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 349839 BT0311 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (NCBI ptt file)
Query= curated2:P37942 (424 letters) >lcl|FitnessBrowser__Btheta:349839 BT0311 lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (NCBI ptt file) Length = 456 Score = 263 bits (672), Expect = 8e-75 Identities = 167/449 (37%), Positives = 245/449 (54%), Gaps = 37/449 (8%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ MP+LGES+TEGTI W V GD + + D + EV T KV+AE+PS G + E++ +E Sbjct: 5 EIKMPKLGESITEGTIVSWSVKVGDVIQEDDVLFEVNTAKVSAEIPSPVAGKVVEILFKE 64 Query: 65 GQTLQVGEMICKIETEGANPAEQK----QEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 G T+ VG ++ ++ G ++++ +E P + E A + K + + ++ YSP Sbjct: 65 GDTVAVGTVVAVVDMGGEEASDEETASGKETPESKENASSDAEKVSSQVAKAEERWYSPV 124 Query: 121 VLRLAGEHGI---DLDQVTGTGAGGRITRKDIQRLIETG--GVQEQNPEELKTA----AP 171 V++LA I +LD + GTG GR+++KDI+ IE G+ E + + T A Sbjct: 125 VIQLARGANIPKEELDSIQGTGYEGRLSKKDIKDYIEKKKRGISEVSKAAIPTGDALTAS 184 Query: 172 APKSA--------SKPEPKEETSYPASAAGDKEIPVTG------------VRKAIASNMK 211 P S S +T A +A K+ P VR+ IA +M Sbjct: 185 MPSSTGGAGSMTTSPVAASVQTPVAAPSAPSKQAPAAANIPGVEVKEMDRVRRIIADHMV 244 Query: 212 RSKTEIPHAWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMN 271 SK PH ++EVDVT +V +R KD+F + EG LT+ +AVA+AL +PQ+N Sbjct: 245 MSKKVSPHVTNVVEVDVTKLVRWREKNKDAFFRREGVKLTYMPVITEAVAKALAAYPQVN 304 Query: 272 SMWAGDKIIQKKDINISIAVATED-SLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLT 330 G I+ KK INI IAV+ D +L VPV+ +AD + G+A I LA K RD KL Sbjct: 305 VSVDGYNILFKKHINIGIAVSLNDGNLIVPVVHDADHLNLNGLAVAIDSLALKARDNKLM 364 Query: 331 ADDMQGGTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVM---DNGMIAVRDMV 387 DD+ GGTFT+ N G+F S+ +IN PQ AIL V I K+P V+ + IA+R + Sbjct: 365 PDDIDGGTFTITNFGTFKSLFGTPVINQPQVAILGVGYIEKKPAVIETPEGDTIAIRHKM 424 Query: 388 NLCLSLDHRVLDGLVCGRFLGRVKQILES 416 L LS DHRV+DG++ G FL + LE+ Sbjct: 425 YLSLSYDHRVVDGMLGGNFLHFIADYLEN 453 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: 493 Number of extensions: 31 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: 456 Length adjustment: 32 Effective length of query: 392 Effective length of database: 424 Effective search space: 166208 Effective search space used: 166208 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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