Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate CCNA_01800 CCNA_01800 pyruvate dehydrogenase E1 component beta subunit
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Caulo:CCNA_01800 Length = 450 Score = 257 bits (657), Expect = 3e-73 Identities = 136/315 (43%), Positives = 194/315 (61%), Gaps = 1/315 (0%) Query: 8 DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67 DA+ AM EEM RD RVF++GE+V + G +K + L ++FG+ RV+DTP+ E AG+G Sbjct: 132 DALRDAMAEEMRRDDRVFLMGEEVAQYQGAYKVSRELLQEFGDRRVIDTPITEHGFAGMG 191 Query: 68 IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127 +GAAM G++PI E +F M A++ II+ AAK Y S IV R P G Sbjct: 192 VGAAMAGLKPIVEFMTWNFAMQAIDHIINSAAKTLYMSGGQIKSSIVFRGPNGAASRVGA 251 Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVPAD 187 HSQ A + N PGLK++ P DAKGLLKAA+RD +PV+F EH+ Y + Sbjct: 252 QHSQDYAAWYGNVPGLKVIAPYDAADAKGLLKAAIRDPNPVVFLEHEMMYGHEFDIPDVE 311 Query: 188 DYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEAI 247 D+V+PIGKA V+R+G D+T++ Y V FAL+AAE LEK+GI+A VVDLRT+ P+D I Sbjct: 312 DWVVPIGKAKVRRQGSDVTLVAYSRMVGFALKAAEELEKEGIAAEVVDLRTIRPMDHATI 371 Query: 248 IEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTME 307 +E+ KT +++ V E + +E+ A I+E LDAP R+ D+P +PYA +E Sbjct: 372 LESVKKTNRLVTVEEGWGPMGVGAEIVARITEFGFDYLDAPPLRVCQEDVP-LPYAANLE 430 Query: 308 KYFMVNPDKVEAAMR 322 + + +K+ A + Sbjct: 431 ALSLPSVEKIVKAAK 445 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: 397 Number of extensions: 17 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: 450 Length adjustment: 30 Effective length of query: 297 Effective length of database: 420 Effective search space: 124740 Effective search space used: 124740 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: 50 (23.9 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