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 199617 SO0425 pyruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase (NCBI ptt file)
Query= curated2:P09062 (423 letters) >FitnessBrowser__MR1:199617 Length = 677 Score = 215 bits (547), Expect = 4e-60 Identities = 139/437 (31%), Positives = 236/437 (54%), Gaps = 36/437 (8%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 I++PDIG+ + V+++E V VGD+I+ DQ + + TDKAT+E+P+P +GK+L+L + G Sbjct: 241 IQVPDIGDA-SNVDVIEVLVSVGDMISADQGLITLETDKATMEVPAPFAGKLLSLTVKVG 299 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125 + ++ GS + IE V A A P A AA ++ PA A+ S Sbjct: 300 DKVSQGSVIATIETTS----VATVSAGAATAPVAQAAAPAPVAQEAAPAPVAAAPSR--- 352 Query: 126 PIVPRQPG-DKPL------ASPAVRKRALDAGIELRYVHGSGPAGRILHEDLDAF----M 174 P VP P P+ ASPAVR+ A + G++L V GSG GRI+ ED+ A+ + Sbjct: 353 PPVPHHPSAGAPVSTGAVHASPAVRRLAREFGVDLTQVTGSGRKGRIMKEDVQAYVKYEL 412 Query: 175 SKPQSAAGQ---TPNG------------YARRTDSEQVPVIGLRRKIAQRMQDAKRRVAH 219 S+P++ A T NG +++ + E++P+ +++ + + H Sbjct: 413 SRPKATAATSVATGNGGGLQVIAAPKVDFSKFGEVEEIPLSRIQKISGPNLHRNWVTIPH 472 Query: 220 FSYVEEIDVTALEALRQQLNSKHGDSRG--KLTLLPFLVRALVVALRDFPQINATYDDEA 277 + +E D+T +E R+Q N + K+T L F+++A+ L+ FP N++ + Sbjct: 473 VTQFDEADITEMEEFRKQQNDAAAKKKADYKITPLVFMMKAVAKTLQQFPVFNSSLSSDG 532 Query: 278 QIITRHGAVHVGIATQGDNGLMVPVLRHAEAGSLWANAGEISRLANAARNNKASREELSG 337 + + + H+G+A NGL+VPV+R + + + E++ ++ AR+ K ++ G Sbjct: 533 ESLIQKKYFHIGVAVDTPNGLVVPVVRDVDKKGIIELSRELADISIRARDGKLKSADMQG 592 Query: 338 STITLTSLGALGGIVSTPVVNTPEVAIVGVNRMVERPVVIDGQIVVRKMMNLSSSFDHRV 397 S T++SLG +GG TP+VN P+VAI+GV++ +P + + M+ LS S+DHRV Sbjct: 593 SCFTISSLGGIGGTAFTPIVNYPDVAILGVSKSEIKPKWNGKEFEPKLMLPLSLSYDHRV 652 Query: 398 VDGMDAALFIQAVRGLL 414 +DG AA F + G+L Sbjct: 653 IDGAMAARFSVTLSGIL 669 Score = 60.8 bits (146), Expect = 1e-13 Identities = 45/123 (36%), Positives = 61/123 (49%), Gaps = 12/123 (9%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 I +PDIG G V ++E V GD I D + + TDKAT+++PSP +G V + G Sbjct: 126 ISVPDIG-GDTDVSVIEVLVAAGDKIEVDAGLITLETDKATMDVPSPFAGVVKEVKVAVG 184 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125 + ++ GS +I +EV G A PA P A A P PAA A A A Sbjct: 185 DKVSQGSLVIMLEVGG---------AAPAAAPQANAPAASAPVAQAAPAA--AVAPVAAV 233 Query: 126 PIV 128 P+V Sbjct: 234 PVV 236 Score = 58.9 bits (141), Expect = 5e-13 Identities = 33/100 (33%), Positives = 56/100 (56%), Gaps = 2/100 (2%) Query: 8 MPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPGEV 67 +PDIG +V+++E VGD +A ++ + V +DKAT++IP+P +G + L G+ Sbjct: 9 VPDIGGD--EVQVIEICAAVGDTLAAEESILTVESDKATMDIPAPFAGVLAELKVAVGDK 66 Query: 68 MAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEP 107 ++ G+ + I+ G+ P A+ A APV A P P Sbjct: 67 VSEGTLIALIQAAGASAQAAAPVAQAAAPAPAPVQAAPAP 106 Lambda K H 0.316 0.133 0.376 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: 704 Number of extensions: 34 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 423 Length of database: 677 Length adjustment: 35 Effective length of query: 388 Effective length of database: 642 Effective search space: 249096 Effective search space used: 249096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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