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 CA265_RS09070 CA265_RS09070 diapophytoene dehydrogenase
Query= curated2:P37942 (424 letters) >FitnessBrowser__Pedo557:CA265_RS09070 Length = 450 Score = 290 bits (742), Expect = 6e-83 Identities = 176/445 (39%), Positives = 255/445 (57%), Gaps = 27/445 (6%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 MA ++ +P++GESV E T+ KW+ PGD ++ D I E+ TDKV++EVPS G + + Sbjct: 1 MAQYELLLPKMGESVAEATVIKWVKQPGDSIDLDDTILEIATDKVDSEVPSPVAGKLVKQ 60 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQ---EQPAASEAAEN-------PVAKSAGAAD 110 + + QVG++I IETEG + + E+P E E P + A D Sbjct: 61 LFAADEVAQVGDVIAIIETEGGDSPTAETPVAEKPITEEKTETIPGIAQLPSENTTVATD 120 Query: 111 QPNKKR-YSPAVLRLAGEHGI---DLDQVTGTGAGGRITRKDIQRLI-ETGGVQEQNPEE 165 + +R YSP V +A + I +LD + G+GA GR+ + D+ I G + Sbjct: 121 FSSSERFYSPLVKSIAAQENISLAELDAIKGSGADGRLNKDDLLDYIARKNGGDPILTQT 180 Query: 166 LKTAAPAP--------KSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEI 217 + AP P K+ S +TS + + GD+ I + +RK IA +M SKT Sbjct: 181 VTITAPVPPVSQITENKATSSAPVVNKTSTTSVSGGDEIIEMDRMRKLIADHMVMSKTTS 240 Query: 218 PHAWTMMEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGD 277 PH + +E DVTNMV +RN +K+SF+K E +TF FV+AVA+A+K+FP +N G Sbjct: 241 PHVTSFVEADVTNMVLWRNKVKNSFEKRENEKITFTPIFVEAVAKAIKDFPMINVSVNGT 300 Query: 278 KIIQKKDINISIAVA-TEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQG 336 +II+K+DINI +A A +L VPVI+NAD+ + G+ K + LA + R+ KL D+ QG Sbjct: 301 QIIKKRDINIGMAAALPSGNLIVPVIRNADQLNLVGLTKAVNDLATRARNSKLKPDETQG 360 Query: 337 GTFTVNNTGSFGSVQSMGIINYPQAAILQVESIVKRPVVMD---NGMIAVRDMVNLCLSL 393 GTFT+ N GSFG+V IIN PQ AIL V +I K+P V++ +IA+R M+ L LS Sbjct: 361 GTFTLTNVGSFGNVMGTPIINQPQVAILAVGAIKKKPAVLETEHGDVIAIRHMMFLSLSY 420 Query: 394 DHRVLDGLVCGRFLGRVKQILESID 418 DHRV+DG + G F+ RV LE D Sbjct: 421 DHRVVDGSLGGMFVRRVADYLEGWD 445 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: 466 Number of extensions: 19 Number of successful extensions: 5 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: 450 Length adjustment: 32 Effective length of query: 392 Effective length of database: 418 Effective search space: 163856 Effective search space used: 163856 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