Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate Ac3H11_3920 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
Query= SwissProt::Q0AVM3 (396 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3920 Length = 403 Score = 312 bits (799), Expect = 1e-89 Identities = 176/397 (44%), Positives = 244/397 (61%), Gaps = 5/397 (1%) Query: 3 REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAG 61 R+ + A RTP G +GG L V + LGAI + + R G+ + +V +GC QAG Sbjct: 5 RQAFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAG 64 Query: 62 L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120 +NVA + AG+P EV TIN++CGSGL AV AA+ IKAG+A +++AGG E+M Sbjct: 65 EDNRNVAHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMS 124 Query: 121 KAPFILPNARWGYRMSMPKGDLID--EMVWGGLTDVFNGYHMGITAENINDMYGITREEQ 178 +APF++P A + + D V + + + M TAEN+ + I RE Q Sbjct: 125 RAPFVMPKAESAFSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQ 184 Query: 179 DAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRKSTPEAMAKLAPAF 237 D RSQ A AI++G EIVPV I KKGD I+ DEHPR+++ EA+AKL Sbjct: 185 DQMALRSQLNAVAAIKAGHLAREIVPVHIPQKKGDAIIVSQDEHPRETSLEALAKLKGVV 244 Query: 238 KKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPA 297 + G+VTAGNASG+ND A A+++ + A + G+KP A+VV A GV P +MG GP PA Sbjct: 245 RPDGTVTAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPA 304 Query: 298 SRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGSS 357 ++K L + GLTID +D+IE NEAFAAQ +AV R LG D +VN GGAIA+GHP+G+S Sbjct: 305 TQKVLAQTGLTIDHMDVIELNEAFAAQGLAVLRALGLKDDDGRVNAWGGAIALGHPLGAS 364 Query: 358 GARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 GAR++ T + + + + L T+CIG G G A+I+E Sbjct: 365 GARLVTTAVNRLHEHAGQYALCTMCIGVGQGIAVILE 401 Lambda K H 0.317 0.135 0.387 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: 451 Number of extensions: 22 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: 396 Length of database: 403 Length adjustment: 31 Effective length of query: 365 Effective length of database: 372 Effective search space: 135780 Effective search space used: 135780 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 (21.7 bits) S2: 50 (23.9 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