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 3609178 Dshi_2566 Transketolase central region (RefSeq)
Query= SwissProt::Q5SLR3 (324 letters) >FitnessBrowser__Dino:3609178 Length = 743 Score = 149 bits (376), Expect = 2e-40 Identities = 105/327 (32%), Positives = 168/327 (51%), Gaps = 21/327 (6%) Query: 10 LNRALDEEMAKDPRVVVLGEDVGKRGGVFLVTEGLLQKYGPDRVMDTPLSEAAIVGAALG 69 LN L + M + +V++GED+G++GGV+ VT+ L Q++G DRV+DT L E +I+G A+G Sbjct: 414 LNFTLTDLMLEHGEIVLMGEDIGRKGGVYGVTQKLAQRFGRDRVIDTLLDEQSILGLAIG 473 Query: 70 MAAHGLRPVAEIQFADYIFPGFDQLVSQVAKLRYRSGGQFTAPLVVRMPSGGGVR--GGH 127 MA +G P+ EIQF Y+ DQL + A L + S GQ+T P+V+R+ G + GGH Sbjct: 474 MAQNGFVPMPEIQFLAYLHNAEDQLRGEAATLPFFSNGQYTNPMVLRIAGLGYQKGFGGH 533 Query: 128 HHSQSPEAHFVHTAGLKVVAVSTPYDAKGLLKAAIR----DEDPVVFLEPKRLY--RSVK 181 H+ + A G+ + ST DA +L+ +R ++ VVFLEP LY R ++ Sbjct: 534 FHNDNALAVLRDIPGVILACPSTGADAARMLRECVRLAREEQRVVVFLEPIALYPMRDLQ 593 Query: 182 EE--------VPEEDYTLPIGKAALRREGKDLTLIGYGTVMPEVLQAAAELAKAGVSAEV 233 + P + +G+ G DL L+ +G +A +L AG+ + Sbjct: 594 GDKDGGWMTRYPPPGERIDLGQVGQHGTGTDLALVSFGNGHYLCHKALPQLRAAGIDPRI 653 Query: 234 LDLRTLMPWDYEAVMNSVAKTGRVVLVSDAPRHASFVSEVAATIAEDLLDMLLAPPIRVT 293 +DLR L P +++ ++ +++V D RH+ V+E + + + LA Sbjct: 654 IDLRWLSPLPERSLLEAIDGIPNILIV-DETRHSGGVAEGLMALLSERTNARLARDTAAD 712 Query: 294 GFDTPYP-YAQDKLYLPTVTRILNAAK 319 F P YA LP+V I AA+ Sbjct: 713 SFIATGPAYAAT---LPSVDSITTAAR 736 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: 510 Number of extensions: 17 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: 743 Length adjustment: 34 Effective length of query: 290 Effective length of database: 709 Effective search space: 205610 Effective search space used: 205610 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