Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate N515DRAFT_0938 N515DRAFT_0938 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_0938 Length = 394 Score = 202 bits (514), Expect = 1e-56 Identities = 141/406 (34%), Positives = 205/406 (50%), Gaps = 35/406 (8%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64 VI RT IG ++ G L AI+ A+++AGI ++V +V+MG + G Sbjct: 7 VIAGAKRTAIG-SFLGQFTGVPTPVLGATAIKAALEQAGIAAQDVNEVLMGCVLPANL-G 64 Query: 65 GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124 AR+A L+AGLP TT+++ C SG++AI L + + V GG ES++ Sbjct: 65 QAPARQAALKAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESMT--- 121 Query: 125 NDKMNTFHAVDPALEAIKGDVYM----------------AMLDTAETVAKRYGISRERQD 168 N H V+ GD + AM E A +Y +RE QD Sbjct: 122 ----NAPHMVNARTGIRYGDGQLVDHMAWDGLTNPYDGKAMGVFGELCADKYHFTREEQD 177 Query: 169 EYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAE 228 +++ES +R AAQQ G F EI P+ T A D+ + DE P A+ Sbjct: 178 AFAIESVKRAQAAQQNGAFAGEIVPV----------TVAGRKGDVVVDTDEQPGRSDIAK 227 Query: 229 GLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPD 288 + A R E TITA ++S +SDGA+A V++S A A+GL+PL ++ EP+ Sbjct: 228 VPSLKPAFRKENGTITAASSSSISDGAAAVVLLSADDAKARGLQPLARIVAHATHSQEPE 287 Query: 289 EMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISV 348 PV A+ ++L + G VDD+ L+E+NEAFAV + +LGI KLNVNGGA ++ Sbjct: 288 WFTTAPVSAIQKVLDKAGWKVDDVDLFEVNEAFAVVAMAPMRELGIPHAKLNVNGGACAL 347 Query: 349 GHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GHP G SG RL L + R K V ++C+GGG +A E++ Sbjct: 348 GHPIGASGTRLVVTLLNALQTRGLKRGVASLCIGGGEATAIAVELL 393 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: 394 Number of extensions: 22 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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