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 Ac3H11_2466 Dihydrolipoamide succinyltransferase component (E2) of 2-oxoglutarate dehydrogenase complex (EC 2.3.1.61)
Query= curated2:P37942 (424 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2466 Length = 422 Score = 228 bits (582), Expect = 2e-64 Identities = 143/419 (34%), Positives = 222/419 (52%), Gaps = 10/419 (2%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MAI ++ +PQL ESV E T+ W G+ V + + E+ TDKV EVP+ G ++E+ Sbjct: 1 MAIVEVKVPQLSESVAEATMLTWKKKAGEAVTVDEILIEIETDKVVLEVPAPSAGVLSEI 60 Query: 61 VGEEGQTLQVGEMICKIETEG-ANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSP 119 + +G T+ ++I KI+TEG A A A + AA P A A A P Sbjct: 61 IQGDGATVVAEQLIAKIDTEGKAGAAAAAPAAAAPAPAAAAPAAAPAAAGGSKGDVAM-P 119 Query: 120 AVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGG-VQEQNPEELKTAAP--APKSA 176 A +L ++ + + V G+G GR+T+ D+ + G P + T P A Sbjct: 120 AAAKLLADNNLSVSAVAGSGKDGRVTKGDVLAAVAGGAKAAVAAPSVIPTGVPSKALPQV 179 Query: 177 SKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRN 236 + P KE+ S ++ +P++ +R +A + +S++ T EV++ ++ R Sbjct: 180 AAPAGKEDLS----GRPEQRVPMSRLRARVAERLLQSQSTNAILTTFNEVNMAPVMDLRK 235 Query: 237 SIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDS 296 +DSF K G L F +FFVKA ALK++P +N+ G+ I+ +I IAV + Sbjct: 236 KFQDSFTKEHGAKLGFMSFFVKAAVHALKKYPVLNASVDGNDIVYHGYFDIGIAVGSPRG 295 Query: 297 LFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGII 356 L VP+++NAD+ + I K I KK +GKL ++M GGTF+++N G+FGS+ S II Sbjct: 296 LVVPILRNADQMSFADIEKKIAEFGKKAAEGKLGIEEMTGGTFSISNGGTFGSMMSTPII 355 Query: 357 NYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 N PQ+AIL V + R +V +NG + VR M L +S DHR++DG L +K LE Sbjct: 356 NPPQSAILGVHATKDRAMV-ENGQVVVRPMNYLAMSYDHRIIDGREAVLGLVAMKDALE 413 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: 411 Number of extensions: 21 Number of successful extensions: 3 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: 422 Length adjustment: 32 Effective length of query: 392 Effective length of database: 390 Effective search space: 152880 Effective search space used: 152880 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