GapMind for Amino acid biosynthesis


Aligments for a candidate for serB in Desulfovibrio vulgaris Hildenborough

Align phosphoserine phosphatase (EC (characterized)
to candidate 208445 DVU2935 phosphoglycerate mutase

         (211 letters)

>lcl|MicrobesOnline__882:208445 DVU2935 phosphoglycerate mutase
          Length = 250

 Score = 47.8 bits (112), Expect = 2e-10
 Identities = 35/108 (32%), Positives = 53/108 (49%), Gaps = 5/108 (4%)

           M +LIL+RH +S WN   R+ G  D DLS  G+ +A   A+ +  E LD  V ++S L R

              T   + +  +     V K  R+ E  +G   G+   E   ++ ED

Lambda     K      H
   0.320    0.136    0.408 

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: 166
Number of extensions: 11
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: 211
Length of database: 250
Length adjustment: 23
Effective length of query: 188
Effective length of database: 227
Effective search space:    42676
Effective search space used:    42676
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 (21.8 bits)
S2: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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