Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate Echvi_2060 Echvi_2060 3-isopropylmalate dehydratase, small subunit
Query= SwissProt::Q58667 (170 letters) >FitnessBrowser__Cola:Echvi_2060 Length = 197 Score = 71.2 bits (173), Expect = 1e-17 Identities = 45/134 (33%), Positives = 68/134 (50%), Gaps = 17/134 (12%) Query: 12 DDVDTDAIIPGPYLRTTDPYELASHCMAGI---DENFPKK-------VKEGDVIVAGENF 61 ++VDTD IIP +L+ T+ + E PK G V+VAG+NF Sbjct: 19 ENVDTDQIIPARFLKATERKGFGDNLFRDWRYDSEGNPKADFVLNDATYSGKVLVAGKNF 78 Query: 62 GCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTD-------EIKDGD 114 G GSSRE A AI G + V++ FA IF NA+N+G++P+ + E++ Sbjct: 79 GSGSSREHAAWAIYDYGFRCVVSSFFADIFKNNALNIGILPVTVTPEFLEEIFAEVEKDP 138 Query: 115 IVEIDLDKEEIVIT 128 E+++D E+ IT Sbjct: 139 ATEVEVDIEKQTIT 152 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: 96 Number of extensions: 7 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: 197 Length adjustment: 19 Effective length of query: 151 Effective length of database: 178 Effective search space: 26878 Effective search space used: 26878 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