Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate RR42_RS10660 RR42_RS10660 pyruvate dehydrogenase
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Cup4G11:RR42_RS10660 Length = 323 Score = 249 bits (636), Expect = 6e-71 Identities = 136/324 (41%), Positives = 201/324 (62%), Gaps = 3/324 (0%) Query: 1 MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60 MS +SY DA+ A++E + D RVF++GEDVGR GG + + GL +FG ERV DTPL+E Sbjct: 1 MSRLSYRDALREALREALANDPRVFLMGEDVGRYGGTYAVSKGLLAEFGPERVRDTPLSE 60 Query: 61 SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120 G GIGAA+ GMRPI E+ +F + A++QI++ AA + S +S P+VVR G Sbjct: 61 LGFTGAGIGAALGGMRPIVEVMTVNFSLLALDQIVNTAALYHHMSGGQFSVPLVVRMATG 120 Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180 G A HS S E +A PG+K++ P+T DA+ +L A+ D DPVL FEH Y + Sbjct: 121 AGRQVAAQHSHSFEGWYAGIPGVKVLAPATIEDARHMLAPALADPDPVLIFEHAALYNM- 179 Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVY 240 + E+P D + I A V+REG D+ ++ YG + ALQAA+ L GI+A V+DLR + Sbjct: 180 EDELP-DVSGVDIRSAKVRREGKDVAIVAYGGTLAKALQAADTLAAKGIAAEVIDLRVLR 238 Query: 241 PLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAM 300 PLD I+ + +K + ++V E + GS+ +EV A I E ++LDAP+ R+ ++P + Sbjct: 239 PLDDATIMASVAKCRRAVIVDEGWRSGSLAAEVMARIVEQVFYELDAPVARVCSEEVP-I 297 Query: 301 PYAPTMEKYFMVNPDKVEAAMREL 324 PYA ME+ + K+ AA+++L Sbjct: 298 PYARHMEEAALPQAGKIVAAVKQL 321 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: 269 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: 323 Length adjustment: 28 Effective length of query: 299 Effective length of database: 295 Effective search space: 88205 Effective search space used: 88205 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 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