GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Sinorhizobium fredii NGR234

Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_015886895.1 NGR_RS03745 aconitate hydratase AcnA

Query= SwissProt::Q9ZND9
         (163 letters)



>NCBI__GCF_000018545.1:WP_015886895.1
          Length = 880

 Score = 47.8 bits (112), Expect = 5e-10
 Identities = 20/49 (40%), Positives = 34/49 (69%)

Query: 52  ILVFGRNAGLGSSREYAPEALKRLGVRAIIAKSYARIFFRNLVNLGIVP 100
           ++V G   G+GSSR++A + +  LG RA++A S+ RI   NL+ +G++P
Sbjct: 740 VVVAGERYGMGSSRDWAAKGVSLLGTRAVLALSFERIHRSNLIGMGVLP 788


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: 287
Number of extensions: 8
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: 880
Length adjustment: 30
Effective length of query: 133
Effective length of database: 850
Effective search space:   113050
Effective search space used:   113050
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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