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_054341133.1 Nant_RS08065 acetyl-CoA C-acyltransferase FadA
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_001305295.1:WP_054341133.1 Length = 392 Score = 308 bits (788), Expect = 2e-88 Identities = 179/406 (44%), Positives = 245/406 (60%), Gaps = 28/406 (6%) Query: 3 EAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61 + I DGIRTP+G+ GG+ +VRA+ L+A ++ LL RNP ++ I+DV+ GC NQ Sbjct: 7 DVVIVDGIRTPMGKSKGGSFRNVRAESLSASIMKGLLARNPNVNPADIEDVVWGCVNQTK 66 Query: 62 EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121 E N+AR A +LAGLP +V G TINRLCGS + AL AA++I G+GD I GGVE M Sbjct: 67 EQGFNIARNALVLAGLPHTVGGQTINRLCGSSMSALHNAAQSIMTGNGDTFIVGGVEHMG 126 Query: 122 RAPFVMG----KAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKIS 177 + G S + +A M M TAE + ++ IS Sbjct: 127 HLNILHGIDLNSEMSKYVAKAAMM---------------------MGITAEMLGKMNGIS 165 Query: 178 REDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRG 237 RE QD F RS + +A+ +G EI+ + + G + ++ DE +RPETT E L+ Sbjct: 166 REMQDEFGARSHRLAHEARETGRFDNEIIAIEGHDANGFKSLLEQDEVIRPETTFEVLQS 225 Query: 238 LKAPFRAN-GVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMG 296 LK F G +TAG +S +DGA+ +++ S A + GL PRA I +MA AG +P +MG Sbjct: 226 LKPAFVPKVGTVTAGTSSAFSDGASGMLVMSAAKAQSLGLKPRAVIRSMAVAGCDPSIMG 285 Query: 297 LGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDD-APHVNPNGGAIAL 355 GPVPAT++ L+RAGL + D+D IELNEAFAAQ L VL+ L L D +VN NGGAIAL Sbjct: 286 YGPVPATQKALKRAGLKMDDIDYIELNEAFAAQGLAVLKGLKLLDRMEENVNLNGGAIAL 345 Query: 356 GHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 GHPLG SG R++ + L ++NG + L TMCIG+GQG+A + ER+ Sbjct: 346 GHPLGCSGTRISTTLLNVLEQKNGTFGLATMCIGMGQGVATVFERL 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: 434 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: 401 Length of database: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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