GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Synechococcus elongatus PCC 7942

Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate Synpcc7942_2548 Synpcc7942_2548 isopropylmalate isomerase small subunit

Query= SwissProt::Q58667
         (170 letters)



>FitnessBrowser__SynE:Synpcc7942_2548
          Length = 202

 Score = 65.9 bits (159), Expect = 4e-16
 Identities = 43/120 (35%), Positives = 66/120 (55%), Gaps = 12/120 (10%)

Query: 3   IKGRAHKF-GDDVDTDAIIPGPYLRTTDPYELASHCMAGIDEN--------FPKKVKEG- 52
           + GRA    G+D+DTD IIP  +LR+     L ++    ID+         F +   +G 
Sbjct: 8   VTGRAVPLVGNDIDTDRIIPARFLRSVTFDGLGANVF--IDDRQQLQGQHPFDQAQYQGA 65

Query: 53  DVIVAGENFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEIKD 112
            V+V   NFGCGSSRE A  AI   GI+A++ +SFA IF+ N +++G+  + A    + +
Sbjct: 66  TVLVVNRNFGCGSSREHAPQAIAKWGIQAIVGESFAEIFFGNCLSLGIPCVTAGAAAVAE 125


Lambda     K      H
   0.318    0.139    0.399 

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: 75
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: 202
Length adjustment: 19
Effective length of query: 151
Effective length of database: 183
Effective search space:    27633
Effective search space used:    27633
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 (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