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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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