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 14859 b0727 dihydrolipoamide acetyltransferase (NCBI)
Query= curated2:P37942 (424 letters) >FitnessBrowser__Keio:14859 Length = 405 Score = 253 bits (645), Expect = 1e-71 Identities = 145/416 (34%), Positives = 229/416 (55%), Gaps = 21/416 (5%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 M+ + +P L ESV + T++ W PGD V + + + E+ TDKV EVP+S G + + Sbjct: 1 MSSVDILVPDLPESVADATVATWHKKPGDAVVRDEVLVEIETDKVVLEVPASADGILDAV 60 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 + +EG T+ +++ ++ EG + K+ + E A P + + ++ N SPA Sbjct: 61 LEDEGTTVTSRQILGRLR-EGNSAG--KETSAKSEEKASTPAQRQQASLEEQNNDALSPA 117 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 + RL EH +D + GTG GGR+TR+D++ K A AP S P Sbjct: 118 IRRLLAEHNLDASAIKGTGVGGRLTREDVE----------------KHLAKAPAKESAPA 161 Query: 181 PKEETSYPASAA-GDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIK 239 + PA AA +K +P+T +RK +A + +K T EV++ ++ R Sbjct: 162 AAAPAAQPALAARSEKRVPMTRLRKRVAERLLEAKNSTAMLTTFNEVNMKPIMDLRKQYG 221 Query: 240 DSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFV 299 ++F+K G L F +F+VKAV +ALK +P++N+ GD ++ ++S+AV+T L Sbjct: 222 EAFEKRHGIRLGFMSFYVKAVVEALKRYPEVNASIDGDDVVYHNYFDVSMAVSTPRGLVT 281 Query: 300 PVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYP 359 PV+++ D + I K I LA K RDGKLT +D+ GG FT+ N G FGS+ S IIN P Sbjct: 282 PVLRDVDTLGMADIEKKIKELAVKGRDGKLTVEDLTGGNFTITNGGVFGSLMSTPIINPP 341 Query: 360 QAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 Q+AIL + +I RP+ + NG + + M+ L LS DHR++DG FL +K++LE Sbjct: 342 QSAILGMHAIKDRPMAV-NGQVEILPMMYLALSYDHRLIDGRESVGFLVTIKELLE 396 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: 381 Number of extensions: 22 Number of successful extensions: 4 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: 405 Length adjustment: 31 Effective length of query: 393 Effective length of database: 374 Effective search space: 146982 Effective search space used: 146982 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