Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_110207571.1 DNK54_RS13705 thiolase family protein
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_003194585.1:WP_110207571.1 Length = 389 Score = 516 bits (1328), Expect = e-151 Identities = 257/389 (66%), Positives = 307/389 (78%), Gaps = 1/389 (0%) Query: 5 VIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNK-LDPGLVDDVITGCVTQAGE 63 +IVDA+R+P GR K G AF E+H +LL+Q ++ L+ER+ +DPG VDDVI GCV+Q GE Sbjct: 1 MIVDAVRTPSGRGKAGGAFAEVHPVDLLSQTVQTLLERSPAVDPGSVDDVIVGCVSQVGE 60 Query: 64 QSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESMSR 123 QSA PGR+AWL AG+P HVPATTIDRKCGSSQQAVHFAAQGI +G YD+V+A G+ESMSR Sbjct: 61 QSATPGRLAWLGAGYPSHVPATTIDRKCGSSQQAVHFAAQGIRSGEYDVVVAGGVESMSR 120 Query: 124 VPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELAATA 183 V MGSAR+G +PYG + R+APGLVSQGVAAELV AK+ LSR +D YSARSH+LAA A Sbjct: 121 VVMGSARMGADPYGARIAERFAPGLVSQGVAAELVTAKWGLSRTQLDEYSARSHDLAAAA 180 Query: 184 RESGAFRREILGISTPNGLVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQIGWNVTA 243 +SGAF REI+ I P G V DETIR GT+ EKL L+ F ND LSARFP++GW++TA Sbjct: 181 SDSGAFAREIIAIEAPAGPVAVDETIRRGTTAEKLAGLKPVFENDALSARFPEVGWSITA 240 Query: 244 GNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPASQRAIKKS 303 GN+SQI+D ASA+L+MS LGL PRAR + V GDDP++MLT PIPA+ + +++S Sbjct: 241 GNSSQITDAASALLIMSRRRCDELGLTPRARIHSMAVVGDDPLLMLTGPIPATHKVLERS 300 Query: 304 GLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPLGASGVRLMTTMLH 363 GL L I H E+NEAFA VPLAW DPA +NPRGGAIALGH LGASG RLMTTMLH Sbjct: 301 GLALSDIGHVELNEAFAPVPLAWLAEFDVDPATVNPRGGAIALGHALGASGARLMTTMLH 360 Query: 364 ALEDSGQRYGLQSMCEAGGMANATIIERL 392 ALED+ Q++GLQ MCEAGGMANATIIERL Sbjct: 361 ALEDNDQQFGLQLMCEAGGMANATIIERL 389 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: 541 Number of extensions: 13 Number of successful extensions: 2 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: 389 Length adjustment: 31 Effective length of query: 361 Effective length of database: 358 Effective search space: 129238 Effective search space used: 129238 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 24 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