GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysU in Magnetospirillum magneticum AMB-1

Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA

Query= SwissProt::Q9ZND9
         (163 letters)



>NCBI__GCF_000009985.1:WP_011386009.1
          Length = 903

 Score = 50.4 bits (119), Expect = 8e-11
 Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 4/83 (4%)

Query: 52  ILVFGRNAGLGSSREYAPEALKRLGVRAIIAKSYARIFFRNLVNLGIVPFESEEVVDALE 111
           I+  G   G GSSR++A +  K LGVRA++A+S+ RI   NLV +G++P +  +   A  
Sbjct: 774 IVFAGTEYGTGSSRDWAAKGPKLLGVRAVVAQSFERIHRSNLVGMGVLPLQFRDGESAAS 833

Query: 112 DG----DEVELDLESGVLTRGEE 130
            G    +E  +   SGVL   +E
Sbjct: 834 LGIAGDEEFHVRGLSGVLRPRQE 856


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: 318
Number of extensions: 13
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: 903
Length adjustment: 30
Effective length of query: 133
Effective length of database: 873
Effective search space:   116109
Effective search space used:   116109
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