Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate CA265_RS18860 CA265_RS18860 alpha-ketoacid dehydrogenase subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Pedo557:CA265_RS18860 Length = 328 Score = 270 bits (689), Expect = 5e-77 Identities = 136/325 (41%), Positives = 210/325 (64%), Gaps = 3/325 (0%) Query: 1 MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60 M + + +A+ AM EEM +D RVF+LGE+V G +K + G+ ++FG +R++DTP+AE Sbjct: 1 MREIQFREALREAMSEEMRKDDRVFLLGEEVAEYNGAYKVSQGMLDEFGAKRIIDTPIAE 60 Query: 61 SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120 AG+ GAA G+ PI E +F + A++QII+ AAKI S +SCP+V R P G Sbjct: 61 LGFAGIATGAATAGLIPIVEFMTFNFSLVAIDQIINGAAKILSMSGGQFSCPMVFRGPTG 120 Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180 HSQ+ E FAN PGLK+V+P+TPYDAKGLLK ++ D+DPV+F E + Y Sbjct: 121 NAGQLGAQHSQNFENWFANTPGLKVVVPATPYDAKGLLKQSIIDQDPVIFMESEVMYG-D 179 Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYG-LCVHFALQAAERLEKDGISAHVVDLRTV 239 KG+VPA++Y + +GKA+V ++G D+T++T+G + A E L K+GI+ V+DLRTV Sbjct: 180 KGDVPAEEYYIELGKANVTKQGTDVTIVTFGKMLTRVVNPAVEELTKEGINVEVIDLRTV 239 Query: 240 YPLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPA 299 P+D + II + KT ++++V E S+ E+A ++ +H LDAP+ R+ D+P Sbjct: 240 RPIDYDTIIASVKKTNRLVVVEEAWPLASLSGEIAFMVQKHAFDYLDAPVLRITCADVP- 298 Query: 300 MPYAPTMEKYFMVNPDKVEAAMREL 324 +PY+PT+ + N ++V A++E+ Sbjct: 299 LPYSPTLIAASLPNAERVVKAVKEV 323 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: 281 Number of extensions: 9 Number of successful extensions: 4 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: 328 Length adjustment: 28 Effective length of query: 299 Effective length of database: 300 Effective search space: 89700 Effective search space used: 89700 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