GapMind for Amino acid biosynthesis


Alignments for a candidate for argA in Caulobacter crescentus NA1000

Align Amino-acid acetyltransferase; N-acetylglutamate synthase; AGS; NAGS; EC (characterized)
to candidate CCNA_02074 CCNA_02074 IAA acetyltransferase

Query= SwissProt::O33289
         (174 letters)

          Length = 156

 Score = 43.9 bits (102), Expect = 1e-09
 Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 10/95 (10%)

           L T+ +A  +F+ A   D    + G GA+  L    GEI+++    A  G G+G A++D 

           L   AR L LQR+ + T   +FF       AR+GF

Lambda     K      H
   0.325    0.141    0.424 

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: 67
Number of extensions: 4
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: 174
Length of database: 156
Length adjustment: 18
Effective length of query: 156
Effective length of database: 138
Effective search space:    21528
Effective search space used:    21528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 43 (21.2 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