Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_075387974.1 BK574_RS20875 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_002019605.1:WP_075387974.1 Length = 393 Score = 576 bits (1484), Expect = e-169 Identities = 289/391 (73%), Positives = 338/391 (86%), Gaps = 1/391 (0%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59 M+EAVIV+GARTPVGKAK+G+LA VRPDDLGA+ +KETLKRAG ++ N IDD+IIGC+ P Sbjct: 1 MREAVIVAGARTPVGKAKRGTLANVRPDDLGALTIKETLKRAGDFDPNQIDDVIIGCSMP 60 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EAEQG+NMARNI ALAGLP TVPAIT+NRYCSSGLQSIAYA+E+IMLG + IAGGAES Sbjct: 61 EAEQGMNMARNISALAGLPNTVPAITINRYCSSGLQSIAYASERIMLGHAKSIIAGGAES 120 Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179 MS +PM GHV PN L E+ PEYYM MG+TAE+VA ++GVSREDQDAFAV SH+ AAKA Sbjct: 121 MSLIPMGGHVIAPNPKLVEEMPEYYMGMGYTAEEVANRFGVSREDQDAFAVESHRRAAKA 180 Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239 +AEGKF+DEIVPV+VT+ +G D+K EK FS DEGVR +TT + L LRPAF G+ Sbjct: 181 IAEGKFEDEIVPVDVTLRSVGADNKLKEKHVTFSVDEGVRAETTVETLGKLRPAFHPKGS 240 Query: 240 VTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRAL 299 VTAGN+SQ SDGAA+V++MDRE+A A GL PL+KFRSFAV GV PE+MGIGPVEAIP+AL Sbjct: 241 VTAGNASQMSDGAASVLVMDREEAKANGLTPLLKFRSFAVAGVAPEIMGIGPVEAIPKAL 300 Query: 300 KLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLS 359 +LAGL L DIGLFELNEAFASQ++QV+R LG+D +KVNVNGGAIALGHPLGC+G KLTL+ Sbjct: 301 ELAGLSLADIGLFELNEAFASQSLQVVRHLGLDLDKVNVNGGAIALGHPLGCSGAKLTLT 360 Query: 360 LIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390 L++EMKRR EQFGVVTMCIGGGMGAAGVFEL Sbjct: 361 LMNEMKRRGEQFGVVTMCIGGGMGAAGVFEL 391 Lambda K H 0.316 0.133 0.377 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: 538 Number of extensions: 12 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: 391 Length of database: 393 Length adjustment: 31 Effective length of query: 360 Effective length of database: 362 Effective search space: 130320 Effective search space used: 130320 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 (21.6 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