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 BPHYT_RS08115 BPHYT_RS08115 dihydrolipoamide succinyltransferase
Query= curated2:P37942 (424 letters) >FitnessBrowser__BFirm:BPHYT_RS08115 Length = 428 Score = 251 bits (642), Expect = 2e-71 Identities = 159/426 (37%), Positives = 234/426 (54%), Gaps = 18/426 (4%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MAI ++ +PQL ESV+E T+ +W PG+ V + + + E+ TDKV EVP+ G + ++ Sbjct: 1 MAIVEVKVPQLSESVSEATMLQWKKKPGEAVAQDEILIEIETDKVVLEVPAPSAGVLAQV 60 Query: 61 VGEEGQTLQVGEMICKIETEG-ANPAEQKQEQPAASEAAENPVAKSAGAADQPN----KK 115 + +G T+ ++I KI+TEG A A + E A EAA P A +A AA + Sbjct: 61 IANDGDTVTADQVIAKIDTEGKAGAAAVEAEVKPAPEAAPAPAAAAAPAAHAASATGANT 120 Query: 116 RYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKS 175 SPA +L E G+ V+GTG GRIT+ D+ T G A APK+ Sbjct: 121 AASPAAGKLMAEKGLGAGDVSGTGRDGRITKGDVL----TAGAPAAKAAPAPAPAAAPKA 176 Query: 176 ASKPEPKEETSYPASA------AGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVT 229 A P + PASA ++ +P++ +R IA + S+ T EV++ Sbjct: 177 AKPSLP--DVKAPASADQWLKDRPEQRVPMSRLRARIAERLLESQQTNAILTTFNEVNMA 234 Query: 230 NMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISI 289 ++ RN KD F+K G L F +FFVKA ALK+FP +N+ G+ I+ +I I Sbjct: 235 PVMDLRNKYKDRFEKEHGVKLGFMSFFVKAAVHALKKFPLVNASIDGNDIVYHGYFDIGI 294 Query: 290 AVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGS 349 AV + L VP+++NAD+ ++ I K I +K +DGKL+ ++M GGTF+++N G FGS Sbjct: 295 AVGSPRGLVVPILRNADQLSLADIEKKIAEFGQKAKDGKLSIEEMTGGTFSISNGGVFGS 354 Query: 350 VQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGR 409 + S IIN PQ+AIL V + +R VV +NG I +R M L LS DHR++DG L Sbjct: 355 MLSTPIINPPQSAILGVHATKERAVV-ENGQIVIRPMNYLALSYDHRIIDGREAVLSLVA 413 Query: 410 VKQILE 415 +K LE Sbjct: 414 MKDALE 419 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: 409 Number of extensions: 23 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: 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