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) >lcl|FitnessBrowser__Koxy:BWI76_RS01360 BWI76_RS01360 acetyl-CoA C-acyltransferase FadA 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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