GapMind for Amino acid biosynthesis


Alignments for a candidate for dapH in Pseudomonas simiae WCS417

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate GFF4535 PS417_23210 serine acetyltransferase

Query= curated2:Q836H8
         (233 letters)

          Length = 260

 Score = 58.9 bits (141), Expect = 9e-14
 Identities = 40/124 (32%), Positives = 61/124 (49%), Gaps = 4/124 (3%)

           + G  ++ GA VG    ID  MG V+G  A +G    +  G  L G           + +

            VV+GA A VL    VG GA V + AVV + VP    V G+P ++I   ++ D+ ++K +

Query: 226 ILEE 229
            + E
Sbjct: 183 AMAE 186

Lambda     K      H
   0.317    0.136    0.381 

Lambda     K      H
   0.267   0.0410    0.140 

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 167
Number of extensions: 12
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 233
Length of database: 260
Length adjustment: 24
Effective length of query: 209
Effective length of database: 236
Effective search space:    49324
Effective search space used:    49324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)

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



Related tools

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