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 BWI76_RS08420 BWI76_RS08420 dihydrolipoamide succinyltransferase
Query= curated2:P37942 (424 letters) >FitnessBrowser__Koxy:BWI76_RS08420 Length = 407 Score = 248 bits (634), Expect = 2e-70 Identities = 144/418 (34%), Positives = 229/418 (54%), Gaps = 23/418 (5%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 M+ + +P L ESV + T++ W PGD V + + + E+ TDKV EVP+S G + + Sbjct: 1 MSSVDILVPDLPESVADATVATWHKKPGDAVVRDEVLVEIETDKVVLEVPASADGILDAV 60 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 + +EG T+ +++ ++ EG + ++ + A E+ P + + ++ N SPA Sbjct: 61 IEDEGATVLSRQILGRLR-EGNSAGKESGAKADAKEST--PAQRQQASLEEQNNDALSPA 117 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 + RL EH +D + GTG GGR+TR+D++ K A AP A P Sbjct: 118 IRRLLAEHSLDAAAIKGTGVGGRLTREDVE----------------KHLANAPAKAPAPA 161 Query: 181 PKEETSYPASAAG---DKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNS 237 + PA G +K +P+T +RK +A + +K T EV++ ++ R Sbjct: 162 AAPAAAAPAPQLGHRSEKRVPMTRLRKRVAERLLEAKNSTAMLTTFNEVNMKPIMDLRKQ 221 Query: 238 IKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSL 297 D+F+K G L F +F+VKAV +ALK +P++N+ GD ++ ++S+AV+T L Sbjct: 222 YGDAFEKRHGIRLGFMSFYVKAVVEALKRYPEVNASIDGDDVVYHNYFDVSMAVSTPRGL 281 Query: 298 FVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIIN 357 PV+++ D + I K I LA K RDGKLT DD+ GG FT+ N G FGS+ S IIN Sbjct: 282 VTPVLRDVDLLGMADIEKKIKELAVKGRDGKLTVDDLTGGNFTITNGGVFGSLMSTPIIN 341 Query: 358 YPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILE 415 PQ+AIL + +I RP+ + NG + + M+ L LS DHR++DG +L +K++LE Sbjct: 342 PPQSAILGMHAIKDRPMAV-NGKVEILPMMYLALSYDHRLIDGRESVGYLVAIKELLE 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: 391 Number of extensions: 24 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: 407 Length adjustment: 31 Effective length of query: 393 Effective length of database: 376 Effective search space: 147768 Effective search space used: 147768 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