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_011912882.1 PST_RS08740 acetyl-CoA C-acyltransferase FadA
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000013785.1:WP_011912882.1 Length = 391 Score = 294 bits (752), Expect = 3e-84 Identities = 173/405 (42%), Positives = 242/405 (59%), Gaps = 24/405 (5%) Query: 2 REAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 R+A I D RTP+GR GG + RA+ ++A + LL RNP++D ++DVI GC NQ Sbjct: 6 RDAVIVDFGRTPMGRSKGGMHRNTRAETMSAQLIDGLLARNPKIDPAEVEDVIWGCVNQT 65 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 E N+ARMA+LL +P + +G T++RLCGS + AL A +AI+ +GD+ + GGVE M Sbjct: 66 LEQGWNIARMASLLTRIPHTSAGQTVSRLCGSSMSALHTAVQAIQTNNGDVFVIGGVEHM 125 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS--MPETAENVAELLKISR 178 + G NP ++ S M TAE + ++ I+R Sbjct: 126 GHVSMMHGVDP-------------------NPQLSLHAAKASGMMGLTAEMLGKMHGITR 166 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 E QD F RS Q KA G +EI+P+ ++ G + +DE +RPETTLE L L Sbjct: 167 EAQDQFGYRSHQLAWKATQEGKFKDEIIPMEGHDENGFLKVFDYDETIRPETTLEGLAEL 226 Query: 239 KAPFRANG-VITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGL 297 K F G +TAG +S + DGA+ +I+ S Q A GL P A + AMA AGV+P +MG Sbjct: 227 KPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAKDLGLQPMAVVRAMALAGVDPAIMGY 286 Query: 298 GPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPH-VNPNGGAIALG 356 GPVP+T++ L+RAGL++ D+ +ELNEAFAAQAL VL++L L D VN +GGAIALG Sbjct: 287 GPVPSTQKALKRAGLTMDDISHVELNEAFAAQALPVLKDLKLLDKMEEKVNLHGGAIALG 346 Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 HP G SGAR++ + + + NG + TMCIG+GQGI+ + ER+ Sbjct: 347 HPFGCSGARISGTLLNVMKQNNGTLGVATMCIGLGQGISTVFERL 391 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: 427 Number of extensions: 18 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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