Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >FitnessBrowser__Smeli:SM_b20589 Length = 400 Score = 337 bits (864), Expect = 4e-97 Identities = 183/400 (45%), Positives = 260/400 (65%), Gaps = 11/400 (2%) Query: 3 REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAG 61 RE + RTP+G FGG+L V + LGAI + + R + E +D+VIFGC QAG Sbjct: 2 REAYICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQAG 61 Query: 62 L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120 +N+AR ++ AG+P V TIN++CGSG+ AV AA+ IK G+A++++AGG E+M Sbjct: 62 EDNRNIARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESMS 121 Query: 121 KAPFILPNARWGYRMSMPKGDLIDEMV-WGGLTDVFNGYH----MGITAENINDMYGITR 175 +APF+LP A + + ++ D + W + + + M T EN+ + Y ++R Sbjct: 122 RAPFVLPKAESAFSRN---AEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDYKVSR 178 Query: 176 EEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRKSTPEAMAKLA 234 E+QDAF RSQ AA A +GR EIV V I +KG +V D DEHPR +T EA+A L Sbjct: 179 EDQDAFALRSQAKAAAAQANGRLASEIVAVTIPQRKGGPVVIDRDEHPRATTIEALAGLK 238 Query: 235 PAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGP 294 F++GG+VTAGNASG+ND AAA+I+ S+E A + G++PMA+++ AS GV P +MG+GP Sbjct: 239 TPFREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMGMGP 298 Query: 295 IPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPI 354 +PAS++ + + G T D D+IE NEAFA+Q +AV R LG AD +VN NGGAIA+GHP+ Sbjct: 299 VPASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNRNGGAIALGHPL 358 Query: 355 GSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 G SGARI T E+ + G + L+T+CIG G G A+ +E Sbjct: 359 GMSGARITGTAALELAETGGRTSLSTMCIGVGQGIAVALE 398 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: 461 Number of extensions: 21 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: 400 Length adjustment: 31 Effective length of query: 365 Effective length of database: 369 Effective search space: 134685 Effective search space used: 134685 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