GapMind for Amino acid biosynthesis


Aligments for a candidate for lysU in Pedobacter sp. GW460-11-11-14-LB5

Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC (characterized)
to candidate CA265_RS15840 CA265_RS15840 3-isopropylmalate dehydratase small subunit

Query= SwissProt::Q58667
         (170 letters)

>lcl|FitnessBrowser__Pedo557:CA265_RS15840 CA265_RS15840
           3-isopropylmalate dehydratase small subunit
          Length = 195

 Score = 72.8 bits (177), Expect = 3e-18
 Identities = 49/135 (36%), Positives = 71/135 (52%), Gaps = 19/135 (14%)

           +++DTD IIP  +L+ T       +        ++N PK           G V+VAG+NF

           GCGSSRE A  AI+  G  AVI+  FA IF  NA+N GL+PI      +A   +  D + 

Query: 115 --IVEIDLDKEEIVI 127
              +E+DL+ + + I

Lambda     K      H
   0.318    0.139    0.399 

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: 111
Number of extensions: 4
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: 170
Length of database: 195
Length adjustment: 19
Effective length of query: 151
Effective length of database: 176
Effective search space:    26576
Effective search space used:    26576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 44 (21.6 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, the preprint 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