Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_055437058.1 ASC41_RS12920 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_001418085.1:WP_055437058.1 Length = 392 Score = 226 bits (575), Expect = 1e-63 Identities = 147/399 (36%), Positives = 221/399 (55%), Gaps = 21/399 (5%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62 E VIVS ARTPIG ++ GAL+ L AI+ A+++ ++P+ V++V+MG +Q G Sbjct: 4 EVVIVSAARTPIG-SFLGALSTIPAPKLGAIAIKGALEKINLNPELVQEVLMGNVVQAG- 61 Query: 63 TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISL 122 TG AR+A + AG+P T TTI++ CASG++ + AA+S+ EI V GG E++SL Sbjct: 62 TGQAPARQAAIFAGIPNTVPCTTINKVCASGMKTVMQAAQSIALGDAEIVVAGGMENMSL 121 Query: 123 VQN-------DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEYSLE 173 + + K VD + DVY AM +A+ A +Y SRE QD Y+++ Sbjct: 122 IPHYFHARSATKFGPATMVDGMQKDGLVDVYDQQAMGVSADACATKYEFSREDQDAYAIQ 181 Query: 174 SQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233 S +R+AAA + GKFN+EI P++ D D+ +++DE + + + L Sbjct: 182 SYKRSAAAWEAGKFNNEIVPVAVPQRRGD---------DVIVTEDEEYK-NVRMDKIPTL 231 Query: 234 KAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIG 293 +A + T+TA NAS ++DGA A V+MS + A GLK L +G EP+ Sbjct: 232 RAAFTKEGTVTAANASTINDGAGAMVLMSREKANELGLKVLATIKGYADAAHEPEWFTTA 291 Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353 P A+P+ L + GL + D+ +E NEAF++ L LG++ +NVNGGA+S+GHP G Sbjct: 292 PSIALPKALNKAGLDIKDVDFFEFNEAFSIVGLANMKILGLNDSNVNVNGGAVSLGHPLG 351 Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 SG R+ L + AK +C GGG SA + E Sbjct: 352 CSGVRILITLLNVLEQNDAKIGAAAICNGGGGASALVLE 390 Lambda K H 0.316 0.134 0.378 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: 395 Number of extensions: 18 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: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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