GapMind for Amino acid biosynthesis

 

Protein HSERO_RS07390 in Herbaspirillum seropedicae SmR1

Annotation: FitnessBrowser__HerbieS:HSERO_RS07390

Length: 359 amino acids

Source: HerbieS 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-isoleucine biosynthesis leuB hi D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized) 72% 99% 558.5 Tartrate dehydrogenase/decarboxylase; TDH; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.93; EC 4.1.1.73; EC 1.1.1.83 71% 538.9
L-leucine biosynthesis leuB hi D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized) 72% 99% 558.5 Tartrate dehydrogenase/decarboxylase; TDH; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.93; EC 4.1.1.73; EC 1.1.1.83 71% 538.9
L-lysine biosynthesis hicdh lo homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized) 38% 99% 224.2 D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) 72% 558.5

Sequence Analysis Tools

View HSERO_RS07390 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...

Sequence

MSKTHRIAVIAGDGIGQEVMPEGLRAVQAASKKFGIDIEFTHFDWAHCNYYAEHGKMMPD
DWFEQLKGFEAIYFGAVGWPATVPDHVSLWGSLLKFRRDFDLYVNLRPVRLMPGVPCPLA
NRKPGDIDFYVVRENTEGEYSSIGGRMYEGTERETVIQESVFSRKGTDRILKFAFDLAQS
RPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDKYHIDILTAHFVLNPDRFDVV
VASNLFGDILSDLGPACAGTIGIAPSANINPTRELPSLFEPVHGSAPDIFGKNIANPVAM
IWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVNGPTTPDLGGKSNTAEVGQAIAAAI

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