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 GFF1733 PGA1_c17570 dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Query= curated2:P37942 (424 letters) >FitnessBrowser__Phaeo:GFF1733 Length = 441 Score = 224 bits (570), Expect = 5e-63 Identities = 136/433 (31%), Positives = 224/433 (51%), Gaps = 22/433 (5%) Query: 5 QMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITELVGEE 64 ++ MP L ++ EGT++KWLV GD V D +AE+ TDK E + G I +++ E Sbjct: 4 EILMPALSPTMEEGTLAKWLVKEGDTVASGDLLAEIETDKATMEFEAVDEGVIGKILIPE 63 Query: 65 GQT-----------LQVGEMICKIETEGANPAEQKQEQ-PAASE-AAENPVAKSAGAADQ 111 G L+ GE I A PA + PAASE AA P + A Sbjct: 64 GSEGVKVNSPIAVLLEDGESADDIGATPAAPAAAANKAAPAASEEAASAPAQATTAATPA 123 Query: 112 P--------NKKRYSPAVLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNP 163 P N+ SP R+A + G+DL Q+ G+G GRI + D++ Sbjct: 124 PAAPQGADGNRIFASPLARRIAADKGLDLSQLNGSGPRGRIVKADVENAKPQAAAAPAAA 183 Query: 164 EELKTAAPAPKSASKPEPKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTM 223 AA A +A ++ + +E+ + G+RK IA+ + +K +PH + Sbjct: 184 APATAAASAAAAAPTGPSADQVARMYEGRTYEEVKLDGMRKTIAARLTEAKQTVPHFYLR 243 Query: 224 MEVDVTNMVAYRNSIKDSFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKK 283 ++ + ++ +R + + G L+ F +KA A AL+ P N++WAGD++++ + Sbjct: 244 RDIQLDALLKFRGELNKQLE-ARGVKLSVNDFIIKACALALQAVPDANAVWAGDRVLKME 302 Query: 284 DINISIAVATEDSLFVPVIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNN 343 ++++AVA E LF PV++N+D K++ ++ ++ LAK+ RD KL + QGG+F ++N Sbjct: 303 ASDVAVAVAIEGGLFTPVLQNSDTKSLSTLSTEMKDLAKRARDRKLAPHEYQGGSFAISN 362 Query: 344 TGSFGSVQSMGIINYPQAAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVC 403 G FG I+N P A IL V + VK+PVV +G +AV ++++ +S+DHRV+DG + Sbjct: 363 LGMFGIDNFDAIVNPPHAGILAVGAGVKKPVVGADGELAVATVMSVTMSVDHRVIDGALG 422 Query: 404 GRFLGRVKQILES 416 L +K LE+ Sbjct: 423 AELLNAIKDNLEN 435 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: 423 Number of extensions: 25 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: 441 Length adjustment: 32 Effective length of query: 392 Effective length of database: 409 Effective search space: 160328 Effective search space used: 160328 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