Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_058929120.1 AU252_RS00950 thiolase family protein
Query= metacyc::G185E-7833-MONOMER (386 letters) >NCBI__GCF_001484605.1:WP_058929120.1 Length = 385 Score = 348 bits (892), Expect = e-100 Identities = 196/389 (50%), Positives = 253/389 (65%), Gaps = 13/389 (3%) Query: 3 EAYVIDAVRTAVG---KRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAI 59 +A V+ A R+AVG G +G+H VDL A R ++D + IDP +DDV GCV + Sbjct: 5 DAVVVLAKRSAVGLGRPEKGVFSGMHSVDLSAQVLRAVVDESGIDPVLIDDVHWGCVSQV 64 Query: 60 GGQAGNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNM 119 G Q+ N+ R + LAAG PE VPG TVDRQCGSSQQ I A IM+G AD+++AGGV+ M Sbjct: 65 GEQSFNVGRNAVLAAGLPESVPGTTVDRQCGSSQQTIHNAAAQIMAGHADIVIAGGVEVM 124 Query: 120 SQIPISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYS 179 S+ P+ S G G P KQ + +Q IS +E+IAEKW LSR ++ + Sbjct: 125 SRTPMFSNTQGGA--GPFGPM--MKQRYPKLVNQGIS----AEMIAEKWGLSRTYLDEMA 176 Query: 180 LTSHERAFAAIRAGHFENEIITVETESGPFRVDEGPRE-SSLEKMAGL-QPLVEGGRLTA 237 + SH RA A G FE EI+ +ET SG D+G R S++EK+AGL P EGG +TA Sbjct: 177 VESHRRAAEATAKGLFEREIVPIETASGTVTTDQGIRPGSTVEKLAGLPNPFKEGGVVTA 236 Query: 238 AMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATRYALDKT 297 ASQ+SDG++A++L S ++ GL+P AR+H +S DP+ MLT PIPAT L + Sbjct: 237 GNASQLSDGSAALMLMSSEKARELGLKPIARVHSVSVIGDDPIMMLTAPIPATAKVLKRA 296 Query: 298 GLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKLFTTMLG 357 GL+I+DI +EINEAFA VV AWL E ADP KVNP GGA+ALGHPLG +GA+L TT+L Sbjct: 297 GLSIEDIGVIEINEAFASVVGAWLSETGADPQKVNPRGGAMALGHPLGGSGARLATTLLH 356 Query: 358 ELERIGGRYGLQTMCEGGGTANVTIIERL 386 ++ G +YGLQTMCEGGG AN TI E L Sbjct: 357 IMQDTGAQYGLQTMCEGGGMANATIFELL 385 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: 414 Number of extensions: 20 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: 385 Length adjustment: 30 Effective length of query: 356 Effective length of database: 355 Effective search space: 126380 Effective search space used: 126380 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 Apr 09 2024. 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