Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate 3610436 Dshi_3817 beta-ketoadipyl CoA thiolase (RefSeq)
Query= SwissProt::Q0AVM3 (396 letters) >FitnessBrowser__Dino:3610436 Length = 400 Score = 320 bits (821), Expect = 3e-92 Identities = 180/399 (45%), Positives = 251/399 (62%), Gaps = 10/399 (2%) Query: 4 EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62 + V+ RTP+G +GG L V + L A+ + + R G+ ++DEVI+G QAG Sbjct: 2 DAVICDGVRTPIGRYGGALSSVRADDLAALPIAALMARNPGVDWARVDEVIYGAANQAGE 61 Query: 63 -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121 +NVAR + AG+P+EV T+N++C SG+ AV AA+ IKAG+ D+ +AGG E+M + Sbjct: 62 DNRNVARMAALLAGLPEEVPGLTVNRLCASGMDAVGAAARGIKAGEYDLAIAGGIESMSR 121 Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITREE 177 APF++P A + + D + W + H M TA+ + Y I+R + Sbjct: 122 APFVMPKAESAFTRAATVHDTT--IGWRFVNPKIAAMHGIDTMPQTADTVAAAYEISRAD 179 Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGK-KGDIVFDTDEHPRKSTPEA-MAKLAP 235 QDAF RSQ A A +G F DEIVPV + + I+ D DEHPR T A +A L Sbjct: 180 QDAFAARSQARWAAADAAGLFADEIVPVPVPQRGSAPILVDRDEHPRPGTDAARLAGLKG 239 Query: 236 AFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPI 295 G SVTAGNASG+ND AAA+++ S A G+ PMA+VV AS GV P VMG+GP+ Sbjct: 240 INGPGLSVTAGNASGVNDGAAALLIASAAAARAHGLTPMARVVGMASAGVAPRVMGIGPV 299 Query: 296 PASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIG 355 PASRK L++AGLT+D +D+IE NEAFA+QS+A R LG AD +VN NGGAIA+GHP+G Sbjct: 300 PASRKLLDRAGLTLDQMDVIELNEAFASQSLATLRQLGLADDDVRVNPNGGAIAMGHPLG 359 Query: 356 SSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 SGAR+++T +++++ G + L T+C+G G GTALI+E Sbjct: 360 MSGARLVLTAAHQLRRTGGRYALCTMCVGVGQGTALILE 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: 487 Number of extensions: 25 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: 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