Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate N515DRAFT_0938 N515DRAFT_0938 acetyl-CoA C-acetyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__Dyella79:N515DRAFT_0938 Length = 394 Score = 252 bits (644), Expect = 1e-71 Identities = 160/399 (40%), Positives = 223/399 (55%), Gaps = 16/399 (4%) Query: 12 IVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGEDNR 71 I A RT IG + G + V LGA IKA E+ + +++VL GC A Sbjct: 8 IAGAKRTAIGSFLGQFTGVPTPVLGATAIKAALEQ-AGIAAQDVNEVLMGCVLPANLGQA 66 Query: 72 DVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRAPF 131 AR + L AGLP V +T+N++CGSGM A+ I+ G +++AGG+ESM+ AP Sbjct: 67 P-ARQAALKAGLPAAVGCTTVNKVCGSGMKAIMLGHDLIKAGSAAVVVAGGMESMTNAPH 125 Query: 132 VMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQDAFA 191 ++ ++ D NP K G+ E A + +RE+QDAFA Sbjct: 126 MVNARTGIRYGDGQLVDHMAWDGLTNPYDGKAMGV-----FGELCADKYHFTREEQDAFA 180 Query: 192 LRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTPFR-EN 250 + S +R AAQ+ G A EI PVT+ RK D +VVDTDE P + + K+ SL FR EN Sbjct: 181 IESVKRAQAAQQNGAFAGEIVPVTVAGRKGD-VVVDTDEQPGRSDIAKVPSLKPAFRKEN 239 Query: 251 GTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAPATRK 310 GT+TA ++S ++DGA A++L AD K L+P AR+VA AT EP P A +K Sbjct: 240 GTITAASSSSISDGAAAVVLLSADDAKARGLQPLARIVAHATHSQEPEWFTTAPVSAIQK 299 Query: 311 VLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGAR 370 VL AG ++ D+D+ E+NEAFA A+A R+LG+P +N NGGA ALGHP+G SG R Sbjct: 300 VLDKAGWKVDDVDLFEVNEAFAVVAMAPMRELGIPH--AKLNVNGGACALGHPIGASGTR 357 Query: 371 LVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIE 409 LV T LN L+ R + + ++CIG G+ A+ +E Sbjct: 358 LVVTLLNALQTR-----GLKRGVASLCIGGGEATAIAVE 391 Lambda K H 0.318 0.133 0.382 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: 379 Number of extensions: 20 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: 415 Length of database: 394 Length adjustment: 31 Effective length of query: 384 Effective length of database: 363 Effective search space: 139392 Effective search space used: 139392 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 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