Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate WP_010876428.1 MTH_RS03725 acetyl-CoA acetyltransferase
Query= BRENDA::I3R3D1 (383 letters) >NCBI__GCF_000008645.1:WP_010876428.1 Length = 383 Score = 297 bits (760), Expect = 4e-85 Identities = 163/382 (42%), Positives = 236/382 (61%), Gaps = 5/382 (1%) Query: 1 MDRVAIIGASMTQFGQR-DAWIRELLAEAGQAALADADVSPDEIEHLYVSNMASGEFEGQ 59 M VA+IG S T+FG+ D R+++ EAG A+ DA V +++ +YV NM++G F Q Sbjct: 1 MRDVAVIGVSQTKFGELWDVSFRDMITEAGLGAIEDAGVEGADLDAMYVGNMSAGLFIKQ 60 Query: 60 TGVPNALAHDLAAMPAYTARIDQTSSSGGAGVYAAWQSVASGASDMTMLVGGEKMTHRST 119 + + +A P + R++ +SGG + + +VASG D+ + G EKMT Sbjct: 61 EHISSLIADHAGLTPIPSTRVEAACASGGLALRSGIMAVASGYHDIVIAAGVEKMT--DV 118 Query: 120 AEATDVIASLTHPV-EYKHGVTLPSFAGLTARLYLDTYDAPRESLGKVAVKNHKNGLDNP 178 + T IA+ + E + GVT PS + AR ++ Y RE L V+V NH+N +NP Sbjct: 119 VDPTPAIATASDQEWEAQQGVTFPSLYAMMARRHMYEYGTTREQLAMVSVINHENASNNP 178 Query: 179 HAQFRKEVDLETVLDSPVVADPLRLYDFCPITDGSAALVFCSESVAREYTDDYVVISGIG 238 AQF +V +E V++S +VADPLRL D PI+DG+AA++ C +AREYTD V + Sbjct: 179 RAQFPMKVTVEQVMNSTMVADPLRLLDCSPISDGAAAVILCPADMAREYTDTPVYVKASA 238 Query: 239 GATDTHVVHERADPTTMGGVVNSSDIAYEMADLEPDDIDVAELHDMFTILEFLQSEDLGF 298 A+ T +H+R D T + VN++ A++MA L P DID+ E+HD F+I L EDLGF Sbjct: 239 QASGTIALHDRRDITRIDATVNAARNAFKMAKLTPGDIDLVEVHDCFSINGILAVEDLGF 298 Query: 299 FEKGEGWKAVEEGVTDRDGELPINTSGGLKSKGHPLGASGVAQVYEIYKQLIGDAGDRQV 358 EKGEG +A E+G+T DG++P+N SGGLK++GHPLGA+G+AQ E+ QL G+AG RQV Sbjct: 299 VEKGEGGRAFEDGMTRIDGDIPVNPSGGLKARGHPLGATGIAQAAEVVWQLRGEAGKRQV 358 Query: 359 D-ADIGLACNVGGFGNCVTTTI 379 + A+IG+ N+GG G I Sbjct: 359 EGAEIGMTHNIGGTGGTAAVHI 380 Lambda K H 0.315 0.132 0.384 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: 416 Number of extensions: 21 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: 383 Length of database: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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: 42 (22.0 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