Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_011650375.1 RL_RS03105 acetyl-CoA C-acetyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_000009265.1:WP_011650375.1 Length = 402 Score = 270 bits (690), Expect = 5e-77 Identities = 160/405 (39%), Positives = 229/405 (56%), Gaps = 16/405 (3%) Query: 1 MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60 M + I D +R+P GR K A E+ + L A+ ++ + +RN LD G VDD+I GCV Sbjct: 1 MTEVFIYDHVRTPRGRGKKDGALHEVPSVRLAAKTLEAIRDRNGLDTGTVDDIIMGCVDP 60 Query: 61 AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120 + A + A AG+ P I R C S AV+F A I GA DIVIA G+ES Sbjct: 61 VMDAGAVIPKAAAFEAGYSTKAPGMQISRFCASGLDAVNFGAGKIAQGADDIVIAGGVES 120 Query: 121 MSRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELA 180 MSRV +G + G PS+ + + QGV+A+L+A KY SR D+D+Y+ S + A Sbjct: 121 MSRVGLGMSG-GAWFMDPSVN--FPAYFMPQGVSADLIATKYGFSRTDVDAYAVESQKRA 177 Query: 181 ATARESGAFRREILGISTPNGL--VEQDETIRPGTSVEKLGTLQASFRNDELSARFPQIG 238 A A E G F + ++ + NGL + +DE +RPGT ++ L +L SF+ F +G Sbjct: 178 AHAWEKGWFDKSVVPVKDQNGLTILAKDEHMRPGTDMQALASLNPSFQMPGEMGGFEAVG 237 Query: 239 WNVT-----------AGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVM 287 AGN+S I DGAS +LL S++ + +G +PRAR AF G DP + Sbjct: 238 IQAHPEIERINYVHHAGNSSGIVDGASVVLLGSKAGGESMGKRPRARIKAFANIGSDPAL 297 Query: 288 MLTAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALG 347 MLT P+ +++ +K+SG+ L ID +E+NEAFA V L + +A D R+N GGAIA+G Sbjct: 298 MLTGPVDVTEKLLKRSGMSLADIDLFELNEAFAAVVLRYMQAFDIDHHRINVNGGAIAMG 357 Query: 348 HPLGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 HPLGA+G ++ T+L LE L ++C GM AT+IER+ Sbjct: 358 HPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATVIERV 402 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: 451 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: 402 Length adjustment: 31 Effective length of query: 361 Effective length of database: 371 Effective search space: 133931 Effective search space used: 133931 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