GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Pseudomonas fluorescens FW300-N1B4

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC 2.3.1.89; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate Pf1N1B4_867 Serine acetyltransferase (EC 2.3.1.30)

Query= curated2:A7HJ58
         (249 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_867
          Length = 258

 Score = 65.9 bits (159), Expect = 8e-16
 Identities = 42/122 (34%), Positives = 61/122 (50%), Gaps = 2/122 (1%)

Query: 125 MMGAVINLGAIIGEGTMID--MNTVIGARARIGKYCHIGAGSVIAGVVEPPSAQPVIIED 182
           + G  I+ GA +G    ID  M  VIG  A IG    +  G  + G       +   +ED
Sbjct: 63  LTGIEIHPGAKVGRRFFIDHGMGIVIGETAEIGNDVTLYQGVTLGGTSWNKGKRHPTLED 122

Query: 183 NVVIGANAVILEGVRVGEHSVVAAGAVVVEDVPPYTVVAGVPAKVIKKVDEKTISKTQLI 242
            VV+GA A +L    VG  + V + AVV + VPP   V G+P ++I K DE+  +K + +
Sbjct: 123 GVVVGAGAKVLGPFTVGAGAKVGSNAVVTKAVPPGATVVGIPGRIIVKSDEEQDAKRKAL 182

Query: 243 EE 244
            E
Sbjct: 183 AE 184


Lambda     K      H
   0.318    0.137    0.375 

Gapped
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: 157
Number of extensions: 8
Number of successful extensions: 2
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: 249
Length of database: 258
Length adjustment: 24
Effective length of query: 225
Effective length of database: 234
Effective search space:    52650
Effective search space used:    52650
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: 47 (22.7 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