Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_041100093.1 SUTH_RS13985 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000828635.1:WP_041100093.1 Length = 402 Score = 321 bits (822), Expect = 3e-92 Identities = 181/402 (45%), Positives = 250/402 (62%), Gaps = 10/402 (2%) Query: 1 MTREVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKRAG-IKAEQIDEVIFGCVLQ 59 MT + + A RTP+G +GGTL + + LGA+ + + R G + E++DEVI+GC Q Sbjct: 1 MTEQAFICDAVRTPIGRYGGTLSGIRTDDLGALPIRALMARNGKVDWERVDEVIYGCANQ 60 Query: 60 AGL-GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTEN 118 AG +NVAR + AG+P V TIN++CGSG+ AV AA+ IK G+ +++AGG E+ Sbjct: 61 AGEDNRNVARMAGLLAGLPVAVAGATINRLCGSGMDAVGTAARAIKTGETALMIAGGVES 120 Query: 119 MDKAPFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGIT 174 M +APF++P A + S D + W + + + M TA+N+ + I Sbjct: 121 MSRAPFVMPKADSAFSRSNAVYDTT--IGWRFVNKLMKQQYGVDSMPETADNVAADFCIG 178 Query: 175 REEQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGDI-VFDTDEHPRKSTP-EAMAK 232 R EQDAF RSQ A A G FKDEI PV I KKG+ +FDTDEHPR T E +AK Sbjct: 179 RAEQDAFALRSQQRWAAAQAKGLFKDEIAPVEIAQKKGESKIFDTDEHPRPDTTLEQLAK 238 Query: 233 LAPAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGL 292 L +VTAGNASG+ND A A+++ S+ A G+ P A+VV+ A+ GV P +MG Sbjct: 239 LKGINGPDLTVTAGNASGVNDGACALLLASEAAAKAHGLTPRARVVAMATAGVAPRIMGF 298 Query: 293 GPIPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGH 352 GP PA +K L GL ++ +D+IE NEAFAAQ +AV RDLG AD +VN GGAIAIGH Sbjct: 299 GPAPAVKKLLALTGLRLEQMDVIELNEAFAAQGLAVTRDLGLADDDARVNPYGGAIAIGH 358 Query: 353 PIGSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 P+G SGAR++ T +Y++ + G + L T+CIG G G A+++E Sbjct: 359 PLGMSGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIE 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: 447 Number of extensions: 24 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 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