GapMind for Amino acid biosynthesis

 

Aligments for a candidate for argA in Pseudomonas simiae WCS417

Align L-amino acid N-acyltransferase MnaT; L-methionine N-acyltransferase; L-methionine sulfoximine/L-methionine sulfone N-acetyltransferase; L-phenylglycine N-acetyltransferase; EC 2.3.1.- (characterized)
to candidate GFF550 PS417_02800 acetyltransferase

Query= SwissProt::P76112
         (172 letters)



>lcl|FitnessBrowser__WCS417:GFF550 PS417_02800 acetyltransferase
          Length = 170

 Score =  224 bits (571), Expect = 6e-64
 Identities = 110/166 (66%), Positives = 124/166 (74%)

Query: 3   IRFARKADCAAIAEIYNHAVLYTAAIWNDQTVDADNRIAWFEARTLAGYPVLVSEENGVV 62
           IR A + D  AI +IYN AVL T AIWN+Q  D  NR AWF AR   GYP+LVS ENG V
Sbjct: 2   IRDATQNDLPAIRDIYNDAVLNTTAIWNEQPADLGNRQAWFSARHALGYPILVSVENGEV 61

Query: 63  TGYASFGDWRSFDGFRHTVEHSVYVHPDHQGKGLGRKLLSRLIDEARDCGKHVMVAGIES 122
           TGYASFGDWR F+GFR++VEHSVYV  D +GKGLG  L+  LI+ AR CGKHVMVA IES
Sbjct: 62  TGYASFGDWRPFEGFRYSVEHSVYVRSDQRGKGLGPLLMEALIERARACGKHVMVAAIES 121

Query: 123 QNQASLHLHQSLGFVVTAQMPQVGTKFGRWLDLTFMQLQLDERTEP 168
            NQAS+ LH+  GF+ T QMPQVG KFGRWLDLTFMQL L+   EP
Sbjct: 122 GNQASIRLHERQGFITTGQMPQVGIKFGRWLDLTFMQLALNPGAEP 167


Lambda     K      H
   0.322    0.136    0.420 

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: 117
Number of extensions: 2
Number of successful extensions: 1
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: 172
Length of database: 170
Length adjustment: 18
Effective length of query: 154
Effective length of database: 152
Effective search space:    23408
Effective search space used:    23408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 43 (21.2 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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