Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 200842 SO1677 acetyl-CoA acetyltransferase (NCBI ptt file)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__MR1:200842 Length = 396 Score = 197 bits (502), Expect = 3e-55 Identities = 132/404 (32%), Positives = 209/404 (51%), Gaps = 29/404 (7%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62 E VIV+ RTP+G +++G+L+ +L AI+ + + P +V++V+MG + G Sbjct: 9 EIVIVAAKRTPMG-SFQGSLSGITSLSLAATAIKALLADTQVAPDKVDEVLMGCVLPAGL 67 Query: 63 TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISL 122 G AR+A L AGLP++ TT+++ C SG++ + LA + ++ + GG ES+S Sbjct: 68 -GQAPARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQ 126 Query: 123 VQ-------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDE 169 + K+ +D +A G AM A+ A +GI+RE+ D Sbjct: 127 APYLLDKARAGIRMGHGKVLDHMFLDGLEDAYTGG---AMGTFAQKTADEFGITREQMDA 183 Query: 170 YSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEG 229 ++L S + AA G F EI P++ V G D+T+ DE P E Sbjct: 184 FALSSLEKANAAINSGAFKTEIVPVT-----VSDRRG-----DVTIDTDEQPG-NARPEK 232 Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289 + L+ + TITA N+S +SDGA+A ++ + A GL L +G ++ EP Sbjct: 233 IPTLRPAFAKDGTITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPAL 292 Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349 PV A+ +LL G S D++ L+E+NEAFA+ + +LG+D K+NVNGGA ++G Sbjct: 293 FTTAPVGAMAKLLSNVGWSKDEVDLFEINEAFAMVTMLAVSELGLDMTKVNVNGGACALG 352 Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393 HP G SGARL + + R K V ++C+GGG +A E+ Sbjct: 353 HPIGCSGARLLVTLIHALKARGLKRGVASLCIGGGEATAMAIEV 396 Lambda K H 0.316 0.134 0.378 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: 429 Number of extensions: 31 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: 395 Length of database: 396 Length adjustment: 31 Effective length of query: 364 Effective length of database: 365 Effective search space: 132860 Effective search space used: 132860 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 (21.6 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