Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_057508008.1 ABB28_RS07330 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_001431535.1:WP_057508008.1 Length = 391 Score = 258 bits (659), Expect = 2e-73 Identities = 161/405 (39%), Positives = 233/405 (57%), Gaps = 18/405 (4%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M+ +I A RT IG + G V LGA + A + + S V +VI GC A Sbjct: 1 MSNIVIAAAKRTAIGSFLGQFNGVPTPTLGATAIAAALEASG-VPASDVTEVIMGCVLPA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 + AR AA+ GLP+S TTLN++CGSG+ A+ ++ G A +++AGG+ESM Sbjct: 60 NL-GQAPARQAAIAGGLPLSTGATTLNKVCGSGMKAIMLGHDLIKAGSASIVVAGGMESM 118 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQG----FGIDSMPETAENVAAQFNI 176 S AP ++ S R+ F ++ V+ + G + +M E AE ++ Sbjct: 119 SNAPHLLPNS-----RTGNRFGN---FQAVDHMAHDGLVNAYDGKAMGEFAECAVDKYQF 170 Query: 177 SRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLA 236 SR +QDA+A+ S +A AA A+G A EIVAV++A RKG +I ++ R D + ++ Sbjct: 171 SREEQDAYAIESVKRAQAAQASGAFADEIVAVKVASRKGEVEISIDEQPTRAD--IAKIP 228 Query: 237 KLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMG 296 L F++ GSVTA ++S ++DGA A++L S E AQ GL+ AR+V AT EP Sbjct: 229 TLRPAFKKDGSVTAASSSSISDGAAAVVLLSEEDAQARGLQPLARIVAHATHSQEPEWFT 288 Query: 297 IGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALG 356 P+ A K+L+ G LAD+D+ E+NEAFA +A +RELG+A D ++N NGGA ALG Sbjct: 289 TAPIGAIHKLLDKAGWTLADVDLFEVNEAFAVVAMAPMRELGIAHD--KLNVNGGACALG 346 Query: 357 HPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 HP+G SGARLV T +H L R G+ + T+CIG G+ A+ IE I Sbjct: 347 HPIGASGARLVVTLVHALRSRGGKRGIATLCIGGGEATAIAIELI 391 Lambda K H 0.319 0.134 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: 369 Number of extensions: 19 Number of successful extensions: 4 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