Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate BPHYT_RS29355 BPHYT_RS29355 pyruvate dehydrogenase subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__BFirm:BPHYT_RS29355 Length = 334 Score = 277 bits (709), Expect = 2e-79 Identities = 145/328 (44%), Positives = 211/328 (64%), Gaps = 13/328 (3%) Query: 4 MSYIDAINLAMKEEMERDSRVFVLGED-------VGRK---GGVFKATAGLYEQFGEERV 53 +++ AIN A+ +EM RD V V+GED G + GGV T GL+ ++ RV Sbjct: 5 ITFSQAINEALSQEMARDETVIVMGEDNAGGAGSPGEQDAWGGVLGVTKGLFHKY-PGRV 63 Query: 54 MDTPLAESAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPI 113 +DTPL+E G +GAA GMRP+AE+ F DF+ +QI ++AAK RY P+ Sbjct: 64 LDTPLSEGGYIGAAVGAAACGMRPVAELMFIDFMGVCFDQIFNQAAKFRYMFGGKAVTPV 123 Query: 114 VVRAPYGGGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEH 173 V+RA G G+ A HSQ + ++F + PGLK+V PSTPYDAKGLL A+RD DPV+F EH Sbjct: 124 VIRAMQGAGLRAAAQHSQMLTSLFTHIPGLKVVCPSTPYDAKGLLIQAIRDNDPVIFCEH 183 Query: 174 KRAYRLIKGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHV 233 K Y +G+VP + Y +P G+A+V R+GDD T+ITYG VH+A +AAE+L KDGI V Sbjct: 184 KLLYSR-EGDVPEESYAIPFGEANVVRDGDDATIITYGRMVHYATEAAEKLAKDGIQVEV 242 Query: 234 VDLRTVYPLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLA 293 +DLRT PLD+E I+E+A++TG+V++V E SI ++++A+I++ L API+ + Sbjct: 243 IDLRTTSPLDEETILESANRTGRVVVVDEANPRCSIATDISALIAQRAFHSLKAPIEMVT 302 Query: 294 GPDIPAMPYAPTMEKYFMVNPDKVEAAM 321 P PA P+A +E ++ + ++ A+ Sbjct: 303 APHTPA-PFAGVLEDMYIPSAAQIAEAV 329 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: 293 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: 327 Length of database: 334 Length adjustment: 28 Effective length of query: 299 Effective length of database: 306 Effective search space: 91494 Effective search space used: 91494 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: 49 (23.5 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