Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate Pf6N2E2_2289 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= SwissProt::Q0AVM3 (396 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2289 Length = 383 Score = 286 bits (733), Expect = 5e-82 Identities = 173/396 (43%), Positives = 248/396 (62%), Gaps = 22/396 (5%) Query: 6 VLVGACRTPVG-TFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQA-GL 62 V+V RTP+G + GG ++ + + A ++ + ++R + ++++VI+GCV Q Sbjct: 1 VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQTLEQ 60 Query: 63 GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDKA 122 G N+AR + IP T++++CGS + A+ AAQ I G+ D+ + GG E+M Sbjct: 61 GWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMG-- 118 Query: 123 PFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYHMGITAENINDMYGITREEQDAFG 182 +SM G +D L MG+TAE + M+GITRE+QDAFG Sbjct: 119 -----------HVSMMHG--VDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFG 165 Query: 183 FRSQTLAAQAIESGRFKDEIVPVVIKGKKGDI-VFDTDEHPR-KSTPEAMAKLAPAFK-K 239 RS LA +A G+FKDEI+P+ + G + +FD DE R ++T E++A L PAF K Sbjct: 166 VRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAALKPAFNPK 225 Query: 240 GGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIPASR 299 GG+VTAG +S I D A+ +IVMS ++A +LGI+PMA + S A GVDP++MG GP+PA++ Sbjct: 226 GGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQ 285 Query: 300 KALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKM-EKVNVNGGAIAIGHPIGSSG 358 KAL++AGL I DID E NEAFAAQ++ V +DL DKM EKVN++GGAIA+GHP G SG Sbjct: 286 KALKRAGLGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSG 345 Query: 359 ARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 ARI TLL M++ G G++T+CIG G G A + E Sbjct: 346 ARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFE 381 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: 430 Number of extensions: 18 Number of successful extensions: 4 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: 383 Length adjustment: 30 Effective length of query: 366 Effective length of database: 353 Effective search space: 129198 Effective search space used: 129198 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