Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_050656999.1 C1M55_RS28700 acetyl-CoA C-acyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_002893965.1:WP_050656999.1 Length = 397 Score = 467 bits (1202), Expect = e-136 Identities = 234/397 (58%), Positives = 297/397 (74%), Gaps = 5/397 (1%) Query: 1 MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60 M +AVIVD +R G+ KPG A + H EL+A V++ + RN LDP LVDDVI GCV Q Sbjct: 1 MTKAVIVDVVRIASGKGKPGGALSGTHPVELMAHVLRSITSRNGLDPALVDDVIGGCVGQ 60 Query: 61 AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120 AGEQ+ R A L+AGFP+ VPATTIDR+CGSSQQA HFAAQG++AGAYDIVIA G+ES Sbjct: 61 AGEQALNITRSAVLSAGFPESVPATTIDRQCGSSQQAAHFAAQGVIAGAYDIVIAAGVES 120 Query: 121 MSRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELA 180 MSRVPMG+ +G++ GP + ARY GLV+QG++AEL+AAK++L R +DS+SA+SH+ A Sbjct: 121 MSRVPMGTTTMGKDASGPGVAARYPEGLVNQGISAELIAAKWKLDRDALDSFSAQSHQRA 180 Query: 181 ATARESGAFRREILGISTPNGLVEQ-----DETIRPGTSVEKLGTLQASFRNDELSARFP 235 A A G F +EIL IS N E DET+R T+ E L L+ SF +++ + RFP Sbjct: 181 AEAAAKGLFDKEILPISVTNAAGETVSHIVDETVRASTTAEGLAGLKPSFYSEKYAQRFP 240 Query: 236 QIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPA 295 + W++T GN+S ++DGASA L+MSE MA +LGL PRARF +F V GDDP+ MLTAPIPA Sbjct: 241 EAQWSITPGNSSPLTDGASAALIMSEEMASKLGLTPRARFHSFSVAGDDPIFMLTAPIPA 300 Query: 296 SQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPLGASGV 355 + + + ++GL +D ID YE+NEAFA VPLAW GADPA+LNP GGAIALGH LG+SG Sbjct: 301 THKVLARAGLSIDDIDTYEVNEAFAPVPLAWAHEFGADPAKLNPWGGAIALGHALGSSGT 360 Query: 356 RLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 RL+TTM++ LE +G RYGLQ+MCE GMANATIIER+ Sbjct: 361 RLLTTMVNHLEATGGRYGLQTMCEGAGMANATIIERI 397 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: 488 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: 392 Length of database: 397 Length adjustment: 31 Effective length of query: 361 Effective length of database: 366 Effective search space: 132126 Effective search space used: 132126 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