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_086511850.1 BZY95_RS21055 dihydrolipoyllysine-residue acetyltransferase
Query= curated2:P37942 (424 letters) >NCBI__GCF_002151265.1:WP_086511850.1 Length = 433 Score = 212 bits (539), Expect = 2e-59 Identities = 143/428 (33%), Positives = 221/428 (51%), Gaps = 33/428 (7%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MAI+++ +P +G+ T+ I + V GD++ DP+ V +DK + +VP+ GT+ EL Sbjct: 1 MAIQEIKVPDIGD-YTDVPIIEIHVQAGDRIQVEDPLITVESDKASMDVPAPAAGTVKEL 59 Query: 61 VGEEGQTLQVGEMICKIETEGA--NPAEQKQEQPAASEAAENPVAKSAGAADQPN----- 113 + G T+ G ++ +E+E A A++K P SE + P A +A AA + Sbjct: 60 KVKLGDTVSEGSLVLLLESEAAAAGGADEKPAAPGGSEGQQGPTAAAAPAAAPTSTASAV 119 Query: 114 -----------KKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQN 162 + SP+ RLA E +DL +V TG GR+T++DI+ + G Sbjct: 120 AAPSGPLADFSRVHASPSARRLARELEVDLTRVPATGLKGRVTQEDIRNFAKGGA----- 174 Query: 163 PEELKTAAPAPKSASK---PEPKEETSYPASAAGDKEI-PVTGVRKAIASNMKRSKTEIP 218 P TAA A P P+ + S G E P++ ++K +N+ R+ +IP Sbjct: 175 PAAQSTAAAASGGGGLDLLPWPQVDFS----KFGPVETQPLSRIKKISGANLHRNWVQIP 230 Query: 219 HAWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDK 278 H E D+T + A+R +K+ G ++ AF +KA LK+FP+ N+ GD+ Sbjct: 231 HVTNHDEADITELEAFRVQFNKDNEKS-GVRVSMLAFMIKAAVATLKQFPEFNASLDGDQ 289 Query: 279 IIQKKDINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGT 338 +I K+ +I A T + L VPVI++AD+K + IA+++ LAK RDGKL D MQGG Sbjct: 290 LILKRYYHIGFAADTPNGLVVPVIRDADKKGVVEIAQEMGTLAKLARDGKLKPDQMQGGC 349 Query: 339 FTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVL 398 FT+++ G G + IIN P+ AI+ V + V D R M+ L LS DHRV+ Sbjct: 350 FTISSLGGIGGLYFTPIINAPEVAIMGVCRSFWKQVSPDGKHSEWRYMLPLSLSWDHRVI 409 Query: 399 DGLVCGRF 406 DG RF Sbjct: 410 DGAAAARF 417 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: 420 Number of extensions: 16 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: 433 Length adjustment: 32 Effective length of query: 392 Effective length of database: 401 Effective search space: 157192 Effective search space used: 157192 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 Apr 09 2024. 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