Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate 351387 BT1859 3-isopropylmalate dehydratase small subunit (NCBI ptt file)
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__Btheta:351387 Length = 200 Score = 60.1 bits (144), Expect = 2e-14 Identities = 44/138 (31%), Positives = 65/138 (47%), Gaps = 19/138 (13%) Query: 12 DDVDTDAIIPGPYLRTTDPYE------LASHCMAGIDENFPKK------VKEGDVIVAGE 59 ++VDTD IIP +L+ T E L D + K G ++VAG+ Sbjct: 19 ENVDTDQIIPARFLKATTREEKFFGDNLFRDWRYNADGSLNKDFVLNDPTYSGQILVAGK 78 Query: 60 NFGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANT-------DEIKD 112 NFG GSSRE A AI G + V++ FA I N +N ++P++ D I Sbjct: 79 NFGSGSSREHAAWAIAGYGFRVVVSSFFADIHKNNELNNFVLPVVVTEGFLQELFDSIFA 138 Query: 113 GDIVEIDLDKEEIVITNK 130 +E++++ E ITNK Sbjct: 139 DPKMEVEVNLPEQTITNK 156 Lambda K H 0.318 0.139 0.399 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: 106 Number of extensions: 8 Number of successful extensions: 2 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: 170 Length of database: 200 Length adjustment: 19 Effective length of query: 151 Effective length of database: 181 Effective search space: 27331 Effective search space used: 27331 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 44 (21.6 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