Align 3-methyl-2-oxobutanoate dehydrogenase subunit alpha; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit alpha; BCKADH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_011781241.1 MVAN_RS20480 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000015305.1:WP_011781241.1 Length = 361 Score = 546 bits (1406), Expect = e-160 Identities = 259/348 (74%), Positives = 291/348 (83%) Query: 18 EPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYTPCR 77 EP+QLV PDG PT E RY RDLP ETL WLYE MVVTRELDTEFVNLQRQGELAL+ CR Sbjct: 12 EPIQLVAPDGAPTPESRYRRDLPPETLAWLYESMVVTRELDTEFVNLQRQGELALFASCR 71 Query: 78 GQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCCAP 137 GQEAAQ+GAAACLRKTDWLFPQYRELG +LVR I P +G WRG WHGGL FT +C AP Sbjct: 72 GQEAAQIGAAACLRKTDWLFPQYRELGAFLVRAIAPAQLGALWRGRWHGGLGFTDRCVAP 131 Query: 138 MSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVFYV 197 +S+PIGT LHAVGAAMAAQRL EDSVTVAFLGDGATSEGD HEALN AAVF PCVF+V Sbjct: 132 VSIPIGTHGLHAVGAAMAAQRLGEDSVTVAFLGDGATSEGDAHEALNLAAVFGAPCVFFV 191 Query: 198 QNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDGPT 257 QNNQWAIS+PV RQ A P++AH+AIGYGMPG+RVDGNDVLAC+AVM +AAARAR G GPT Sbjct: 192 QNNQWAISVPVERQHAGPTLAHRAIGYGMPGVRVDGNDVLACFAVMEQAAARAREGGGPT 251 Query: 258 LIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVTAR 317 IEAVTYR+GPHTT+DDPTRYRS EEV+ W DPI RYRTYL+ G+W+QRLEE+V R Sbjct: 252 FIEAVTYRMGPHTTSDDPTRYRSDEEVEHWRARDPIARYRTYLEHTGVWTQRLEERVAHR 311 Query: 318 AKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAELAR 365 ++ +R+ELRDAV PD D+ EVF TVY +ITP L QR++L AELA+ Sbjct: 312 SQRLRAELRDAVITEPDIDIGEVFDTVYHDITPDLARQRDELLAELAK 359 Lambda K H 0.320 0.134 0.413 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: 509 Number of extensions: 12 Number of successful extensions: 1 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: 367 Length of database: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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: 49 (23.5 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