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 AZOBR_RS14080 AZOBR_RS14080 dihydrolipoamide succinyltransferase
Query= curated2:P37942 (424 letters) >FitnessBrowser__azobra:AZOBR_RS14080 Length = 417 Score = 251 bits (640), Expect = 4e-71 Identities = 156/415 (37%), Positives = 224/415 (53%), Gaps = 14/415 (3%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ +P LGESV+E T+++WL GD V + + E+ TDKV EV + GT+ E+V + Sbjct: 4 EIKVPTLGESVSEATVARWLKKVGDAVAADEALVELETDKVTLEVNAPSAGTLAEIVAAD 63 Query: 65 GQTLQVGEMICKIETEGAN-PAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYS---PA 120 G + VG ++ + GA A K PAA AA P A A A + PA Sbjct: 64 GANVGVGALLGVLGEAGAAVAAPAKAAAPAA--AAPAPAAAPAAAPAPAGASALADAGPA 121 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 +L E G+D Q+ G+G GRIT+ D+ P AAPA S Sbjct: 122 ARKLVAEKGLDASQIAGSGKDGRITKGDVID-------HAAKPAAAPAAAPAAASQKYQW 174 Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240 AA ++ + +T +R+ IA +K ++ T EVD+TN++A RN KD Sbjct: 175 TAGTAGDRPRAAQEERVRMTRLRQRIAERLKEAQNSAAMLTTFNEVDMTNVMALRNEYKD 234 Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300 F+K L F +FFVKA QALKE P +N+ G ++ K +I +AV T L VP Sbjct: 235 FFEKRHKVRLGFMSFFVKAAIQALKEIPAVNAEIDGTDLVYKNYYDIGVAVGTPQGLVVP 294 Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360 ++++AD+ I I L KK RDGKL+ D++ GGTFT++N G +GS+ S IIN PQ Sbjct: 295 IVRDADKLGFAQIEGKIGELGKKGRDGKLSMDELTGGTFTISNGGVYGSLMSTPIINPPQ 354 Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 +AIL + +RPVV+ NG I +R M+ L LS DHR++DG FL R+K+ +E Sbjct: 355 SAILGMHKTQERPVVV-NGKIEIRPMMYLALSYDHRIIDGKEAVTFLVRIKENIE 408 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: 437 Number of extensions: 17 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: 417 Length adjustment: 32 Effective length of query: 392 Effective length of database: 385 Effective search space: 150920 Effective search space used: 150920 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