Align acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized)
to candidate WP_110804969.1 C8J30_RS06880 acetyl-CoA C-acetyltransferase
Query= ecocyc::ACETYL-COA-ACETYLTRANSFER-MONOMER (394 letters) >NCBI__GCF_003217355.1:WP_110804969.1 Length = 403 Score = 263 bits (671), Expect = 9e-75 Identities = 167/418 (39%), Positives = 229/418 (54%), Gaps = 40/418 (9%) Query: 1 MKNCVIVSAVRTAIGS--FNGSLASTSAIDLGATVIKAAIERAKIDSQHVDEVIMGNVLQ 58 M I A RT G +GSL +++ L A ++ A ER + V++VI GNV Q Sbjct: 1 MTEAYIYDACRTPRGKGRADGSLHEVTSVALSARLLDAVAERNGLTGHAVEDVIWGNVTQ 60 Query: 59 AG-LGQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMEN 117 G G AR A+L SGL E++ G ++N+ C SG+++V LAA ++AG + +AGG+E Sbjct: 61 VGEQGGCLARSAVLLSGLDESIPGLSINRFCASGMEAVNLAANQVKAGAGAAYIAGGVEM 120 Query: 118 MSLAPYLLDAKARSGYRLGDGQVYDVILRDGLMCATHGYHMGITAENVAKEYGITREMQD 177 MS D A + + L T+ GI+A+ +A EYG TREM D Sbjct: 121 MSRVAMGSDGAA-------------IAVDPSLAMKTYFVPQGISADVIATEYGFTREMAD 167 Query: 178 ELALHSQRKAAAAIESGAFTAEIVPVNVVTRKKTFVFSQDEFPKANSTAEALGALRPAFD 237 LA+ SQR+AA A F IVPV + + +DE+ + +T E L L+PAF Sbjct: 168 ALAVESQRRAAEAWAENRFAKSIVPVR--DQNGLIILERDEYLRPGTTMEDLAKLKPAFK 225 Query: 238 KAGTVT----------------------AGNASGINDGAAALVIMEESAALAAGLTPLAR 275 G V AGN+SGI DGAAA++I + A GL P AR Sbjct: 226 DMGEVMPGFDKVAMLKYPHLERIEHIHHAGNSSGIVDGAAAVLIGSKEFGEAHGLKPRAR 285 Query: 276 IKSYASGGVPPALMGMGPVPATQKALQLAGLQLADIDLIEANEAFAAQFLAVGKNLGFDS 335 I++ A G P +M GPVP T+K L+ +G+ ++DIDL E NEAFAA L + Sbjct: 286 IRATAKIGTDPTIMLTGPVPVTEKILRDSGMSISDIDLFEVNEAFAAVVLRFMQAFDVGQ 345 Query: 336 EKVNVNGGAIALGHPIGASGARILVTLLHAMQARDKTLGLATLCIGGGQGIAMVIERL 393 +KVNVNGGA+ALGHP+GA+GA I+ TLL ++ RD + GLATLCI G G A +IER+ Sbjct: 346 DKVNVNGGAMALGHPLGATGAIIIGTLLDELERRDLSTGLATLCIASGMGAATIIERV 403 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: 414 Number of extensions: 14 Number of successful extensions: 5 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: 403 Length adjustment: 31 Effective length of query: 363 Effective length of database: 372 Effective search space: 135036 Effective search space used: 135036 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