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 RR42_RS12935 RR42_RS12935 dihydrolipoamide succinyltransferase
Query= curated2:P37942 (424 letters) >FitnessBrowser__Cup4G11:RR42_RS12935 Length = 415 Score = 248 bits (633), Expect = 2e-70 Identities = 159/428 (37%), Positives = 230/428 (53%), Gaps = 35/428 (8%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MAI + +PQL ESV E T+ W PG+ V + + + E+ TDKV EVP+ G ++++ Sbjct: 1 MAIVDVKVPQLSESVAEATMLNWKKKPGEAVAQDEILIEIETDKVVLEVPAPSAGVLSQI 60 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 + +G T+ E+I KI+TE A PAA AA P A +A AA P+ Sbjct: 61 IRNDGDTVVADEVIAKIDTEATAGAVA----PAA--AAPAPAAPAAAAAPAAAGAVAMPS 114 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 +L E G+ QV GTG GRIT+ D+ TAAPAP A+K Sbjct: 115 AAKLMAEGGLSAGQVAGTGKDGRITKGDVLAA---------------TAAPAPAPAAKAA 159 Query: 181 PKEETSYPA----------SAAGDK---EIPVTGVRKAIASNMKRSKTEIPHAWTMMEVD 227 P + PA +A GD+ +P++ +R IA + +S++ T EV+ Sbjct: 160 PAPAAAKPALQQVAAPMDFAALGDRPEERVPMSRLRARIAERLLQSQSTNAILTTFNEVN 219 Query: 228 VTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINI 287 + ++ RN KD F+K G L F +FFVKA ALK+FP +N+ G+ I+ +I Sbjct: 220 MKPVMDLRNKYKDRFEKEHGVKLGFMSFFVKAAVHALKKFPLINASIDGNDIVYHGYFDI 279 Query: 288 SIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSF 347 IAV + L VP+++NAD+ ++ I K I K RDGKL+ +++ GGTF+++N G+F Sbjct: 280 GIAVGSPRGLVVPILRNADQMSLADIEKKIAEFGAKARDGKLSLEELTGGTFSISNGGTF 339 Query: 348 GSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFL 407 GS+ S IIN PQ+AIL V + RPVV D G I +R M L +S DHR++DG L Sbjct: 340 GSMLSTPIINPPQSAILGVHATKDRPVVED-GQIVIRPMNYLAMSYDHRIIDGREAVLGL 398 Query: 408 GRVKQILE 415 +K LE Sbjct: 399 VAMKDALE 406 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: 404 Number of extensions: 22 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: 415 Length adjustment: 32 Effective length of query: 392 Effective length of database: 383 Effective search space: 150136 Effective search space used: 150136 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