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_065398074.1 BBI00_RS06900 2-oxo acid dehydrogenase subunit E2
Query= curated2:P37942 (424 letters) >NCBI__GCF_001684965.1:WP_065398074.1 Length = 435 Score = 283 bits (724), Expect = 7e-81 Identities = 177/443 (39%), Positives = 264/443 (59%), Gaps = 28/443 (6%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MA ++ +P +GE V E TI WL GD V + D + E+ TDKV+++VP+ +G I ++ Sbjct: 1 MAEYKLLLPSMGEGVMEATIITWLFNEGDNVKEDDSVVEIATDKVDSDVPTPVSGKIVKI 60 Query: 61 VGEEGQTLQVGEMICKIETEGANPA--EQKQEQPAASEAAEN------PVAKSAGAADQP 112 + ++ + +VGE I +E EG A E + E PAA+ AE P+ ++ A + Sbjct: 61 LKQKDEVAKVGEAIAILEIEGEGTASEEVQAETPAAAPDAETLKTIEQPLQQTIAANVEF 120 Query: 113 NKKRY-SPAVLRLAGEHGI---DLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKT 168 + Y SP V +A + I +L + G+G GRIT++DI + G Q P+ Sbjct: 121 SGDLYLSPLVKSIAQQENISEAELKSIKGSGLEGRITKEDILAYVANRGTQP-TPQ---- 175 Query: 169 AAPAPKSASKPEPKEETSYPAS----AAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMM 224 AAP ++AS P+P S PA+ +AGD+ IP+ +RK IA NM ++K PH + + Sbjct: 176 AAPV-QAASTPQPA--VSAPAATIPVSAGDEIIPMDRMRKIIAENMVKAKQIAPHVTSFI 232 Query: 225 EVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKD 284 E DVTN+V +RN K F+K EG LTF FVKAV +A+++FP +N G+ II+KK+ Sbjct: 233 ETDVTNVVKWRNKNKAVFEKREGEKLTFMPIFVKAVVKAIQDFPMINVSVNGENIIKKKN 292 Query: 285 INISIAVATED-SLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNN 343 INI +A A D +L VPVIKNAD+ ++ G+AK I LA + R+ KL +D QG T+T++N Sbjct: 293 INIGMATALPDGNLIVPVIKNADQLSLSGLAKAINDLAYRARNKKLRPEDTQGATYTISN 352 Query: 344 TGSFGSVQSMGIINYPQAAILQVESIVKRPVVM---DNGMIAVRDMVNLCLSLDHRVLDG 400 GSFG++ II PQ AIL + +IVK+P V+ D +IA+R+++ + S DHRV+DG Sbjct: 353 VGSFGNLMGTPIIPQPQVAILAIGAIVKKPAVLETADGDVIAIRNLMFMSHSYDHRVVDG 412 Query: 401 LVCGRFLGRVKQILESIDEKTSV 423 + G L V LE+ D T + Sbjct: 413 SLGGMMLKHVHDYLENWDLNTEI 435 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: 414 Number of extensions: 23 Number of successful extensions: 6 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