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) >FitnessBrowser__Btheta:349839 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:
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