Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate N515DRAFT_2688 N515DRAFT_2688 acetyl-CoA acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_2688 Length = 401 Score = 281 bits (718), Expect = 3e-80 Identities = 171/397 (43%), Positives = 230/397 (57%), Gaps = 11/397 (2%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQQG 61 +A IV+ RTP+GKA RG T +L H I + +A GID + DV++G AM + Sbjct: 7 DAYIVAATRTPVGKAPRGVFRNTRPDDMLAHVIRAVMAQAPGIDAHRIGDVIVGCAMPEA 66 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 G N+AR LL AGLP T G T++R C+SG+QAIA AA + ++ + G ES+S Sbjct: 67 EQGMNVARIGLLLAGLPDTVPGVTVNRFCSSGVQAIAQAADRIRLGEADLMIAAGTESMS 126 Query: 122 LVQNDKMNTFHAVDPAL---EAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRT 178 +V M A++P + E I + M TAE VAK++ ISRE QD ++ S R Sbjct: 127 MVP--MMGHKVAMNPGIFDNEHI--GIAYGMGITAENVAKQWKISREEQDTFAAASHERA 182 Query: 179 AAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAV-- 236 AA + G+F DEI P D AT ++ + DEGPRP +T E L LK V Sbjct: 183 LAAIKAGEFKDEITPFKLDDHYPDLATRSIKTDSRLIDTDEGPRPGSTVEVLGKLKPVFR 242 Query: 237 RGE-GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPV 295 G+ G ++TAGN+SQ SDGA A ++ S+ GL P+ F G PD MGIGP Sbjct: 243 NGQFGGSVTAGNSSQTSDGAGAVLLASEAAIKEYGLTPIARFVSYSVAGVRPDIMGIGPK 302 Query: 296 FAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMS 355 A+P+ LK+ G++ D + ELNEAFA Q L LG+DP K+N GGAI++GHP G + Sbjct: 303 EAIPKALKQAGMTQDQLDWIELNEAFAAQSLAVIKDLGLDPSKINPLGGAIALGHPLGAT 362 Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 GA A + RRRK KY +VTMC+G GMG+AG+FE Sbjct: 363 GAIRAATLVHGMRRRKQKYGMVTMCIGTGMGAAGIFE 399 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: 417 Number of extensions: 16 Number of successful extensions: 4 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: 401 Length adjustment: 31 Effective length of query: 364 Effective length of database: 370 Effective search space: 134680 Effective search space used: 134680 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