Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate WP_011869007.1 MMARC5_RS06370 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q58667 (170 letters) >NCBI__GCF_000016125.1:WP_011869007.1 Length = 161 Score = 218 bits (555), Expect = 4e-62 Identities = 102/162 (62%), Positives = 130/162 (80%), Gaps = 4/162 (2%) Query: 1 MIIKGRAHKFGDDVDTDAIIPGPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGEN 60 M I G+ H FGDD+DTDAIIPG YL+TTD YELASHCMAGIDE+FP+ VKEGD +VAGEN Sbjct: 1 MKITGKVHVFGDDIDTDAIIPGAYLKTTDEYELASHCMAGIDEDFPEMVKEGDFLVAGEN 60 Query: 61 FGCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIAN--TDEIKDGDIVEI 118 FGCGSSREQA IAIKYCGIKA+I +SFARIFYRN IN+G+ PI + +KDGD++E+ Sbjct: 61 FGCGSSREQAPIAIKYCGIKAIIVESFARIFYRNCINLGVFPIECKGISKHVKDGDLIEL 120 Query: 119 DLDKEEIVITNKNKTIKCETPKGLEREILAAGGLVNYLKKRK 160 DL+ +++++ K+K + C P G ++I+ GGL+NY KK+K Sbjct: 121 DLENKKVIL--KDKVLDCHIPTGTAKDIMDEGGLINYAKKQK 160 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: 158 Number of extensions: 5 Number of successful extensions: 3 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: 161 Length adjustment: 18 Effective length of query: 152 Effective length of database: 143 Effective search space: 21736 Effective search space used: 21736 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: 43 (21.2 bits)
This GapMind analysis is from Apr 10 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