GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Azospirillum brasilense Sp245

Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase

Query= SwissProt::Q9ZND9
         (163 letters)



>FitnessBrowser__azobra:AZOBR_RS02985
          Length = 896

 Score = 53.9 bits (128), Expect = 7e-12
 Identities = 30/78 (38%), Positives = 48/78 (61%), Gaps = 9/78 (11%)

Query: 52  ILVFGRNAGLGSSREYAPEALKRLGVRAIIAKSYARIFFRNLVNLGIVPFESEE------ 105
           +++ G+  G GSSR++A +  K LG+RA+IA+S+ RI   NLV +GI+P + ++      
Sbjct: 769 VVIAGKEYGTGSSRDWAAKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRND 828

Query: 106 -VVDALE--DGDEVELDL 120
             +D  E  D D +E DL
Sbjct: 829 LALDGTETFDIDGIEQDL 846


Lambda     K      H
   0.322    0.144    0.432 

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: 277
Number of extensions: 10
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: 163
Length of database: 896
Length adjustment: 30
Effective length of query: 133
Effective length of database: 866
Effective search space:   115178
Effective search space used:   115178
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: 49 (23.5 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