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_083442155.1 NITAL_RS11440 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= SwissProt::P9WIS3 (367 letters) >NCBI__GCF_000969705.1:WP_083442155.1 Length = 375 Score = 360 bits (923), Expect = e-104 Identities = 188/359 (52%), Positives = 237/359 (66%), Gaps = 2/359 (0%) Query: 5 SRRPSGMLMSVDLEPVQLVGPDGTPTAERRYHRDLPEETLRWLYEMMVVTRELDTEFVNL 64 S P G L + EPV+L+ PDGT + + DL ++ L LY M VTR LD E +NL Sbjct: 10 SADPDGFLPTS--EPVRLLEPDGTFHEDPDHPVDLSDDELVELYRRMAVTRRLDRESINL 67 Query: 65 QRQGELALYTPCRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTW 124 QRQG+L +Y C GQEAAQVG+A+ L K DW+FP YRELG +VRG+ G + +RGTW Sbjct: 68 QRQGQLGVYASCLGQEAAQVGSASALAKQDWIFPSYRELGAAVVRGVDAGALLHLYRGTW 127 Query: 125 HGGLQFTTKCCAPMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALN 184 +S+PIGTQ LHA G AM A+ D V + + GDG TSEGD HEA+N Sbjct: 128 LSDHDPYEYNFGLLSIPIGTQALHATGLAMGARFDDNPLVALTYFGDGGTSEGDPHEAMN 187 Query: 185 FAAVFTTPCVFYVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMA 244 FAAVF P +F+VQNNQ+AIS+P+ RQT AP++AHKAIGYGMPG+R DGNDVLA YAV Sbjct: 188 FAAVFEAPVIFFVQNNQYAISVPLDRQTKAPTLAHKAIGYGMPGVRCDGNDVLASYAVTK 247 Query: 245 EAAARARAGDGPTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQG 304 A RAR G GPT IEA+TYR+ HTT+DDP+RYR+++E+ A DP+ R R +L +G Sbjct: 248 RAVERARRGGGPTFIEAMTYRMEAHTTSDDPSRYRTKDELADAAKTDPLLRMRNFLGHRG 307 Query: 305 LWSQRLEEQVTARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAEL 363 LWS LE K + LRD+++DAP D EVF VY + T + QR +LRAEL Sbjct: 308 LWSDDLEASCDEAGKEAATALRDSIYDAPHGDPMEVFDHVYVDDTGHYERQRAELRAEL 366 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: 413 Number of extensions: 12 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: 367 Length of database: 375 Length adjustment: 30 Effective length of query: 337 Effective length of database: 345 Effective search space: 116265 Effective search space used: 116265 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