Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_050465357.1 AKL27_RS23765 acetyl-CoA C-acyltransferase
Query= metacyc::G185E-7833-MONOMER (386 letters) >NCBI__GCF_001189915.1:WP_050465357.1 Length = 390 Score = 378 bits (971), Expect = e-109 Identities = 203/392 (51%), Positives = 269/392 (68%), Gaps = 8/392 (2%) Query: 1 MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60 M EAY++ AVRTA G+R G L+G HP DL A L+DRT IDP +DDVI GCV G Sbjct: 1 MAEAYIVAAVRTASGRRNGRLSGWHPADLAAQTLDALVDRTGIDPELIDDVIMGCVGQAG 60 Query: 61 GQAGNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMS 120 QA NI R + LA+ PE VPG ++DRQCGSSQQA+ F AQA+MSGT D+++A GV++MS Sbjct: 61 EQALNIGRNAVLASKLPESVPGTSIDRQCGSSQQALHFAAQAVMSGTMDIVIAAGVESMS 120 Query: 121 QIPISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYSL 180 ++P+ +A ++ GF S + + Q RY + SQF G+EL+A+K+ L ++ M+R++L Sbjct: 121 RVPMGTATDFLQKNGFGSFMSPAMQ--ARYPGKRFSQFDGAELVAQKYALQKDAMDRFAL 178 Query: 181 TSHERAFAAIRAGHFENEIITVET-----ESGPFRVDEGPR-ESSLEKMAGLQPLVEGGR 234 SH +A AA +AG F NEI VE +S + DEG R ++SLE +A ++ L EGG Sbjct: 179 ESHRKAAAATQAGLFANEITPVEIRLENGDSEWHQTDEGIRYDASLESIAKVKLLSEGGT 238 Query: 235 LTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATRYAL 294 TAA SQISDGA+A+L+ +E +K + P ARIHHI DPV ML P+ AT +L Sbjct: 239 ATAASTSQISDGAAALLIVNEAGLKKLNVAPLARIHHIGLLGHDPVIMLEAPVHATLKSL 298 Query: 295 DKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKLFTT 354 K G+ IDDID E+NEAFA + +AWL+ ADP ++N NGGAIALGHPLGA+GA+L TT Sbjct: 299 KKAGMTIDDIDLFEVNEAFASIPLAWLQGTGADPQRLNVNGGAIALGHPLGASGARLMTT 358 Query: 355 MLGELERIGGRYGLQTMCEGGGTANVTIIERL 386 ++ L + R+GLQTMCE GG ANVTI+ERL Sbjct: 359 LVNALHQKQKRFGLQTMCELGGLANVTIVERL 390 Lambda K H 0.317 0.134 0.389 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: 406 Number of extensions: 13 Number of successful extensions: 3 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: 386 Length of database: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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