Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_011842153.1 RSPH17029_RS16020 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000015985.1:WP_011842153.1 Length = 399 Score = 326 bits (836), Expect = 6e-94 Identities = 179/396 (45%), Positives = 253/396 (63%), Gaps = 6/396 (1%) Query: 4 EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62 +V + RTP+G +GG L V + LGA+ + + R G+ E +D+VIFGC QAG Sbjct: 3 QVFICDYIRTPIGRYGGALSPVRADDLGAVPLKALMARNGGVDWEAVDDVIFGCANQAGE 62 Query: 63 -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121 +NVAR + AG+P VT TIN++CGSG+ AV AA+ I AG+AD+++AGG E+M + Sbjct: 63 DNRNVARMSALLAGLPVGVTGTTINRLCGSGMDAVLTAARQIAAGEADLVIAGGVESMSR 122 Query: 122 APFILPNARWGYRMSMPKGDLID--EMVWGGLTDVFNGYHMGITAENINDMYGITREEQD 179 APF+LP A + S D V + + M T +N+ +GI+RE QD Sbjct: 123 APFVLPKAGTAFTRSAEIHDTTIGWRFVNPAMEAAYGVDPMPQTGQNVACDFGISREAQD 182 Query: 180 AFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDIV-FDTDEHPRKSTPEAMAKLAPAFK 238 A SQT AA A +GR EI PV++ ++G+ V + DEHPR +TPEA+AKL P F Sbjct: 183 AMALASQTKAAAAQANGRLAQEITPVLVPQRRGEPVRVEQDEHPRATTPEALAKLKPLFA 242 Query: 239 KGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPAS 298 GGSVTAGN+SG+ND AAA+I+ S+ G+ P+A+V+ A+ GV P +MG+GP+PA+ Sbjct: 243 -GGSVTAGNSSGVNDGAAALILASEAAVRRHGLTPIARVLGGATAGVPPRIMGIGPVPAA 301 Query: 299 RKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGSSG 358 K + + GLT + D+IE NEAFAAQ +A R LG A++ +VN NGGAIA+GHP+G SG Sbjct: 302 LKLMARLGLTTEAFDVIELNEAFAAQGVATLRQLGIAEEDARVNPNGGAIALGHPLGMSG 361 Query: 359 ARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 ARI T ++Q+ G ++ L+ +CIG G G A+ +E Sbjct: 362 ARITGTAALQLQRTGGRRALSAMCIGVGQGIAIALE 397 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: 485 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: 399 Length adjustment: 31 Effective length of query: 365 Effective length of database: 368 Effective search space: 134320 Effective search space used: 134320 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