GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Sinorhizobium fredii NGR234

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate WP_012708954.1 NGR_RS23345 acyltransferase

Query= SwissProt::O34981
         (236 letters)



>NCBI__GCF_000018545.1:WP_012708954.1
          Length = 162

 Score = 63.2 bits (152), Expect = 3e-15
 Identities = 49/164 (29%), Positives = 73/164 (44%), Gaps = 52/164 (31%)

Query: 92  ARIEPGAIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVL-----GGRATVGKNC 146
           ARI P A I D V          G  I    V+GE ++ID  V +      G  T+G+ C
Sbjct: 8   ARISPLADIEDSVR---------GTRI----VVGEASVIDSFVKIKPAGGSGDLTIGRFC 54

Query: 147 HIGAGSVLAG----------------VIEP------------------PSAKPVVIEDDV 172
           ++ +G V                      P                  PS   +V+E+DV
Sbjct: 55  YVNSGCVFYTGNGIRIADDVLIAANCTFAPVNHAFKDKGRLIREQGFEPSRGGIVVEEDV 114

Query: 173 VIGANAVVLEGVTVGKGAVVAAGAIVVNDVEPYTVVAGTPAKKI 216
            +GAN+V+L+G  + KG V+AAG+IV  +VE YT+  G P +++
Sbjct: 115 WVGANSVILDGAILRKGCVIAAGSIVRGEVEAYTICGGNPLRRL 158


Lambda     K      H
   0.313    0.134    0.364 

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: 124
Number of extensions: 9
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: 236
Length of database: 162
Length adjustment: 20
Effective length of query: 216
Effective length of database: 142
Effective search space:    30672
Effective search space used:    30672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 44 (21.6 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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