Align acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized)
to candidate WP_039104024.1 FPB0191_RS03365 acetyl-CoA C-acyltransferase
Query= ecocyc::ACETYL-COA-ACETYLTRANSFER-MONOMER (394 letters) >NCBI__GCF_000807275.1:WP_039104024.1 Length = 392 Score = 429 bits (1102), Expect = e-125 Identities = 226/392 (57%), Positives = 284/392 (72%), Gaps = 1/392 (0%) Query: 1 MKNCVIVSAVRTAIGSFNGSLASTSAIDLGATVIKAAIERAKIDSQHVDEVIMGNVLQAG 60 MK VIVSA RTAIG FNGS+AS AI+LG VI+ A++R ++D+ VDEVI+GNV+Q+G Sbjct: 1 MKKVVIVSATRTAIGHFNGSIASIDAIELGKIVIEDALKRIELDTSFVDEVIIGNVIQSG 60 Query: 61 LGQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMENMSL 120 LGQNPARQ+ LK+ L+ + FT+NKVCGSGLK++ LAAQ+I AG ++AGGMENMS Sbjct: 61 LGQNPARQSALKANLSNNIPAFTINKVCGSGLKAITLAAQSILAGDNHIMIAGGMENMSQ 120 Query: 121 APYLLDAKARSGYRLGDGQVYDVILRDGLMCATHGYHMGITAENVAKEYGITREMQDELA 180 APYL++ K R G Q+YD ++ DGL C+ + YHMG+TAE +AK Y I+R QD+ A Sbjct: 121 APYLINNKCRWNLNQGKNQLYDTLVNDGLYCSINHYHMGMTAEILAKMYDISRSDQDQFA 180 Query: 181 LHSQRKAAAAIESGAFTAEIVPVNVVTRKKTFVFSQDEFPKANSTAEALGALRPAFDKAG 240 L S + A AI +G F EIVP+ V T K+ ++F QD+ PK N + + L L P F K G Sbjct: 181 LRSHQLAQKAISNGEFIDEIVPITVKTGKEKYIFQQDQLPKFNLSLDHLSDLIPIF-KKG 239 Query: 241 TVTAGNASGINDGAAALVIMEESAALAAGLTPLARIKSYASGGVPPALMGMGPVPATQKA 300 TVT GN S ++DGAAAL+IM E+ A GL PLA I+SYASG V P LMG+G V AT+ A Sbjct: 240 TVTTGNISNLSDGAAALIIMSENRAKQLGLRPLAYIRSYASGAVNPNLMGLGSVSATKLA 299 Query: 301 LQLAGLQLADIDLIEANEAFAAQFLAVGKNLGFDSEKVNVNGGAIALGHPIGASGARILV 360 L+ A L L+DIDLIEA E FAAQFLA+ L FD K N+ GG IALGHPIG+SGARILV Sbjct: 300 LKKASLNLSDIDLIEAGETFAAQFLALCYELDFDLSKTNIRGGTIALGHPIGSSGARILV 359 Query: 361 TLLHAMQARDKTLGLATLCIGGGQGIAMVIER 392 TLL+ M DK GLATL IGGG GI++++ER Sbjct: 360 TLLYTMIHHDKQFGLATLGIGGGLGISIILER 391 Lambda K H 0.317 0.132 0.364 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: 354 Number of extensions: 12 Number of successful extensions: 2 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: 394 Length of database: 392 Length adjustment: 31 Effective length of query: 363 Effective length of database: 361 Effective search space: 131043 Effective search space used: 131043 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 (21.7 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