Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate AO356_20395 AO356_20395 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20395 Length = 401 Score = 271 bits (692), Expect = 3e-77 Identities = 169/423 (39%), Positives = 234/423 (55%), Gaps = 44/423 (10%) Query: 1 MREAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCAN 58 M +A I D +RTP G+ GAL SV+ +L L L R LD +DD++LGC Sbjct: 1 MTQALIFDALRTPRGKGKADGALHSVKPVNLMGGLLSALRQRMD-LDTSQVDDIVLGCVT 59 Query: 59 QAGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVE 118 GE ++A+ A L+A SV+G +NR C SGL+A+ AA +++G DL++AGGVE Sbjct: 60 PVGEQGADIAKTAALVANWDVSVAGVQLNRFCASGLEAVNLAAMKVRSGFEDLVVAGGVE 119 Query: 119 SMSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISR 178 SMSR P A A Q+ + + Q G D +A L SR Sbjct: 120 SMSRVPMGSDGGAWALDPQSNL---------QGHFIPQGIGADL-------IATLEGFSR 163 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 ED D +AL SQQ+ A+A++ G + +V V +++ G+V + HDE +R ++TLE L L Sbjct: 164 EDVDRYALHSQQKAARARADGSFDKSLVAV--RDQNGIVL-LDHDEFIRADSTLEGLGKL 220 Query: 239 KAPFRANG--------------------VITAGNASGVNDGAAALIIASEQMAAAQGLTP 278 K F A G V T GN+SG+ DGAA ++I SE A GL P Sbjct: 221 KPSFEAMGQMGFDGTALRVYSHVERIHHVHTPGNSSGIVDGAALMLIGSEAKGRAMGLQP 280 Query: 279 RARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELG 338 RARIVA A +P +M GP PATR+ L +AGL + D+D+ E+NEAFA+ L +R++ Sbjct: 281 RARIVATAVTSTDPTIMLTGPAPATRKALAKAGLRVEDIDLFEVNEAFASVVLKFIRDMA 340 Query: 339 LPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMIL 398 + D VN NGG+IALGHPLG +G + EL R RY L T+C+G G GIA ++ Sbjct: 341 I--DPAKVNVNGGSIALGHPLGATGCAILGTLLDELEARRLRYGLATLCVGGGMGIATVI 398 Query: 399 ERV 401 ER+ Sbjct: 399 ERL 401 Lambda K H 0.319 0.135 0.384 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: 424 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: 401 Length of database: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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