Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_004299880.1 C665_RS03170 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000310185.1:WP_004299880.1 Length = 401 Score = 340 bits (873), Expect = 3e-98 Identities = 187/397 (47%), Positives = 261/397 (65%), Gaps = 6/397 (1%) Query: 4 EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62 + + A RTP+G +GGTL V + LGA+ + + R + ++++I+GC QAG Sbjct: 3 QAFICDAIRTPIGRYGGTLASVRADDLGAVPLKALMTRNPQVDWTAVEDIIYGCANQAGE 62 Query: 63 -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121 +NVAR + AG+P EV T+N++CGSG+ A+ LAA+ IK+G+ ++++AGG E+M + Sbjct: 63 DNRNVARMSGLLAGLPIEVPGTTVNRLCGSGMDAIGLAARSIKSGETELMIAGGVESMSR 122 Query: 122 APFILPNARWGYRMSMPKGDLID--EMVWGGLTDVFNGYHMGITAENINDMYGITREEQD 179 APF++ A + S D + + ++ + M TA+N+ + I+R +QD Sbjct: 123 APFVMGKAESAFSRSAAIYDTTIGWRFINPLMKKLYETHSMPQTADNVAADFDISRADQD 182 Query: 180 AFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPR-KSTPEAMAKLAPAF 237 AF RSQ A A +GRFKDE+VPVVI KKGD IVFDTDEHPR ++T E +AKL Sbjct: 183 AFALRSQQRWAAAHAAGRFKDELVPVVIPRKKGDPIVFDTDEHPRPETTLEMLAKLKGVN 242 Query: 238 KKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPA 297 SVTAGNASG+ND A A+++ S A + G+ P A+VV+ A+ GV P +MG GP PA Sbjct: 243 GPELSVTAGNASGVNDGACALLLASDAAAAKHGLTPRARVVAMATAGVAPRIMGFGPAPA 302 Query: 298 SRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGSS 357 RK L KAGLT+D +D+IE NEAFAAQ +AV RDLG AD E+VN NGGAIA+GHP+G S Sbjct: 303 VRKVLAKAGLTLDQMDVIELNEAFAAQGLAVLRDLGLADDEERVNPNGGAIALGHPLGMS 362 Query: 358 GARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 GAR++ T YE+Q+R + L T+CIG G G A+I+E Sbjct: 363 GARLVTTAAYELQRRNGRYALCTMCIGVGQGIAMIIE 399 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: 443 Number of extensions: 24 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: 401 Length adjustment: 31 Effective length of query: 365 Effective length of database: 370 Effective search space: 135050 Effective search space used: 135050 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 24 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