Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_058931411.1 AU252_RS15005 thiolase family protein
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_001484605.1:WP_058931411.1 Length = 403 Score = 275 bits (703), Expect = 2e-78 Identities = 171/414 (41%), Positives = 230/414 (55%), Gaps = 31/414 (7%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EA +V RTP+G+ Y GAL+A L I AV RAG+DP +E+V++G A Sbjct: 1 MVEAFLVGGVRTPVGR-YGGALSAVRPDDLAALVIREAVSRAGLDPDSIEEVILGNANGA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G N+AR A+L AGLP+ G T++R CASGL AI A+ + ++ + GG ES+ Sbjct: 60 GEENRNVARMAVLLAGLPLHIPGITVNRLCASGLSAIIQASHMIKSGAADVVIAGGVESM 119 Query: 121 SLVQ--NDKMNTFHA--------------VDPALE----AIKGDVYMAMLDTAETVAKRY 160 S +K T A V+P + A G + +M +TAE VA+ Sbjct: 120 SRAPWAQEKPATAFAKPGQIFDTSIGWRFVNPLFQKGGLARDGKMTYSMPETAEEVARVD 179 Query: 161 GISRERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEG 220 GI+RE D +++ S R+ AA G+F DEI P++ K + + DEG Sbjct: 180 GITREDADAFAVRSHERSLAAIAAGRFRDEIVPVTVKSRKAETV----------VDTDEG 229 Query: 221 PRPETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGM 280 PR TT E LAGL+ V G +TAGN+S L+DGASA ++ S+ A GL P Sbjct: 230 PRAGTTLEVLAGLRPVVPGGSVVTAGNSSTLNDGASAIIVASEAAIARLGLTPRARIIDG 289 Query: 281 VSYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLN 340 S GCEP+ MGIGPV A ++L R GLS D+G ELNEAFA Q L +LG+DP+ +N Sbjct: 290 ASAGCEPEIMGIGPVPATQKVLARSGLSASDLGAVELNEAFATQSLASMRRLGLDPDTVN 349 Query: 341 VNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 +GGAIS+GHP G SG+R+A L R A+ + TMCVG G G+A L E V Sbjct: 350 NDGGAISLGHPLGSSGSRIAITLLGRMEREDARIGLATMCVGVGQGTAMLLERV 403 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: 433 Number of extensions: 21 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: 403 Length adjustment: 31 Effective length of query: 364 Effective length of database: 372 Effective search space: 135408 Effective search space used: 135408 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