GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Pseudomonas stutzeri RCH2

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 GFF855 Psest_0869 Acetyltransferase (isoleucine patch superfamily)

Query= curated2:C4L2D4
         (235 letters)



>FitnessBrowser__psRCH2:GFF855
          Length = 182

 Score = 67.0 bits (162), Expect = 2e-16
 Identities = 40/108 (37%), Positives = 58/108 (53%), Gaps = 20/108 (18%)

Query: 123 IGDGSMVDMNAVIGARGTLGKNVHLGAGAVVAGVLEPPSKD----------------PVI 166
           +G+G+ ++ N VI         VH+GAGA +   ++  + D                P+ 
Sbjct: 78  LGEGAFLNFNCVI----LDVVEVHIGAGAQIGPAVQLYTADHPRDPEARRSGVEFGRPIN 133

Query: 167 IEDGVMIGANAVILEGVRVGENAVVAAGSVVTQDVPPGVVVAGTPARI 214
           I   V +G  A+IL GV +G++AV+ AGSVVT+DVP G  V G PARI
Sbjct: 134 IGRNVWVGGGAIILPGVTIGDDAVIGAGSVVTRDVPAGATVVGNPARI 181


Lambda     K      H
   0.315    0.133    0.360 

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: 83
Number of extensions: 7
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: 235
Length of database: 182
Length adjustment: 21
Effective length of query: 214
Effective length of database: 161
Effective search space:    34454
Effective search space used:    34454
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

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