Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate AO353_19955 AO353_19955 pyruvate dehydrogenase
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19955 Length = 326 Score = 245 bits (626), Expect = 9e-70 Identities = 135/322 (41%), Positives = 199/322 (61%), Gaps = 3/322 (0%) Query: 5 SYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIA 64 +Y +A+ A++E ++RD RVF++GEDVGR GG + + GL E FG ER+ D PL+E Sbjct: 6 TYREALREALREALQRDPRVFLMGEDVGRYGGSYAVSLGLLEAFGPERIRDAPLSELGFV 65 Query: 65 GVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVH 124 G GIGAA+ GMRPI E+ +F + A++ +++ AA +R+ S +S P+VVR G G Sbjct: 66 GAGIGAALGGMRPIVEIMTVNFSLLALDPLMNTAAALRHMSGGQFSVPLVVRMATGAGRQ 125 Query: 125 GALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEV 184 A HS S+E +A+ PGLKI+ P+T DA+G+L A+ D DPVL FEH + Y L +GE Sbjct: 126 LAAQHSHSLEGWYAHIPGLKILAPATVEDARGMLWPALLDPDPVLIFEHAQLYSL-EGET 184 Query: 185 PADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDK 244 + L I A V+R G D+T+I YG + AL AAE+L +GI V+DLR + PLD Sbjct: 185 -GEWQTLDISSAKVRRAGKDLTLIAYGGTLGKALAAAEQLAGEGIDCEVIDLRVLRPLDD 243 Query: 245 EAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAP 304 + I+ + KT + L+V E + GS+ +E+ I E F+LDAP R+ ++P +PY Sbjct: 244 QTIMASVCKTRRALVVDEGWRSGSLSAEIITRIVEQGFFELDAPPSRVCSAEVP-IPYPR 302 Query: 305 TMEKYFMVNPDKVEAAMRELAE 326 +E+ + + AA REL + Sbjct: 303 HLEEAALPQVSTIVAAARELCQ 324 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: 244 Number of extensions: 10 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: 326 Length adjustment: 28 Effective length of query: 299 Effective length of database: 298 Effective search space: 89102 Effective search space used: 89102 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