Align Homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate Dsui_2347 Dsui_2347 aconitate hydratase 1
Query= SwissProt::Q9ZND9 (163 letters) >FitnessBrowser__PS:Dsui_2347 Length = 898 Score = 50.4 bits (119), Expect = 8e-11 Identities = 38/121 (31%), Positives = 58/121 (47%), Gaps = 20/121 (16%) Query: 53 LVF-GRNAGLGSSREYAPEALKRLGVRAIIAKSYARIFFRNLVNLGIVPFESEEVVDA-- 109 LVF G G GSSR++A + + LGVRA++A+S+ RI NLV +G++P + + A Sbjct: 771 LVFAGEEYGTGSSRDWAAKGTRLLGVRAVVARSFERIHRANLVGMGVLPLQFKAGTSAAS 830 Query: 110 --LEDGDEVELDLESGVL----------TRGEER-----FALRPPPPFLLEALKEGSLLD 152 L+ + +L G L TR + R R P +E + G +L Sbjct: 831 LGLDGSEHFDLPGADGPLQAQQDLMLRITRSDGRVEQVPLLCRIDTPIEVEYFRHGGILP 890 Query: 153 Y 153 Y Sbjct: 891 Y 891 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: 898 Length adjustment: 30 Effective length of query: 133 Effective length of database: 868 Effective search space: 115444 Effective search space used: 115444 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.
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