Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_058860019.1 AS188_RS15780 acetyl-CoA C-acyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_001482365.1:WP_058860019.1 Length = 399 Score = 335 bits (859), Expect = 1e-96 Identities = 190/408 (46%), Positives = 260/408 (63%), Gaps = 27/408 (6%) Query: 1 MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60 M E + RT +G YG +L V DL A +K AV AGI P DV+EVILGN AG Sbjct: 1 MTEAFLVGGARTPVGRYGGALSSVRPDDLAALVVKHAVTDAGIDPHDVDEVILGNANGAG 60 Query: 61 L-GQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMS 119 +N AR A AG P +P +T+N++C S L + +A+ +IKAG ADV++AGG+E+MS Sbjct: 61 EENRNVARMAWLLAGFPDTVPGITVNRLCASSLSAIIMASHMIKAGAADVVVAGGVESMS 120 Query: 120 RAPYLAN-------------NARWGYRMGNAKFV--DEMITDGLWDAFNDYHMGITAENI 164 RAP++ + G+R N +F D+M Y M TAE + Sbjct: 121 RAPWVMEKPATAFAKPGEVFDTSIGWRFTNPEFKKHDKMT----------YSMPETAEEV 170 Query: 165 AERWNISREEQDEFALASQKKAEEAIKSGQFKDEIVPVVIKGRKG-ETVVDTDEHPRFGS 223 A I+RE+ D FA+AS +KA AI +G+F DEIVPV +KGRKG ETVVDTDE PR G+ Sbjct: 171 AAVDGITREDADAFAVASHEKAIAAIDAGRFADEIVPVTVKGRKGAETVVDTDEGPRPGT 230 Query: 224 TIEGLAKLKPAFKKDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGV 283 T++ LAKL+P VTAGN+S LND A+ ++++S A++ G+ A+IV SAGV Sbjct: 231 TMDVLAKLRPVVTHGSVVTAGNSSSLNDGASAILVVSERAAEKYGLTARARIVDGASAGV 290 Query: 284 DPAIMGYGPFYATKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGA 343 P IMG GP AT+ +E+ GW + +L +E NEAFA+QSLA + L D VN +GGA Sbjct: 291 APEIMGLGPVPATQKVLERTGWGIGDLGAVELNEAFASQSLACIRRLGLDEGIVNNDGGA 350 Query: 344 IALGHPIGASGARILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391 IALGH +G+SG+R++VTL+ M++ A++GLAT+C+G GQGTA+L+EK Sbjct: 351 IALGHALGSSGSRLVVTLLGRMEREGAERGLATMCVGVGQGTAMLVEK 398 Lambda K H 0.315 0.132 0.375 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: 447 Number of extensions: 19 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: 392 Length of database: 399 Length adjustment: 31 Effective length of query: 361 Effective length of database: 368 Effective search space: 132848 Effective search space used: 132848 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