis metH hi methionine synthase; EC 2.1.1.13 (characterized) 62% 99% 1478.4
L-methionine biosynthesis metH hi metH: methionine synthase (EC 2.1.1.13) (TIGR02082) 100% 1739.8
L-methionine biosynthesis B12-reactivation-domain hi Met_synt_B12 (PF02965) 100% 414.3
L-methionine biosynthesis split_metH_1 lo Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized) 31% 86% 103.2 methionine synthase; EC 2.1.1.13 62% 1478.4

Sequence Analysis Tools

View WP_012709542.1 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

MSAASLFGELSPKPDGSEIFRALNQAAAERILIMDGAMGTEIQQLGFVEDHFRGERFGGC
ACHQQGNNDLLTLTQPKAIEEIHYRYALAGADILETNTFSSTRIAQADYGMEDMVYDLNR
DGARLARRAAKRAEAEDGRRRFVAGALGPTNRTASISPDVNNPGYRAVSFDDLRLAYAEQ
VRGLIDGGADIILIETIFDTLNAKAAIFATQEVFAEKKIHLPVMVSGTITDLSGRTLSGQ
TPTAFWYSVRHAAPFTIGLNCALGADAMRAHIDELSTVADTLVCAYPNAGLPNEFGRYDE
SPETMAAQIEAFVRDGLVNIVGGCCGSTPAHIRAIAEAVQKYPPRQVPEIERRMRLSGLE
PFTLTDEIPFVNVGERTNVTGSAKFRKLITTGDYAAALDVARDQVANGAQIIDINMDEGL
IDSTRAMVEFLNLVASEPDIACVPVMIDSSKWEVIEAGLKCVQGKALVNSISLKEGEEAF
LHHARLVRAYGAAVVVMAFDEKGQADSRARKVEICRRAYRLLTEEVGFPPEDIIFDPNIF
AVATGIDEHNNYGVDFIEATHEIIATLPHVHVSGGVSNLSFSFRGNEPVREAMHAVFLYH
AIQAGMDMGIVNAGQLAVYDAIDPELREACEDVVLNRRPDATERLLEIAERYRGQGGAQG
KEKDLAWRQWPVAKRLEHALVNGITEFIEADTEEARLAAERPLHVIEGPLMAGMNVVGDL
FGAGKMFLPQVVKSARVMKQAVAVLLPYMEAEKLANGGEGTRASAGKILMATVKGDVHDI
GKNIVGVVLACNNYEIIDLGVMVPSAKILEVARQEKVDAIGLSGLITPSLDEMVHVASEL
EREGFDIPLLIGGATTSRVHTAVKINPRYGLGQTVYVTDASRAVGVVSSLLSPEARDGYK
ETVRAEYLKVADAHARNEAEKRRLPLSQARANASKLDWDAYRPKTPSFLGTRVFESWDLA
ELARYIDWTPFFQTWELKGVYPRILDDEHQGPAARQLFADAQAMLEKIIAEKWFAPKAVV
GFWPAGSAGDDIRLFTDERRERELATFFTLRQQLAKRDGRPNVALADFVAPVESGRRDYL
GGFVVTAGIEEVAIAERFERANDDYSSILVKALADRFAEAFAERMHEYVRKELWGYAPDE
SFTPQELIAEPYTGIRPAPGYPAQPDHTEKETLFRLLDAEAAIGVRLTENYAMWPGSSVS
GLYVGHPDAYYFGVAKIERDQVEDYATRKRMGVREVERWLSPILNYVPMRETQAAE

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