Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate WP_041750801.1 BBTA_RS20845 pyruvate dehydrogenase complex E1 component subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >NCBI__GCF_000015165.1:WP_041750801.1 Length = 465 Score = 277 bits (708), Expect = 4e-79 Identities = 144/318 (45%), Positives = 204/318 (64%), Gaps = 3/318 (0%) Query: 8 DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67 +A+ AM EEM RD VF++GE+V G +K T GL ++FG RVMDTP+ E AG+G Sbjct: 147 EALRDAMAEEMRRDGDVFIMGEEVAEYQGAYKVTQGLLQEFGARRVMDTPITEHGFAGIG 206 Query: 68 IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127 +GAAM G++PI E +F M A++QII+ AAK Y S C IV R P G A Sbjct: 207 VGAAMAGLKPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGCSIVFRGPNGAAARVAA 266 Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVP-A 186 HSQ + +++ PGLK+V P + DAKGLLKAA+RD +PV+F E++ Y GEVP Sbjct: 267 QHSQDYSSWYSHIPGLKVVAPYSAADAKGLLKAAIRDPNPVIFLENEVLYG-HSGEVPKL 325 Query: 187 DDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEA 246 DDYV+PIGKA + R G D+T+I++ + +AL+AA+ L K+GI A V+DLRT+ P+D + Sbjct: 326 DDYVIPIGKARIARSGKDVTIISWSNGMTYALKAADELAKEGIEAEVIDLRTLRPMDTDT 385 Query: 247 IIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTM 306 II + KTG+ + V E + + +E+AA I EH LDAP+ R++G D+P MPYA + Sbjct: 386 IIASVKKTGRAVTVEEGWAQSGVGAEIAARIMEHAFDYLDAPVTRVSGKDVP-MPYAANL 444 Query: 307 EKYFMVNPDKVEAAMREL 324 EK + + +V A + + Sbjct: 445 EKLALPSAAEVVQAAKSV 462 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: 411 Number of extensions: 17 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: 465 Length adjustment: 30 Effective length of query: 297 Effective length of database: 435 Effective search space: 129195 Effective search space used: 129195 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 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