Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_011840657.1 RSPH17029_RS04440 acetyl-CoA C-acetyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_000015985.1:WP_011840657.1 Length = 403 Score = 292 bits (747), Expect = 1e-83 Identities = 165/408 (40%), Positives = 252/408 (61%), Gaps = 21/408 (5%) Query: 1 MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60 M +A I DA+R+P G+ +P A E+ + L A+V+ + ERN LD V+DVI G TQ Sbjct: 1 MTEAYIYDALRTPRGKGRPDGALHEVTSVALSAKVLNAVKERNHLDGAAVEDVIWGNATQ 60 Query: 61 AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120 GEQ R A L + + +P +I+R C S +AV+ AA + AGA + IA G+E Sbjct: 61 VGEQGGCLARSAVLLSDLDESIPGLSINRFCASGMEAVNLAANQVRAGAGEAYIAGGVEM 120 Query: 121 MSRVPMGS--ARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHE 178 MSRV MGS A + +P +M+ + P QG++A+++A +Y SR + D+ + S + Sbjct: 121 MSRVAMGSDGAAVAADP-SLAMKTYFVP----QGISADIIATRYGFSRDEADALAVESQK 175 Query: 179 LAATARESGAFRREILGISTPNG--LVEQDETIRPGTSVEKLGTLQASFRN--------D 228 AA A G F R ++ + NG ++E+DE +RPGT ++ LG L+ +F+ D Sbjct: 176 RAAAAWAEGRFARSVVPVRDQNGVTILERDEYLRPGTDMQSLGALKPAFKEMGEQMPGFD 235 Query: 229 ELSA-RFPQ---IGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDD 284 +L+ ++P+ + AGN+S I DGA+A+L+ S + + GL+PRAR A G D Sbjct: 236 KLALMKYPELERVEHIHHAGNSSGIVDGAAAVLIGSRAFGEAHGLRPRARIRATAKIGTD 295 Query: 285 PVMMLTAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAI 344 P +MLT P+P +Q+ ++++G+++ ID +E+NEAFA V L +Q+A G DPAR+NP GGAI Sbjct: 296 PTIMLTGPVPVTQKILREAGMQISDIDLFEVNEAFAAVVLRFQQAFGVDPARVNPNGGAI 355 Query: 345 ALGHPLGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 A+GHPLGA+G ++ T+L LE + + GL ++C A GM ATIIER+ Sbjct: 356 AMGHPLGATGAIIIGTLLDELERTDRSVGLATLCVASGMGAATIIERV 403 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: 437 Number of extensions: 18 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: 392 Length of database: 403 Length adjustment: 31 Effective length of query: 361 Effective length of database: 372 Effective search space: 134292 Effective search space used: 134292 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 Apr 10 2024. 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