GapMind for Amino acid biosynthesis


Alignments for a candidate for dapH in Klebsiella michiganensis M5al

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate BWI76_RS00615 BWI76_RS00615 galactoside O-acetyltransferase

Query= curated2:B1IMX1
         (236 letters)

          Length = 196

 Score = 66.6 bits (161), Expect = 3e-16
 Identities = 31/67 (46%), Positives = 43/67 (64%)

           S P  IED V +G   +I  GV IGK SV+ AGS+V   +P NVV AG P +I++E+  +

Query: 224 TKDKTKL 230
            K+K +L
Sbjct: 187 DKNKYQL 193

 Score = 26.2 bits (56), Expect = 5e-04
 Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 21/83 (25%)

           D+     +     II D V +G       G +IN G  IG+ +++   +VV        N

             + A  V AGV       PC I
Sbjct: 164 RSIPANVVAAGV-------PCRI 179

Lambda     K      H
   0.315    0.136    0.375 

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: 136
Number of extensions: 10
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 236
Length of database: 196
Length adjustment: 22
Effective length of query: 214
Effective length of database: 174
Effective search space:    37236
Effective search space used:    37236
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: 42 (22.0 bits)
S2: 45 (21.9 bits)

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