Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_025273353.1 HALAL_RS0107190 acetyl-CoA C-acyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_000527155.1:WP_025273353.1 Length = 387 Score = 355 bits (911), Expect = e-102 Identities = 199/401 (49%), Positives = 264/401 (65%), Gaps = 24/401 (5%) Query: 1 MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60 M++ VI A RSP+ KPG A +E+H ++ A V + + R+ L P VDDVI GCV+Q Sbjct: 1 MREVVIGSAARSPVAVGKPGGALSEIHPVDVAAPVFQTALNRSGLLPDQVDDVIVGCVSQ 60 Query: 61 AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120 EQS R LAAG+P+ VP TT+DR+CGS QQA+ FA + +G D+V+A G+ES Sbjct: 61 VDEQSWNIARNIVLAAGWPETVPGTTVDRQCGSGQQAIAFATALVASGQADVVVAGGVES 120 Query: 121 MSRVPMGSARIGQNPYGPSMEARYAPGL-------VSQGVAAELVAAKYELSRHDMDSYS 173 MSRVPMGS+ PYG ++ ARYA L +QGVAAE +AAK+ + R M+ ++ Sbjct: 121 MSRVPMGSSSADGKPYGEAVRARYAEQLDTTRTLPFNQGVAAEKIAAKWGIDRAAMERFA 180 Query: 174 ARSHELAATARESGAFRREILGISTPNGLVEQDETIRPGTSVEKLGTLQASFRNDELSAR 233 SH+ AA+AR++G F REI+ P E DE IR TS+EKL L+ +F D Sbjct: 181 LASHQKAASARDAGDFDREIV----PFDEYEVDEGIR-DTSLEKLAGLKPAFSED----- 230 Query: 234 FPQIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPI 293 ++TAG ASQISDGA+A+++MS + L KP AR V G DPVMML I Sbjct: 231 -----GSITAGLASQISDGAAAVVVMSAEKSSTLRRKPMARVVDHAAVGSDPVMMLDGVI 285 Query: 294 PASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALG--ADPARLNPRGGAIALGHPLG 351 PA+++ + ++G+ D+I +E+NEAFA VP+AW +A G AD RLNPRGGAIALGHPLG Sbjct: 286 PATEKILGRTGMSPDEIGVFEVNEAFASVPMAWAQATGLAADDERLNPRGGAIALGHPLG 345 Query: 352 ASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 A+G RL T++LH ++DSGQRYG+Q MCE GGMANAT+ E L Sbjct: 346 ATGARLSTSLLHYMQDSGQRYGMQVMCEGGGMANATVYELL 386 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: 478 Number of extensions: 22 Number of successful extensions: 5 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 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