Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate Echvi_4039 Echvi_4039 aconitate hydratase 1
Query= SwissProt::Q9ZND9 (163 letters) >FitnessBrowser__Cola:Echvi_4039 Length = 925 Score = 49.7 bits (117), Expect = 1e-10 Identities = 26/77 (33%), Positives = 45/77 (58%) Query: 52 ILVFGRNAGLGSSREYAPEALKRLGVRAIIAKSYARIFFRNLVNLGIVPFESEEVVDALE 111 +++ G+ G GSSR++A + LG+ A+IA+SY RI NLV +G++P + E A Sbjct: 796 VVLAGKEYGSGSSRDWAAKGTTLLGIHAVIAESYERIHRSNLVGMGVLPLQFAEGQSASS 855 Query: 112 DGDEVELDLESGVLTRG 128 G + + ++ +T G Sbjct: 856 LGLDGKEEITIEGITEG 872 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: 15 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: 925 Length adjustment: 30 Effective length of query: 133 Effective length of database: 895 Effective search space: 119035 Effective search space used: 119035 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: 50 (23.9 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