Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_086510452.1 BZY95_RS13540 acetyl-CoA C-acetyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_002151265.1:WP_086510452.1 Length = 391 Score = 260 bits (665), Expect = 4e-74 Identities = 159/395 (40%), Positives = 232/395 (58%), Gaps = 18/395 (4%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA 96 DVV+V RRTAI G G +L + V+ +L + +Q+ ++ +G VL G Sbjct: 3 DVVIVAARRTAIGAFG-GSLAGIAASDLGALVIKDILASTGVAADQIDEVLLGQVLTAGV 61 Query: 97 GAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLA 156 G AR A + +P VP T+N+ C SGL+A+ IR G ++ +A G E+MS + Sbjct: 62 GQNPARQAAIKAGLPAAVPAMTINKVCGSGLKALHLATQAIRCGDAELIIAGGQENMSAS 121 Query: 157 DRGNPGNITSRLMEKEKARDCLIP-----------MGITSENVAERFGISREKQDTFALA 205 P + + M KA D ++ MGIT+EN+AE++GI+RE+ D FA A Sbjct: 122 PHVLPNSRNGQRMGDWKAIDTMVHDGLWDAFNDYHMGITAENLAEKYGITREEMDEFAAA 181 Query: 206 SQQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFK 265 SQQKAA A +G F+ +IVPV + KG + DE R + + LA ++PAFK Sbjct: 182 SQQKAAAAIREGRFKGQIVPVE--IPQRKGDP--VVFDTDENPR-EVSADKLAGMRPAFK 236 Query: 266 KDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAI 325 KDG+ TAGN+S ++DGAAA+++ +KA+ELGL L + +Y+ GV P IMGIGPA A Sbjct: 237 KDGTITAGNASSINDGAAAVMICSAAKAKELGLEPLARIAAYSNAGVDPAIMGIGPAPAT 296 Query: 326 PVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGAR 385 L+KAG ++ D+D+ E NEAFA+QA ++L KVN GGA+ALGHP+G +G R Sbjct: 297 RRCLEKAGWSLDDLDLIEANEAFAAQALSVNKELGWDTSKVNVNGGAIALGHPIGASGCR 356 Query: 386 QVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 +++LL+E+ R + G+ ++CIG G G A E Sbjct: 357 VLVSLLHEMIARDAKK-GLATLCIGGGQGVALAIE 390 Lambda K H 0.317 0.134 0.385 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: 433 Number of extensions: 26 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: 424 Length of database: 391 Length adjustment: 31 Effective length of query: 393 Effective length of database: 360 Effective search space: 141480 Effective search space used: 141480 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