Align 2-oxoisovalerate dehydrogenase subunit beta; Branched-chain alpha-keto acid dehydrogenase E1 component beta chain; BCKDH E1-beta; EC 1.2.4.4 (characterized)
to candidate GFF3312 PGA1_c33640 putative 2-oxoisovalerate dehydrogenase (fused subunits alpha and beta)
Query= SwissProt::Q5SLR3 (324 letters) >FitnessBrowser__Phaeo:GFF3312 Length = 729 Score = 157 bits (397), Expect = 8e-43 Identities = 96/273 (35%), Positives = 154/273 (56%), Gaps = 16/273 (5%) Query: 6 MVQALNRALDEEMAKDPRVVVLGEDVGKRGGVFLVTEGLLQKYGPDRVMDTPLSEAAIVG 65 M + +N AL + M +VV+GEDVG++GGV+ VT+ L Q++G DRV+DT L E +I+G Sbjct: 396 MSRLINWALTDLMLAHGELVVMGEDVGRKGGVYGVTQKLQQRFGQDRVIDTLLDEQSILG 455 Query: 66 AALGMAAHGLRPVAEIQFADYIFPGFDQLVSQVAKLRYRSGGQFTAPLVVRMPSGGGVR- 124 A+GM +G P+ EIQF Y+ DQ+ + A L + S GQF+ P+V+R+ G + Sbjct: 456 LAIGMGHNGFVPIPEIQFLAYLHNAEDQIRGEAATLPFFSNGQFSNPMVLRIAGLGYQKG 515 Query: 125 -GGHHHSQSPEAHFVHTAGLKVVAVSTPYDAKGLLKAAIR----DEDPVVFLEPKRLY-- 177 GGH H+ + A G+ + S +A +L+ A+R ++ VVF+EP LY Sbjct: 516 FGGHFHNDNSLAVLRDIPGIVIACPSDGAEAAMMLREAVRLAREEQRVVVFVEPIALYPM 575 Query: 178 ---RSVKE-----EVPEEDYTLPIGKAALRREGKDLTLIGYGTVMPEVLQAAAELAKAGV 229 + K+ P+ D + +G+ + +G DL ++ YG QA A+LA GV Sbjct: 576 RDLHAAKDGGWMRHYPKPDQRIALGEVGVHGDGTDLAIVTYGNGRYLAAQAQADLAAKGV 635 Query: 230 SAEVLDLRTLMPWDYEAVMNSVAKTGRVVLVSD 262 +A V+DLR L P EA++ + A ++++V + Sbjct: 636 AARVVDLRWLAPLPKEALLAAAAACDKILIVDE 668 Lambda K H 0.319 0.136 0.389 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: 437 Number of extensions: 18 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: 324 Length of database: 729 Length adjustment: 34 Effective length of query: 290 Effective length of database: 695 Effective search space: 201550 Effective search space used: 201550 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: 52 (24.6 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