GapMind for Amino acid biosynthesis


Alignments for a candidate for trpD_1 in Sinorhizobium meliloti 1021

Align Glutamine amidotransferase of anthranilate synthase (characterized, see rationale)
to candidate SMc00394 SMc00394 GMP synthase

Query= uniprot:B8DM46_DESVM
         (192 letters)

          Length = 520

 Score = 53.9 bits (128), Expect = 5e-12
 Identities = 37/122 (30%), Positives = 55/122 (45%), Gaps = 7/122 (5%)

           +PV G+C G Q +    G  V+ G     G+          LF G+ S   +G  H + +

              +R    P+   V A +       +    R +  VQFHPE V TPDG +++ANF   +

Query: 190 AG 191
Sbjct: 197 AG 198

Lambda     K      H
   0.325    0.142    0.453 

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: 293
Number of extensions: 23
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: 192
Length of database: 520
Length adjustment: 27
Effective length of query: 165
Effective length of database: 493
Effective search space:    81345
Effective search space used:    81345
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 (21.5 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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