Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_017599366.1 D471_RS0114985 acetyl-CoA C-acyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000341125.1:WP_017599366.1 Length = 380 Score = 276 bits (705), Expect = 9e-79 Identities = 170/403 (42%), Positives = 235/403 (58%), Gaps = 25/403 (6%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M EA+I +RTP+G GAL++V DL A L+EL+ R +D ++DV++GC QA Sbjct: 1 MAEAYIVGAVRTPVGTKKGALAAVHPADLGAHVLKELVTRTG-VDPAAVEDVVMGCVTQA 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 G ++AR A L AG P+SV G TI+R CGS A+ FAA+ + +G DL++A GVE+M Sbjct: 60 GPQALDLARTAWLSAGFPESVPGVTIDRQCGSSQQAVHFAAQGVMSGTQDLVVASGVENM 119 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPET--AENVAELLKISR 178 P MG A F+ + GW +++GT + + A+ + E R Sbjct: 120 GMVP--MG-ANVQFAIDNGLGLYGEGW-------VERYGTQEISQFRGAQLMCEKWGYKR 169 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 E+ + FAL S QR A+A G ++I P+ + DE +R +TTLE++ GL Sbjct: 170 EELERFALESHQRAARAIEDGRFDDQIAPLA---------GVARDEGVRADTTLEKMAGL 220 Query: 239 KAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLG 298 K P R +TA AS ++ GA A+++ASE+ GLTP ARIV ++ G +P M Sbjct: 221 K-PLREGWELTAAVASQISVGAGAVLLASERAVREHGLTPLARIVQLSLVGDDPVYMLTA 279 Query: 299 PVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHP 358 P+PATR L++AGL+I D+DV E+NEAFA + + ELG D VNPNGGAIALGHP Sbjct: 280 PIPATRIALDKAGLTIDDIDVTEINEAFAPVPMSWIEELGA--DPAKVNPNGGAIALGHP 337 Query: 359 LGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 LG +GA L +ELHR GRY L TMC G GQ ++ERV Sbjct: 338 LGATGAVLMTKLVNELHRSGGRYGLQTMCEGGGQANVTVIERV 380 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: 423 Number of extensions: 19 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: 401 Length of database: 380 Length adjustment: 31 Effective length of query: 370 Effective length of database: 349 Effective search space: 129130 Effective search space used: 129130 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 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