Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate BPHYT_RS29415 BPHYT_RS29415 3-hydroxyisobutyrate dehydrogenase
Query= metacyc::MONOMER-11664 (295 letters) >FitnessBrowser__BFirm:BPHYT_RS29415 Length = 296 Score = 165 bits (418), Expect = 1e-45 Identities = 100/288 (34%), Positives = 151/288 (52%), Gaps = 8/288 (2%) Query: 3 IAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELVIT 62 + IGLG MG +AR+L++AG +++ DL VL GG +P + A E+V+T Sbjct: 5 VGVIGLGAMGLGVARSLLRAGLKVHACDLRSEVLNAFVAEGGVGCATPAELGAQCEVVVT 64 Query: 63 MLPAAAHVRSVYLNDDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPVSG 122 ++ AA +V + G +A ++PG + +T+ P A + K A G+ M DAPVSG Sbjct: 65 LVVNAAQTEAVLFGEQGAVAAMKPGRVVIASATVAPDFAIQLGKRIEAAGLQMLDAPVSG 124 Query: 123 GTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCG-EVGTGQIAKICNNLLLGISM 181 G AA+G +T M A +A+ + VL M + G E G G KI N LL G+ + Sbjct: 125 GAARAASGEMTMMTSGPAAAYAACEDVLAAMAGKVYRLGSEHGAGSKVKIINQLLAGVHI 184 Query: 182 IGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGAE 241 +EAMALG G+D L +I S G W + N P I+ + YT + Sbjct: 185 AVAAEAMALGLREGVDPDALYEVITHSAGNSWMFE--NRVPHIL-----NGDYTPLSAVD 237 Query: 242 LMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVE 289 + +KDLGL + AR++ P+ L A A Q++ S G GG+D SA+++ Sbjct: 238 IFVKDLGLVLDTARRSKFPLPLSAAAHQMFMMASTAGHGGEDDSAVIK 285 Lambda K H 0.317 0.134 0.386 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: 232 Number of extensions: 15 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: 295 Length of database: 296 Length adjustment: 26 Effective length of query: 269 Effective length of database: 270 Effective search space: 72630 Effective search space used: 72630 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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