Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate WP_012647510.1 GEOB_RS12065 thiolase family protein
Query= BRENDA::I3R3D1 (383 letters) >NCBI__GCF_000022265.1:WP_012647510.1 Length = 390 Score = 169 bits (427), Expect = 2e-46 Identities = 117/359 (32%), Positives = 182/359 (50%), Gaps = 12/359 (3%) Query: 4 VAIIGASMTQFGQRDAWIRELLAEAGQAALADADVS-PDEIEHLYVSNMASGEFEGQTGV 62 V I G T+FG+ L EA A+ +++ PD ++ YV N + GQT V Sbjct: 7 VYIAGVGETKFGKHTVDFDVLGREAALQAMRGSNIDRPDMVQSAYVGNGMNDMVTGQT-V 65 Query: 63 PNALAHDLAAMPAYTARIDQTSSSGGAGVYAAWQSVASGASDMTMLVGGEKMT-HRSTAE 121 L +P + S+G V+ A + VA+G +D+++ VG E T HR + Sbjct: 66 FRGLGMCGPNLPIIN--VQSACSAGAMAVFCAIKDVATGVTDLSIGVGCENHTMHRQSGA 123 Query: 122 ATDVIASLTHPVEYKHGVTLPSFAGLTARLYLDTYDAPRESLGKVAVKNHKNGLDNPHAQ 181 A S +E HG + + A Y+ A E L + VKN K+ NPHA Sbjct: 124 AFSAARS---DIETMHGAVMTGKYAMRATRYMHETGATIEDLAMITVKNRKHATHNPHAW 180 Query: 182 FRKEVDLETVLDSPVVADPLRLYDFCPITDGSAALVFCSESVAREY-TDDYVVISGIGGA 240 F+ + +E V++S +VA P+ L C I DG+AA+V S+ + ++ V ++G+ Sbjct: 181 FKGPITIEEVVNSRMVAYPMTLQQCCGIADGAAAVVVGSKEMMKKLGIAKPVRVAGV--V 238 Query: 241 TDTHVVHERADPTTMGGVVNS-SDIAYEMADLEPDDIDVAELHDMFTILEFLQSEDLGFF 299 ++ H R T + + S+ YE + + PD++++ ELHD FTI E L E +G Sbjct: 239 VESGPYHNRPRDITGDDITETTSEKLYEESGIGPDEVNILELHDAFTISELLYYECMGLC 298 Query: 300 EKGEGWKAVEEGVTDRDGELPINTSGGLKSKGHPLGASGVAQVYEIYKQLIGDAGDRQV 358 +KGEG K + +G + G+ ++ GG+ S GHP+GASG AQV + KQL G+ G QV Sbjct: 299 KKGEGLKFLRDGQSTYGGKCVVSPRGGMLSYGHPIGASGAAQVAQNVKQLRGECGGHQV 357 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: 393 Number of extensions: 25 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: 390 Length adjustment: 30 Effective length of query: 353 Effective length of database: 360 Effective search space: 127080 Effective search space used: 127080 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