Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase
Query= SwissProt::Q0AVM3 (396 letters) >FitnessBrowser__Koxy:BWI76_RS16135 Length = 400 Score = 329 bits (844), Expect = 7e-95 Identities = 172/398 (43%), Positives = 256/398 (64%), Gaps = 9/398 (2%) Query: 4 EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62 + + A RTP G FGGTL + + L A+ + ++R G+ +ID+VI+GC QAG Sbjct: 3 QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGE 62 Query: 63 -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121 +NVAR ++ AG+P+ V T+N++CGS L A+ +AA+ IK+G+ +++AGG E+M + Sbjct: 63 DNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSR 122 Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITREE 177 APF++ A + +M D + W + + M TAEN+ D + I+R + Sbjct: 123 APFVMGKAESAFSRTMRMEDTT--IGWRFINPQMKALYGVDSMPETAENVADDFAISRAD 180 Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRKSTPEAMAKLAPA 236 QDAF RSQ A A E+GRF DE++ V + +KG+ ++F DEHPR +T EA+A+L Sbjct: 181 QDAFALRSQLRTAAAQEAGRFADELIAVSVPQRKGEPLLFSRDEHPRTTTAEALARLRGV 240 Query: 237 FKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPIP 296 + G+VTAGNASG+ND A A+++ S++ ++P+A+VV A+ GV P +MG GP P Sbjct: 241 VRPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATAGVAPRIMGFGPAP 300 Query: 297 ASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIGS 356 A RK L + GLT+ +D+IE NEAFAAQ++AV RDLG D VN NGGAIA+GHP+G+ Sbjct: 301 AVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGHPLGA 360 Query: 357 SGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 SG R+ +T Y++++ G + L T+CIG G G ALI+E Sbjct: 361 SGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIE 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: 447 Number of extensions: 23 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