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 7024533 Shewana3_1711 2-oxoglutarate dehydrogenase E2 component (RefSeq)
Query= curated2:P37942 (424 letters) >FitnessBrowser__ANA3:7024533 Length = 397 Score = 246 bits (628), Expect = 9e-70 Identities = 154/415 (37%), Positives = 229/415 (55%), Gaps = 27/415 (6%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 M+IE + +P L ESV + TI+ W V G++V++ + ++ TDKV EV + G I E Sbjct: 1 MSIE-IKVPVLPESVADATIATWHVKVGEQVSRDQNLVDIETDKVVLEVVAPEDGHIGEF 59 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 + +EG T+ ++I K A QE A A PVA AA + + SP+ Sbjct: 60 LFQEGDTVLGEQVIAKFIAG----AVSGQEVTKAEAEAAAPVA---AAATEESNDALSPS 112 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 V RL EH +D +V GTG GGRIT++D++ I++ APK+A+ Sbjct: 113 VRRLLAEHNVDASKVKGTGVGGRITKEDVEAFIKS----------------APKAAAPAA 156 Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240 P + A+ +K +P+T +RK IA+ + +K T EV++ ++ R +D Sbjct: 157 PAVQPL--AAGRSEKRVPMTRLRKTIANRLLEAKNSTAMLTTFNEVNMKPIMDIRKQYQD 214 Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300 F+K G L F +F+VKAV +ALK FP++N+ GD I+ ++SIAV+T L P Sbjct: 215 IFEKRHGIRLGFMSFYVKAVTEALKRFPEVNASIDGDDIVYHNYFDVSIAVSTPRGLVTP 274 Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360 V+++ D ++ I K + LA K RDGKLT DM GG FTV N G FGS+ S I+N PQ Sbjct: 275 VLRDTDTMSLADIEKAVRDLAIKGRDGKLTVADMTGGNFTVTNGGVFGSLMSTPILNLPQ 334 Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 +AIL + +I RP+ + NG + + M+ L LS DHR++DG FL +K LE Sbjct: 335 SAILGMHAIKDRPMAV-NGQVEILPMMYLALSYDHRIVDGRESVGFLVAIKDFLE 388 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: 359 Number of extensions: 16 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: 397 Length adjustment: 31 Effective length of query: 393 Effective length of database: 366 Effective search space: 143838 Effective search space used: 143838 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