GapMind for Amino acid biosynthesis


Alignments for a candidate for dapH in Shewanella sp. ANA-3

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate 7025668 Shewana3_2818 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase (RefSeq)

Query= curated2:Q8TY70
         (245 letters)

          Length = 274

 Score =  104 bits (259), Expect = 2e-27
 Identities = 71/187 (37%), Positives = 98/187 (52%), Gaps = 34/187 (18%)

           VPL  A+Y E     E +R+ P A +R+   +GK  V +M + +N+GA + +GTMVD  A

            VGS A++GKNVH+  G  I GVLEP  A P +IED+  IGA + I+EGV V +G+V++ 

Query: 204 GAVVTED---------------VPPSKVVAG------------VPARVVKDVDKKTEAKT 236
           G  + +                VP   VV                A +VK VD KT  K 

Query: 237 QIVDALR 243
            I + LR
Sbjct: 265 GINELLR 271

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: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 245
Length of database: 274
Length adjustment: 24
Effective length of query: 221
Effective length of database: 250
Effective search space:    55250
Effective search space used:    55250
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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