Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate CCNA_00820 CCNA_00820 3-ketoacyl-CoA thiolase
Query= metacyc::G185E-7833-MONOMER (386 letters) >FitnessBrowser__Caulo:CCNA_00820 Length = 390 Score = 378 bits (970), Expect = e-109 Identities = 199/394 (50%), Positives = 271/394 (68%), Gaps = 12/394 (3%) Query: 1 MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60 M EAY++ A RTA G++GG ++G HP DL L+DR+ DPA ++DVI GCV +G Sbjct: 1 MGEAYIVAAARTAGGRKGGRVSGWHPADLAGEVLNALVDRSGADPALIEDVIMGCVGQVG 60 Query: 61 GQAGNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMS 120 QA NIAR + LA+ PE VP +VDRQCGSSQQ+I F A +MSG D+++A GV++MS Sbjct: 61 EQAINIARNAVLASKLPESVPATSVDRQCGSSQQSIHFAAATVMSGAMDIVIAAGVESMS 120 Query: 121 QIP--ISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERY 178 ++P +SSA+ FG T +S + RY + SQF G+E++A+K++LSRE+++ + Sbjct: 121 RVPMGLSSALPYKNGFG----TYKSPRMEERYPGIQFSQFAGAEMLAKKYDLSREQLDAF 176 Query: 179 SLTSHERAFAAIRAGHFENEIITVETESGPFRV-----DEGPR-ESSLEKMAGLQPLVEG 232 +L SH+RA AA + G F EI+ ++ V DEG R ++++E + G++ L E Sbjct: 177 ALASHQRAMAATKGGKFAAEIVPIKVTLPDGSVETHDADEGIRWDATMESIGGVKLLSED 236 Query: 233 GRLTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATRY 292 GRLTAA +SQI DGA+ V++ +ER +K G+ P ARIHH++ DPV ML PIPAT+ Sbjct: 237 GRLTAATSSQICDGAAGVMIVNERGLKALGVAPLARIHHMTVIGHDPVIMLEAPIPATQK 296 Query: 293 ALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKLF 352 AL++ G+ IDDID E+NEAFA V AWL+ DP K+N NGGAIALGHPLG +GAKL Sbjct: 297 ALERAGMKIDDIDLYEVNEAFASVPTAWLQVTGGDPDKLNVNGGAIALGHPLGGSGAKLM 356 Query: 353 TTMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386 TT++ L+ G RYGLQTMCEGGG ANVTI+ERL Sbjct: 357 TTLVHALKDRGARYGLQTMCEGGGLANVTIVERL 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: 452 Number of extensions: 18 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 17 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