Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_058860019.1 AS188_RS15780 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_001482365.1:WP_058860019.1 Length = 399 Score = 249 bits (636), Expect = 1e-70 Identities = 159/407 (39%), Positives = 221/407 (54%), Gaps = 25/407 (6%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MTEA +V ARTP+G+ Y GAL++ L ++HAV AGIDP +V++V++G A Sbjct: 1 MTEAFLVGGARTPVGR-YGGALSSVRPDDLAALVVKHAVTDAGIDPHDVDEVILGNANGA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G N+AR A L AG P T G T++R CAS L AI +A+ + ++ V GG ES+ Sbjct: 60 GEENRNVARMAWLLAGFPDTVPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESM 119 Query: 121 S---LVQNDKMNTFHAVDPALEAIKG------------DVYMAMLDTAETVAKRYGISRE 165 S V F + G + +M +TAE VA GI+RE Sbjct: 120 SRAPWVMEKPATAFAKPGEVFDTSIGWRFTNPEFKKHDKMTYSMPETAEEVAAVDGITRE 179 Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225 D +++ S + AA G+F DEI P++ K GA + + DEGPRP T Sbjct: 180 DADAFAVASHEKAIAAIDAGRFADEIVPVTVK-----GRKGA----ETVVDTDEGPRPGT 230 Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285 T + LA L+ V G +TAGN+S L+DGASA +++S++ A GL S G Sbjct: 231 TMDVLAKLRPVVTHGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGV 290 Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGA 345 P+ MG+GPV A ++L+R G + D+G ELNEAFA Q L C +LG+D +N +GGA Sbjct: 291 APEIMGLGPVPATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLGLDEGIVNNDGGA 350 Query: 346 ISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 I++GH G SG+RL L R A+ + TMCVG G G+A L E Sbjct: 351 IALGHALGSSGSRLVVTLLGRMEREGAERGLATMCVGVGQGTAMLVE 397 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: 430 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 399 Length adjustment: 31 Effective length of query: 364 Effective length of database: 368 Effective search space: 133952 Effective search space used: 133952 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