Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_012112924.1 XAUT_RS04530 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000017645.1:WP_012112924.1 Length = 402 Score = 317 bits (811), Expect = 5e-91 Identities = 175/393 (44%), Positives = 250/393 (63%), Gaps = 13/393 (3%) Query: 12 RTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL-GQNVARQ 69 RTP+G + G LKDV + L A + +R G+ E +D+VI GC QAG ++VAR Sbjct: 11 RTPIGRYAGALKDVRADDLAAHPIRVLKERNPGVDWEAVDDVILGCANQAGEDNRDVARM 70 Query: 70 CMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKAPFILPNA 129 + AG+P T+N++CGSGL AV + A+ I GDAD+I+AGG E+M +APF+ A Sbjct: 71 AALLAGLPVSAPGTTVNRLCGSGLDAVGIGARAIMTGDADLIVAGGVESMTRAPFVQGKA 130 Query: 130 RWGYRMSMPKGDLIDEMV-WGGLTDVFNGYH----MGITAENINDMYGITREEQDAFGFR 184 + + + ++ D + W + + + M T EN+ + + ++R +QD F +R Sbjct: 131 QEAFSR---QAEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDFQVSRADQDLFAYR 187 Query: 185 SQTLAAQAIESGRFKDEIVPVVIKGKKGDIV-FDTDEHPR-KSTPEAMAKLAPAFKK-GG 241 SQ A ++G F EI P+ +KGKKG ++ + DEHPR ++T E +A L F+K GG Sbjct: 188 SQQRVKAAQDAGFFAREIAPIEVKGKKGAVIRVEADEHPRAETTLEQLAGLKAPFRKAGG 247 Query: 242 SVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPASRKA 301 +VTAGNASG+ND A A+I+ S+ A + G+ P A+VVS GV P +MG+GP PA+RK Sbjct: 248 TVTAGNASGVNDGAGALILASEAAAKKYGLTPRARVVSVVQAGVPPRIMGIGPAPATRKL 307 Query: 302 LEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGSSGARI 361 LEK GL + DIDLIE NEAFAAQ++AV R LG D E VN NGGAIA+GHP+G SGAR+ Sbjct: 308 LEKNGLALADIDLIELNEAFAAQALAVLRQLGLPDDAEHVNPNGGAIALGHPLGMSGARL 367 Query: 362 LVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 +T + ++ RG + +AT+CIG G G A ++E Sbjct: 368 AMTAVSALEVRGGTRAVATMCIGVGQGIAALIE 400 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: 475 Number of extensions: 20 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: 402 Length adjustment: 31 Effective length of query: 365 Effective length of database: 371 Effective search space: 135415 Effective search space used: 135415 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 Apr 09 2024. 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