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 WP_009781680.1 MED217_RS16440 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_000152985.1:WP_009781680.1 Length = 411 Score = 249 bits (637), Expect = 8e-71 Identities = 161/434 (37%), Positives = 232/434 (53%), Gaps = 51/434 (11%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MA+E M +P GES+TE I++WLV GD V K IAEV +DK E+P+ +G IT L Sbjct: 1 MALE-MKVPSPGESITEVEIAQWLVEDGDYVEKDQAIAEVDSDKATLELPAEASGIIT-L 58 Query: 61 VGEEGQTLQVGEMICKIETEGANP---------------AEQKQEQPAASEAAENPVAKS 105 EEG + VGE++C I+T+ A P AE K+E P+ S E K Sbjct: 59 KAEEGDAVAVGEVVCLIDTDAAKPEGDSSGDKEEQKEEKAEPKKEAPSKSSTPEQAQDKK 118 Query: 106 AGAADQPNKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEE 165 A+ P SPA + E GID V GTG GRIT++D + G Sbjct: 119 TYASGSP-----SPAAKKTLDEKGIDAKDVKGTGRDGRITKEDAVNAQPSMGT------- 166 Query: 166 LKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMME 225 P + S+ E + + S +R+ +A + K E T E Sbjct: 167 -------PGTGSRGESRSKMSM--------------LRRKVAERLVSVKNETAMLTTFNE 205 Query: 226 VDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDI 285 VD+T + R+ K+ FK G +L F +FF A +AL+ +P +NSM G +++ Sbjct: 206 VDMTPIFDLRSKYKEDFKAKHGVSLGFMSFFTLACVRALEMYPAVNSMIDGKEMVSYDFK 265 Query: 286 NISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTG 345 +ISIAV+ L VPVI+NA+ + +G+ ++ LA + RDG++T D+M GGTFT+ N G Sbjct: 266 DISIAVSGPKGLMVPVIRNAENLSFRGVESEVKRLALRARDGQITVDEMTGGTFTITNGG 325 Query: 346 SFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGR 405 FGS+ S IIN PQ+AIL + +IV+RP+V D G IA+ ++ + LS DHR++DG Sbjct: 326 VFGSMLSTPIINPPQSAILGMHNIVERPIVRDGG-IAIAPIMYVALSYDHRIIDGKESVG 384 Query: 406 FLGRVKQILESIDE 419 FL VK+ LE+ +E Sbjct: 385 FLVAVKEALENPEE 398 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: 425 Number of extensions: 25 Number of successful extensions: 5 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: 411 Length adjustment: 32 Effective length of query: 392 Effective length of database: 379 Effective search space: 148568 Effective search space used: 148568 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 24 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