Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_066917847.1 ACG33_RS00350 acetyl-CoA acetyltransferase
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_001579945.1:WP_066917847.1 Length = 384 Score = 367 bits (942), Expect = e-106 Identities = 197/394 (50%), Positives = 269/394 (68%), Gaps = 14/394 (3%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 M EA+IV A+R+ GR+GG L+ H ADL A V+ ALVER A +DVI GCV +G Sbjct: 1 MPEAFIVDALRSPTGRRGGSLAQVHGADLGAHVIKALVERNAVPAAEYDDVIFGCVDTIG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 AG++AR A L + +P +VPGT++DRQCGSSQQA+HFAAQAVMSG D+V+A GV++M+ Sbjct: 61 ALAGDIARTAWLVAGMPLNVPGTTIDRQCGSSQQAVHFAAQAVMSGTQDVVLAGGVQTMS 120 Query: 121 RVPMGLSSQLPAKNGFGVP--KSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYAL 178 +P+ + GF P +S G +AR+ +QF A+ IA +++SRE ++ +A Sbjct: 121 SIPISSAMLAGRPLGFTTPFAESKGWQARFGDAPVNQFYAAQRIADHWNISREAMEIFAK 180 Query: 179 QSHQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEG- 237 +SH RA+ A GRF E++P GE DE R +TLE + +++ + Sbjct: 181 ESHDRALKAMAEGRFDREVVPF---------GEF-LMDETARV-STLEKMATLQPVDPAY 229 Query: 238 GRVTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEV 297 ++TAA +S +CD A+ ++VV+EA LK+ G+KP AR+ ++V+ DP+ L AP+PAT Sbjct: 230 PKITAAVSSSVCDAASAVLVVSEAALKRYGLKPRARIVHLSVLADDPIWHLTAPIPATRN 289 Query: 298 ALKKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLM 357 ALKKAG+++ DIDL E+NEAFA V +AWL+ TG AR+NV+GGAIALGHPLG SG KLM Sbjct: 290 ALKKAGMKLEDIDLVEINEAFASVVMAWLQETGYPHARINVNGGAIALGHPLGASGTKLM 349 Query: 358 TTLVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 TTL+H L G RYGLQTMCEGGG ANVTI+ER+ Sbjct: 350 TTLLHELERTGGRYGLQTMCEGGGQANVTIIERM 383 Lambda K H 0.317 0.132 0.379 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: 456 Number of extensions: 15 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: 391 Length of database: 384 Length adjustment: 30 Effective length of query: 361 Effective length of database: 354 Effective search space: 127794 Effective search space used: 127794 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