GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Klebsiella michiganensis M5al

Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate BWI76_RS00965 BWI76_RS00965 acetolactate synthase 2 small subunit

Query= BRENDA::P0ADG1
         (87 letters)



>FitnessBrowser__Koxy:BWI76_RS00965
          Length = 85

 Score =  124 bits (312), Expect = 2e-34
 Identities = 67/87 (77%), Positives = 74/87 (85%), Gaps = 2/87 (2%)

Query: 1  MMQHQVNVSARFNPETLERVLRVVRHRGFHVCSMNMAAASDAQNINIELTVASPRSVDLL 60
          MMQHQV + ARFNPETLERVLRVVRHRGF +C+MNM  A+DA+NINIELTVAS R V+LL
Sbjct: 1  MMQHQVALQARFNPETLERVLRVVRHRGFQICAMNMETAADARNINIELTVASQRPVELL 60

Query: 61 FSQLNKLVDVAHVAICQSTTTSQQIRA 87
          FSQL+KLVDVA V I Q   TSQQIRA
Sbjct: 61 FSQLSKLVDVACVEIQQ--PTSQQIRA 85


Lambda     K      H
   0.323    0.128    0.354 

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: 61
Number of extensions: 2
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: 87
Length of database: 85
Length adjustment: 9
Effective length of query: 78
Effective length of database: 76
Effective search space:     5928
Effective search space used:     5928
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 38 (20.7 bits)
S2: 38 (19.2 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