Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_033100436.1 JG50_RS0107240 acetyl-CoA C-acetyltransferase
Query= SwissProt::P45855 (393 letters) >NCBI__GCF_000763315.1:WP_033100436.1 Length = 393 Score = 508 bits (1307), Expect = e-148 Identities = 254/392 (64%), Positives = 313/392 (79%), Gaps = 1/392 (0%) Query: 1 MRKTVIVSAARTPFGKFGGVLKEVKAAELGGIVMKEALQQAGVSGDDVEGNVMGMVVQAG 60 M K VI+ ARTPFGKFGG LK+V A ELGG ++ AL++AGV+ + V+ +MGMV+Q G Sbjct: 1 MVKAVILGGARTPFGKFGGALKDVPAVELGGTAIRAALERAGVAAEMVDEVIMGMVLQGG 60 Query: 61 SGQIPSRQAARLAGMPWSVPSETLNKVCASGLRAVTLCDQMIRAQDADILVAGGMESMSN 120 +GQIPSRQAARLAG+ W V +ET+NKVCASGLR+VTL DQ+IRA DA ++VAGGMESMSN Sbjct: 61 AGQIPSRQAARLAGLGWEVGTETINKVCASGLRSVTLADQIIRAGDAGVVVAGGMESMSN 120 Query: 121 IPYAVPAGRWGARMGDGELRDLMVYDGLTCAFDEVHMAVHGNTAAKEYAISRREQDEWAL 180 PY +P+GR+G RMGDG++ DLM++DGL CAF +VHM VHG+ AKEY ++R EQD WAL Sbjct: 121 APYILPSGRFGQRMGDGKMVDLMIHDGLWCAFHDVHMIVHGSNTAKEYNVTREEQDAWAL 180 Query: 181 RSHARAAKAADEGKFQDEIVPVNWIGRKGKPNVVDKDEAIRRDTSLDQLAKLAPIYASDG 240 RSH RA +A + G+F DEI PV + K + VVD+DEA+R DT+L++L+ L P+Y DG Sbjct: 181 RSHQRALEAINHGRFADEITPVT-VKVKKQEIVVDRDEAVRADTTLEKLSGLKPVYLQDG 239 Query: 241 SITAGNAPGVNDGAGAFVLMSEEKAAELGKRPLATILGFSTTGMPAHELAAAPGFAINKL 300 +ITAGNAPGVNDGA A V+ S EKA ELG +PLA+ILG + M A + P +AI KL Sbjct: 240 TITAGNAPGVNDGAAALVVASSEKAQELGIKPLASILGHAAVAMEAKDFPITPAYAIKKL 299 Query: 301 LKKNGLTVQDIDLFEVNEAFASVVLTCEKIVGFDLEKVNVNGGAIALGHPIGASGARILM 360 LKK+GLTV IDLFE+NEAFA+V L K++G D K+NVNGGA+ALGHPIGASGARIL+ Sbjct: 300 LKKHGLTVAQIDLFEINEAFAAVALANSKLLGIDPGKLNVNGGAVALGHPIGASGARILL 359 Query: 361 TLVYELKRRGGGLGVAAICSGAAQGDAVLVQV 392 TL+ ELKRRGGGLGVAAICSGAAQGDAVLV+V Sbjct: 360 TLIMELKRRGGGLGVAAICSGAAQGDAVLVKV 391 Lambda K H 0.317 0.134 0.387 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: 16 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: 393 Length of database: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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