Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate Dsui_2218 Dsui_2218 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase
Query= curated2:P37942 (424 letters) >FitnessBrowser__PS:Dsui_2218 Length = 402 Score = 233 bits (595), Expect = 6e-66 Identities = 147/413 (35%), Positives = 225/413 (54%), Gaps = 21/413 (5%) Query: 3 IEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVG 62 I + +PQL ESV E T+ W G+ V++ + + ++ TDKV E+P+ G I +++ Sbjct: 2 IIDVKVPQLSESVAEATLVSWHKKAGEAVSRDENLIDIETDKVVLELPAPDAGVIVKIIK 61 Query: 63 EEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPAVL 122 +G T+ GE+I +I+TE A A AA+ AA P +A AA SPA Sbjct: 62 GDGDTVVSGEVIAQIDTE-AKAAAGAAPAAAAAPAAAAPAPVAAAAAPAAAAGTASPAAR 120 Query: 123 RLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPEPK 182 ++ E GI V+GTG GGR+T++D G Q K AAPA + + Sbjct: 121 KILDEKGIAAADVSGTGRGGRVTKEDAV------GAQA------KAAAPAVAAPA----- 163 Query: 183 EETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKDSF 242 S P ++ +P+T +R IA + +SK E T EV++ ++A R D F Sbjct: 164 --VSIPLGDRPEQRVPMTRLRARIAERLLQSKNENAILTTFNEVNMAPVMALRKQYGDKF 221 Query: 243 KKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVPVI 302 +K G L F FFVKA ALK++P +N+ G+ I+ I+I IAV + L VP++ Sbjct: 222 EKEHGVRLGFMGFFVKAAVAALKKYPILNASVDGNDIVYHGYIDIGIAVGSPRGLVVPIL 281 Query: 303 KNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQAA 362 ++AD+ +I I K I +K +DGK++ +++ GGTF+++N G FGS+ S IIN PQ+A Sbjct: 282 RDADQMSIADIEKKIAEYGQKAKDGKISIEELTGGTFSISNGGVFGSMLSTPIINPPQSA 341 Query: 363 ILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 IL + + R VV +NG + VR + L +S DHR++DG L +K+ LE Sbjct: 342 ILGIHATKDRAVV-ENGQVVVRPINYLAMSYDHRIIDGREAVLGLVTMKEALE 393 Lambda K H 0.312 0.129 0.359 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: 391 Number of extensions: 18 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: 424 Length of database: 402 Length adjustment: 31 Effective length of query: 393 Effective length of database: 371 Effective search space: 145803 Effective search space used: 145803 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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