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_013075388.1 BTUS_RS06885 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_000092905.1:WP_013075388.1 Length = 435 Score = 221 bits (563), Expect = 3e-62 Identities = 155/430 (36%), Positives = 222/430 (51%), Gaps = 31/430 (7%) Query: 8 MPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEEGQT 67 +P+LGES+ E TI W GD V K + +AEV TDKVN EV S G + ++ G+T Sbjct: 6 VPELGESIVEATILSWRKNEGDPVAKGETVAEVETDKVNVEVASEEDGVLEAILKPAGET 65 Query: 68 LQVGEMICKIETEGANPA-EQKQEQPAASEAAENPVAK--SAGAADQPNKKRYSPAVLRL 124 + VGE I +I + A+ A E QPA + P K +AG + R A Sbjct: 66 VFVGETIARIRSGAADQAAEHTPNQPARGQEPTPPETKHPNAGEKGLAVESRPVEASRGK 125 Query: 125 AGEHGID------LDQVTGTGAGGRIT-RKDIQRLIETGGVQEQNPEELKTAAPAPKSAS 177 G D LDQ T + T R QR Q P+ AAPA SA+ Sbjct: 126 TGPQTADNPSPAALDQATAPSSVTSPTPRTPSQR---RRARQADGPQ----AAPAT-SAA 177 Query: 178 KPEPKEETSYPASAAG------------DKEIPVTGVRKAIASNMKRSKTEIPHAWTMME 225 + E E + PA+ ++ IP+T R+ IA + +K T E Sbjct: 178 RTEVVREATAPAAPVAPGTTAASPLRPDEERIPMTRRRQTIARRLLEAKQSTAMLTTFNE 237 Query: 226 VDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDI 285 +D++ ++ R KD FK+ G L F +FF +A ALK FP +N+ G++I+ K Sbjct: 238 IDMSAVLDLRRRRKDQFKEEHGVGLGFMSFFTRAAVGALKAFPMLNAEIEGNEIVVKHHY 297 Query: 286 NISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTG 345 +I IAVAT L VPV+++AD T I I LAK+ R+G L ++QGGTFT+ N G Sbjct: 298 DIGIAVATPAGLVVPVVRDADRLTFAEIESRIADLAKRAREGTLHPQELQGGTFTITNGG 357 Query: 346 SFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGR 405 FGS+ S I+N PQ IL + +I +RPV ++ G I +R M+ + LS DHR++DG + Sbjct: 358 VFGSLFSTPILNPPQVGILGMHAIKERPVAVE-GQIVLRPMMYVALSYDHRIVDGAEAVQ 416 Query: 406 FLGRVKQILE 415 FL +VK+++E Sbjct: 417 FLVKVKEMVE 426 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: 446 Number of extensions: 20 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: 435 Length adjustment: 32 Effective length of query: 392 Effective length of database: 403 Effective search space: 157976 Effective search space used: 157976 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 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