Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate WP_011906984.1 SARO_RS19585 TPP-dependent acetoin dehydrogenase complex, E1 protein subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >NCBI__GCF_000013325.1:WP_011906984.1 Length = 327 Score = 224 bits (571), Expect = 2e-63 Identities = 131/323 (40%), Positives = 191/323 (59%), Gaps = 4/323 (1%) Query: 4 MSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAI 63 M Y A+ L + EEM RD +F++G+ V GG F GL +FG +RV+D +AE+ Sbjct: 6 MGYNAAMGLGLVEEMRRDDSIFIMGQGVVT-GGWFGMEKGLVAEFGNDRVLDCGIAEAFE 64 Query: 64 AGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGV 123 AG+ GAA+ GM+P+ M F DF + A ++I + AK RY D V+ P G Sbjct: 65 AGLAAGAAIAGMKPVINMGFGDFALIAGDEIYHKLAKWRYMHGLDVPMTAVIIFPIGAMG 124 Query: 124 HGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGE 183 HS E + + PGLK+V+PST DAKGL+KAA+R+ +PVL F + +G+ Sbjct: 125 GAGPEHSSCTEVLGMHFPGLKVVVPSTAEDAKGLMKAALREPNPVL-FHSVQGLGWSRGD 183 Query: 184 VPAD-DYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPL 242 VP D D+V+PIGKA +R G D++++TYG +L+AAERL +GI A V+DLR++ PL Sbjct: 184 VPLDPDFVVPIGKAVTRRRGADLSIVTYGSMAPRSLKAAERLASEGIDAEVIDLRSLVPL 243 Query: 243 DKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPY 302 D E ++E+ S+T + ++V E + +E+AA I E FDLDAP+ RL D P Sbjct: 244 DWEHVLESVSRTHRAMVVHEAFRTAGPGAEIAAQIQERAFFDLDAPVLRLGARDFPLCQN 303 Query: 303 APTMEKYFMVNPDKVEAAMRELA 325 A +E+ + + D + A R LA Sbjct: 304 A-DLEQAAIPSVDAIAAEARRLA 325 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: 305 Number of extensions: 16 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: 327 Length of database: 327 Length adjustment: 28 Effective length of query: 299 Effective length of database: 299 Effective search space: 89401 Effective search space used: 89401 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