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 201092 SO1931 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase (NCBI ptt file)
Query= curated2:P37942 (424 letters) >FitnessBrowser__MR1:201092 Length = 395 Score = 242 bits (618), Expect = 1e-68 Identities = 152/415 (36%), Positives = 227/415 (54%), Gaps = 29/415 (6%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 M+IE + +P L ESV + TI+ W V G +V++ + ++ TDKV EV + G I E Sbjct: 1 MSIE-IKVPVLPESVADATIATWHVKVGQQVSRDQNLVDIETDKVVLEVVAPEDGHIGEF 59 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 + EG T+ ++I K + E + Q A A A A+D+ N SP+ Sbjct: 60 LFHEGDTVLGEQVIAKFIAGAVSGQEVTKAQAEA--------AAPAVASDESNDA-LSPS 110 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 V RL EH +D +V GTG GGRIT++D++ I++ APK+A+ Sbjct: 111 VRRLLAEHNVDASKVKGTGVGGRITKEDVEAFIKS----------------APKAAASAA 154 Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240 P + A+ +K +P+T +RK IA+ + +K T EV++ ++ R +D Sbjct: 155 PVVQPL--AAGRSEKRVPMTRLRKTIANRLLEAKNSTAMLTTFNEVNMKPIMDIRKQYQD 212 Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300 F+K G L F +F+VKAV +ALK FP++N+ GD I+ ++SIAV+T L P Sbjct: 213 IFEKRHGIRLGFMSFYVKAVTEALKRFPEVNASIDGDDIVYHNYFDVSIAVSTPRGLVTP 272 Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360 V+++ D ++ I K + LA K RDGKLT DM GG FTV N G FGS+ S I+N PQ Sbjct: 273 VLRDTDTMSLADIEKAVRDLAIKGRDGKLTVADMTGGNFTVTNGGVFGSLMSTPILNLPQ 332 Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 +AIL + +I RP+ + NG + + M+ L LS DHR++DG FL +K LE Sbjct: 333 SAILGMHAIKDRPMAV-NGQVEILPMMYLALSYDHRIIDGRESVGFLVAIKDFLE 386 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: 354 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: 395 Length adjustment: 31 Effective length of query: 393 Effective length of database: 364 Effective search space: 143052 Effective search space used: 143052 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