Align Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 (characterized)
to candidate WP_010876462.1 MTH_RS03905 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q58667 (170 letters) >NCBI__GCF_000008645.1:WP_010876462.1 Length = 170 Score = 153 bits (386), Expect = 2e-42 Identities = 86/157 (54%), Positives = 104/157 (66%), Gaps = 2/157 (1%) Query: 2 IIKGRAHKFGDDVDTDAIIPGPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGENF 61 II+GR +FGD+VDTD IIPG YLRT ELASH M G F +V++GD+IVAG NF Sbjct: 4 IIRGRVWRFGDNVDTDMIIPGRYLRTFSLDELASHVMEGARPEFASQVRKGDIIVAGRNF 63 Query: 62 GCGSSREQAVIAIKYCGIKAVIAKSFARIFYRNAINVGLIPIIANTDEIKDGDIVEIDLD 121 GCGSSREQA +A+K+ G+ A+IA+SFARIFYRNAIN+GL I+A D DGD V IDL Sbjct: 64 GCGSSREQAPVALKHAGVVAIIAESFARIFYRNAINIGLPVIMAKVD-ADDGDEVSIDLR 122 Query: 122 KEEIVITNKNKTIKCETPKGLEREILAAGGLVN-YLK 157 +I + + IL GGLVN YLK Sbjct: 123 SGQIRNLTAGSEYRMKPFNDYMLSILEDGGLVNHYLK 159 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: 129 Number of extensions: 3 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: 170 Length adjustment: 18 Effective length of query: 152 Effective length of database: 152 Effective search space: 23104 Effective search space used: 23104 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