Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate WP_055434954.1 ASC41_RS01930 pyruvate dehydrogenase complex E1 component subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >NCBI__GCF_001418085.1:WP_055434954.1 Length = 325 Score = 283 bits (725), Expect = 3e-81 Identities = 140/324 (43%), Positives = 214/324 (66%), Gaps = 2/324 (0%) Query: 1 MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60 M + + +AI AM EEM RD ++++GE+V G +KA+ G+ ++FG +RV+DTP+AE Sbjct: 1 MKTIQFREAICEAMSEEMRRDESIYLMGEEVAEYNGAYKASKGMLDEFGAKRVIDTPIAE 60 Query: 61 SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120 AG+ IG+ M G RPI E +F + ++QII+ AAKIR S CPIV R P G Sbjct: 61 LGFAGIAIGSTMTGNRPIVEYMTFNFSLVGIDQIINNAAKIRQMSGGQLKCPIVFRGPTG 120 Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180 HSQ+ E+ FAN PGLK+V+PS PYDAKGLLKAA+RD+DPV+F E ++ Y Sbjct: 121 SAGQLGATHSQAFESWFANTPGLKVVVPSNPYDAKGLLKAAIRDDDPVIFMESEQMYG-D 179 Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVY 240 KGEVP +Y +P+G AD+KREG D+T++++G + A +AA+ L K+GIS ++DLRTV Sbjct: 180 KGEVPEGEYTIPLGVADIKREGTDVTIVSFGKIIKEAYKAADELAKEGISCEIIDLRTVR 239 Query: 241 PLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAM 300 PLDKEA++++ KT +++++ E G++ +E+ I+ LDAP+ ++ D PA Sbjct: 240 PLDKEAVLKSVKKTNRLVVLEEAWPFGNVSTELTYIVQSEAFDYLDAPVVKINTADTPA- 298 Query: 301 PYAPTMEKYFMVNPDKVEAAMREL 324 PY+P + ++ + +V A++++ Sbjct: 299 PYSPVLLAEWLPDYTEVIKAVKKV 322 Lambda K H 0.319 0.136 0.392 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: 285 Number of extensions: 9 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: 327 Length of database: 325 Length adjustment: 28 Effective length of query: 299 Effective length of database: 297 Effective search space: 88803 Effective search space used: 88803 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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