Align Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase
Query= curated2:P44873 (393 letters) >FitnessBrowser__Dyella79:N515DRAFT_3009 Length = 427 Score = 191 bits (486), Expect = 3e-53 Identities = 137/431 (31%), Positives = 211/431 (48%), Gaps = 49/431 (11%) Query: 2 ENVVIVSAVRTPIGSFNGALSSVSAVDLGAIVIQEAIKRANIESALVNEVIMGNVLQAGL 61 + V ++ +R P N A + V + V+ ++R + + EV MG V++ Sbjct: 6 KRVGVIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVERFRLHGEELGEVAMGAVIKHSS 65 Query: 62 GQNPARQAALKAGIEKEIPSLTINKVCGSGLKSVALGAQSIISGDADIVVVGGMENMSQA 121 N AR+A L +G+ P +T + CG+ L + + A I +G + + GG + S Sbjct: 66 EWNLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTSDV 125 Query: 122 PYLLDSKVRQGV-----------KMGNLTLRDTMIE-----DGLTCASNHYHMGITAENI 165 P +L + R+ + KM T ++ E G+ MG E + Sbjct: 126 PIVLGERFRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGDHCERM 185 Query: 166 AEQYGISRQAQDELALRSQTLASQAVQLGVFDKEIVPVMVKTRKGDIIVSRDEYPKADTT 225 A+++ I R+AQD LAL S + A + G F+ +VP +G + RD + +AD++ Sbjct: 186 AKEWHIGREAQDRLALESHQKLAAAYEAGFFEDLVVPF-----RG---LKRDGFLRADSS 237 Query: 226 AEGLAKLKPAFKK---EGTVTAGNASGINDGAAALILVSESKAHALGLKAIAKIRSYASG 282 E L LKPAF K GT+TAGN++G++DGAAA++L S+ A GLK A Sbjct: 238 MEKLGTLKPAFDKISGHGTLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLDAEVA 297 Query: 283 GVDPSVMGLG----PVPATQKALKKAGINLDDIDLIEANEAFASQFL------------- 325 VD V G G P A + L + G+ L D D E +EAFA+Q L Sbjct: 298 AVD-FVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESETYCR 356 Query: 326 ---GVGKDL-NLDMNKTNIHGGAIALGHPIGASGARILVTLLHNLIEKDKKLGLATLCIG 381 G+ + L ++D K N+HG ++A GHP A+GARI+ TL L EK GL ++C Sbjct: 357 NRLGLEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLISICTA 416 Query: 382 GGQGISMIVER 392 GG G++ I+ER Sbjct: 417 GGMGVTAILER 427 Lambda K H 0.315 0.133 0.360 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: 375 Number of extensions: 14 Number of successful extensions: 6 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: 393 Length of database: 427 Length adjustment: 31 Effective length of query: 362 Effective length of database: 396 Effective search space: 143352 Effective search space used: 143352 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 17 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