Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate BWI76_RS01360 BWI76_RS01360 acetyl-CoA C-acyltransferase FadA
Query= BRENDA::Q0KAI3 (392 letters) >FitnessBrowser__Koxy:BWI76_RS01360 Length = 387 Score = 283 bits (725), Expect = 5e-81 Identities = 175/401 (43%), Positives = 238/401 (59%), Gaps = 23/401 (5%) Query: 1 MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERN-KLDPGLVDDVITGCVT 59 M+Q VIVDA+R+PMGRSK G AF + A +L A +++ L+ RN L+ +DD+ GCV Sbjct: 1 MEQVVIVDAVRTPMGRSK-GGAFRHVRADDLSAHLMRSLLSRNPSLEASAIDDIYWGCVQ 59 Query: 60 QAGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIE 119 Q EQ R A L A P VPATT++R CGSS QA+H AA+ IM G + + G+E Sbjct: 60 QTLEQGFNIARNAALLAEIPHSVPATTVNRLCGSSMQALHDAARMIMTGDASVCLIGGVE 119 Query: 120 SMSRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHEL 179 M VPM + P + A G+ AE++A + +SR D ++ARSH Sbjct: 120 HMGHVPMSHGV----DFHPGLSRNVAKAAGMMGLTAEMLARLHGISREMQDQFAARSHAR 175 Query: 180 AATARESGAFRREIL--GISTPNGLVEQ---DETIRPGTSVEKLGTLQASFRNDELSARF 234 A A +SGAF+ EI+ G +G+++ DE IRP T+VE L L+ +F Sbjct: 176 AWAATQSGAFKTEIIPTGGHDADGVLKSYSYDEVIRPETTVEALAALRPAFD-------- 227 Query: 235 PQIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIP 294 P G VTAG +S +SDGA+AMLLMSES A+ LGLKPRAR + V G DP +M P+P Sbjct: 228 PVTG-TVTAGTSSALSDGAAAMLLMSESRARELGLKPRARVRSMAVVGCDPSIMGYGPVP 286 Query: 295 ASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALG---ADPARLNPRGGAIALGHPLG 351 AS+ A+KK+GL ID +E+NEAFA L + LG ++N GGAIALGHPLG Sbjct: 287 ASKLALKKAGLSASDIDVFEMNEAFAAQILPCIKDLGLMEQIDEKINLNGGAIALGHPLG 346 Query: 352 ASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 SG R+ TT+++ +E ++GL +MC G AT+ ER+ Sbjct: 347 CSGARISTTLINQMERKDAQFGLATMCIGLGQGIATVFERV 387 Lambda K H 0.318 0.132 0.384 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: 418 Number of extensions: 16 Number of successful extensions: 6 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: 392 Length of database: 387 Length adjustment: 30 Effective length of query: 362 Effective length of database: 357 Effective search space: 129234 Effective search space used: 129234 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