GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Methylomonas methanica MC09

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 WP_013817130.1 METME_RS23160 antibiotic acetyltransferase

Query= curated2:Q032G9
         (257 letters)



>NCBI__GCF_000214665.1:WP_013817130.1
          Length = 181

 Score = 67.8 bits (164), Expect = 1e-16
 Identities = 50/152 (32%), Positives = 75/152 (49%), Gaps = 4/152 (2%)

Query: 90  KDYTIEFEGRNSAVPLLDTRAINARIEPGAIIRDQVMI-GDNAVIMMGAIINIGAEIGEG 148
           KD   EF     A  LL T+        G  +   V+I G+N V      I   +EI   
Sbjct: 2   KDQIKEFLKACRAKYLLITKYRGTTAGKGFHVGKNVIIRGNNCVFGDYVFIGENSEIAPA 61

Query: 149 TMIDMGAVLGGRATVGKNSHI--GAGAVLAGVIEPASAEPVRVGDNVLVGANAVVIEGVQ 206
             I   A++     +  + HI    G  +     P S +   +G +VL+G  A+V+ GV 
Sbjct: 62  VTIGNYAMISSYVAITGSDHIYNKPGVAIRFSGRPDSVK-THIGHDVLIGHGAIVMRGVT 120

Query: 207 VGSGSVVAAGAIVTQDVPENVVVAGVPARTIK 238
           +G+G+V+A+GA+VT+DVP   V+ GVPA+ IK
Sbjct: 121 IGNGAVIASGAVVTKDVPAYAVMGGVPAKFIK 152


Lambda     K      H
   0.316    0.134    0.368 

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: 126
Number of extensions: 12
Number of successful extensions: 4
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: 257
Length of database: 181
Length adjustment: 22
Effective length of query: 235
Effective length of database: 159
Effective search space:    37365
Effective search space used:    37365
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: 45 (21.9 bits)

This GapMind analysis is from Apr 10 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