Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >FitnessBrowser__Putida:PP_1377 Length = 400 Score = 341 bits (874), Expect = 2e-98 Identities = 180/398 (45%), Positives = 261/398 (65%), Gaps = 9/398 (2%) Query: 4 EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62 +V + A RTP+G FGG L V + L A+ + I+R G++ +Q+DEV FGC QAG Sbjct: 3 DVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQVDEVFFGCANQAGE 62 Query: 63 -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121 +NVAR ++ AG+P+ + T+N++C SG+ AV A + I +G+ ++++AGG E+M + Sbjct: 63 DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESMSR 122 Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITREE 177 APF++ A Y +M D + W + + + M TA+N+ D Y ++R + Sbjct: 123 APFVMGKAESAYSRNMKLEDTT--IGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDIVFDTDEHPR-KSTPEAMAKLAPA 236 QDAF RSQ AA A +G F +EIVPV I KKG+I+ + DEH R ++T EA+ KL P Sbjct: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGEIIVERDEHLRPETTLEALTKLKPV 240 Query: 237 FKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIP 296 +VTAGNASG+ND AAA+I+ S + G+ P A+V+ ASGGV P VMG+GP+P Sbjct: 241 NGPDKTVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 Query: 297 ASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGS 356 A RK E+ G+ + D D+IE NEAFA+Q +AV R+LG AD +VN NGGAIA+GHP+G Sbjct: 301 AVRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 Query: 357 SGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 SGAR+++T L++++K G +KGLAT+C+G G G AL +E Sbjct: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIE 398 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: 453 Number of extensions: 18 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: 400 Length adjustment: 31 Effective length of query: 365 Effective length of database: 369 Effective search space: 134685 Effective search space used: 134685 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