Align 2-oxoisovalerate dehydrogenase subunit alpha 2, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate AZOBR_RS25395 AZOBR_RS25395 acetoin dehydrogenase
Query= SwissProt::Q84JL2 (472 letters) >FitnessBrowser__azobra:AZOBR_RS25395 Length = 316 Score = 138 bits (348), Expect = 2e-37 Identities = 98/313 (31%), Positives = 151/313 (48%), Gaps = 5/313 (1%) Query: 133 IYSDMVTLQIMDNIFYEAQRQGRLSFYA-TAIGEEAINIASAAALTPQDVIFPQYREPGV 191 +Y+ M +++ + + EA + G+++ Y +IG+EAI A A L DV+ +R G Sbjct: 3 LYATMQRIRVFETLADEAHKAGQVAGYIHLSIGQEAIAAAVGANLRADDVLTSTHRGHGH 62 Query: 192 LLWRGFTLQEFANQCFGNKSDYGKGRQMPVHYGSNKLNYFTVSATIATQLPNAVGAAYSL 251 + +G + G G+ +H + + +A LP AVGAA+++ Sbjct: 63 TIAKGADPLAMFRELCGRAGGTCGGKGGSMHIADFSVGMLGANGVVAAGLPIAVGAAHAI 122 Query: 252 KMDKKDACAVTYFGDGGTSEGDFHAALNIAAVMEAPVLFICRNNGWAISTPTSDQFRSDG 311 + +D AV +FGDG T+ G F ALN AA PVLF+C +NG+ +T T G Sbjct: 123 ALKGEDRIAVCFFGDGATNRGPFLEALNWAAAFRLPVLFVCEDNGYGATTRTGSVSAGGG 182 Query: 312 VVVKGRAYGIRSIRVDGNDALAMYSAVHTAREMAIRE-QRPILIEALTYRVGHHSTSDDS 370 V+ + GI VDGND LA A A A+R+ P + A TYR H++SD + Sbjct: 183 PGVRAESLGIPVTVVDGND-LAAVDAAAAALVRAVRDGGGPQFLHARTYRFRGHTSSDPA 241 Query: 371 TRYRSAGEIEWWNKARNPLSRFRTWIESNGWWSDKTESDLRSRIKKEMLEALRVAEKTEK 430 T YR A E+ +PL R + G D E R ++ + AL A + Sbjct: 242 T-YRDAAEVRAQLAGNDPLQRAAATLAELGVTPDALERVERHE-RETLAAALATALDSPW 299 Query: 431 PNLQNMFSDVYDV 443 P+L+ F+DV D+ Sbjct: 300 PDLRTAFTDVQDI 312 Lambda K H 0.318 0.132 0.394 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: 329 Number of extensions: 17 Number of successful extensions: 5 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: 472 Length of database: 316 Length adjustment: 30 Effective length of query: 442 Effective length of database: 286 Effective search space: 126412 Effective search space used: 126412 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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