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 5209178 Shew_1656 2-oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase (RefSeq)
Query= curated2:P37942 (424 letters) >FitnessBrowser__PV4:5209178 Length = 396 Score = 249 bits (637), Expect = 8e-71 Identities = 150/415 (36%), Positives = 227/415 (54%), Gaps = 28/415 (6%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 M+IE + +P L ESV + TI+ W V G++V++ + ++ TDKV EV + G+I E Sbjct: 1 MSIE-IKVPVLPESVADATIATWHVKAGEQVSRDQNLVDIETDKVVLEVVAPEDGSIVEF 59 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 + EEG T+ +I K E +EQ A+ A A A + + SP+ Sbjct: 60 LAEEGDTVLAEAVIAKFVAGAVAGQEVSKEQAEAA-------APQAEATSEESNDALSPS 112 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 V RL EH +D ++ GTG GGRIT++D++ I++ APA K+A+ Sbjct: 113 VRRLIAEHNLDAAKIKGTGVGGRITKEDVEAFIKS--------------APAAKAAAPA- 157 Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240 P K +P+T +RK IA+ + +K T EV++ ++ R ++ Sbjct: 158 ----VVAPLGERSQKRVPMTRLRKTIANRLLEAKNSTAMLTTFNEVNMKPIMNIRKQYQE 213 Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300 F+K G L F +F+VKAV +ALK FP++N+ GD I+ ++SIAV+T L P Sbjct: 214 LFEKKHGIRLGFMSFYVKAVTEALKRFPEVNASIDGDDIVYHNYFDVSIAVSTPRGLVTP 273 Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360 V+++ D ++ I +++ LA K RDGKLT DDM GG FTV N G FGS+ S I+N PQ Sbjct: 274 VLRDTDTMSLADIERNVRDLAIKGRDGKLTVDDMTGGNFTVTNGGVFGSLMSTPILNLPQ 333 Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 +AIL + +I RP+ + NG + + M+ L LS DHR++DG FL +K LE Sbjct: 334 SAILGMHAIKDRPMAV-NGQVEILPMMYLALSYDHRIIDGRESVGFLVAIKDFLE 387 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: 351 Number of extensions: 19 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: 396 Length adjustment: 31 Effective length of query: 393 Effective length of database: 365 Effective search space: 143445 Effective search space used: 143445 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