Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_012047377.1 BBTA_RS35760 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000015165.1:WP_012047377.1 Length = 402 Score = 325 bits (832), Expect = 2e-93 Identities = 181/403 (44%), Positives = 251/403 (62%), Gaps = 12/403 (2%) Query: 3 REVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEA-IKRAGIKAEQIDEVIFGCVLQAG 61 R+V + A RTP+G FGG+L V + L A + K + +DEV FGC QAG Sbjct: 2 RDVFICDAVRTPIGRFGGSLAKVRTDDLAATPLKALKAKHPNLDWAAVDEVFFGCANQAG 61 Query: 62 L-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMD 120 +NVAR ++ AG+P + T+N++C SGL AV A + I+AG+ D+ +AGG E+M Sbjct: 62 EDNRNVARMALLLAGLPDSIPGQTLNRLCASGLDAVGAAGRAIRAGEVDLAIAGGVESMT 121 Query: 121 KAPFILPNARWGYRMSMPKGDLIDEMV-WGGLTDVFNGYH----MGITAENINDMYGITR 175 +APF+ A + S ++ D + W + + + M T EN+ + + ++R Sbjct: 122 RAPFVQGKATEAFSRS---AEIFDTTIGWRFINPLMKQQYGVDSMPETGENVAEEFQVSR 178 Query: 176 EEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKG-KKGDIVFDTDEHPR-KSTPEAMAKL 233 +QDAF RSQ A QAI SG F EI PV + G K G I D DEHPR ++T E +AKL Sbjct: 179 ADQDAFAIRSQQRAGQAIASGYFAAEITPVSVPGGKAGPITVDKDEHPRPETTLEGLAKL 238 Query: 234 APAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLG 293 P + G+VTAGNASG+ND AAA+I+ S+ + G+ P A+V+ AS GV P +MG+G Sbjct: 239 KPIVRNPGTVTAGNASGVNDGAAAMILASEAAVKKHGLTPRARVLGLASAGVPPRIMGIG 298 Query: 294 PIPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHP 353 P+PA RK +E+ GL I D DLIE NEAFA+Q IA R LG A+ + VN +GGAIA+GHP Sbjct: 299 PVPAVRKLMERLGLKITDFDLIELNEAFASQGIACLRQLGVAEDADFVNPHGGAIALGHP 358 Query: 354 IGSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVEAL 396 +G SGARI +T ++ ++ RG K+ LAT+C+G G G AL VE L Sbjct: 359 LGMSGARIAMTAVHGLEVRGGKRALATMCVGVGQGVALAVEKL 401 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: 444 Number of extensions: 23 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: 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 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