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 CCNA_01803 CCNA_01803 pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase component
Query= curated2:P37942 (424 letters) >FitnessBrowser__Caulo:CCNA_01803 Length = 428 Score = 216 bits (549), Expect = 1e-60 Identities = 137/418 (32%), Positives = 221/418 (52%), Gaps = 13/418 (3%) Query: 8 MPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEG-Q 66 MP L ++ EGT++KW V GD V D IAE+ TDK EV + G + ++ G + Sbjct: 7 MPALSPTMEEGTLAKWHVKVGDTVKAGDVIAEIETDKATMEVEAVDEGVVEAILVPAGTE 66 Query: 67 TLQVGEMICKIETEGANPAEQ-KQEQPAASEAAENPVAKSAGAADQP--------NKKRY 117 ++V +I K+ EG +PA K E P A+ AA P A A A P ++ Sbjct: 67 NVKVNALIAKLAGEGDSPAPAPKVEAPKAAAAAPVPAAAPAPAVPAPAAPVAADGSRVLA 126 Query: 118 SPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSAS 177 SP RLA G+DL + GTG GR+ + D++ ++G + AA AP +A+ Sbjct: 127 SPLARRLASAAGLDLKALKGTGPHGRVVKSDVEAA-KSGAPAAKAAPASAPAAVAPTAAA 185 Query: 178 KPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237 + + A +P+ G+RK IA M S ++PH +++++ ++A R Sbjct: 186 PRQIQSLEQMGIPAGSYDLVPLDGMRKTIARRMTESFRDVPHFPLTIDLEIDALLAARAK 245 Query: 238 IKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSL 297 I +K +G ++ +KA A ALK+ P+ N+ + + I +I++AVA + L Sbjct: 246 INSLLEK-QGVKVSVNDIVIKAAAVALKQVPEANASYTPEGIAMHHHADIAVAVAVDGGL 304 Query: 298 FVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIIN 357 P+I+ A+ K + I+ ++ LA++ +D KL ++ QGGTF+++N G FG IIN Sbjct: 305 ITPIIRKAETKGLAQISAEMKDLAQRAKDKKLKPEEFQGGTFSISNLGMFGIKSFASIIN 364 Query: 358 YPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 PQ AI+ V + +RPVV NG I V ++ + L+ DHRV+DG V +FL + ++E Sbjct: 365 EPQGAIMSVGAGEQRPVV-KNGEIKVATVMTVTLTCDHRVVDGSVGAKFLAAFRPLIE 421 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: 430 Number of extensions: 27 Number of successful extensions: 6 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: 428 Length adjustment: 32 Effective length of query: 392 Effective length of database: 396 Effective search space: 155232 Effective search space used: 155232 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: 51 (24.3 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