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_066324593.1 BLR17_RS15680 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_900100165.1:WP_066324593.1 Length = 393 Score = 300 bits (767), Expect = 7e-86 Identities = 172/387 (44%), Positives = 239/387 (61%), Gaps = 7/387 (1%) Query: 40 VVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDV-NLRPEQLGDICVGNVL-QPGAG 97 +V RTA+ +A +G F+ PDEL + + ++ ++ + +++ D+ VGN + + G Sbjct: 6 IVKAYRTAVGKAPKGLFRFKRPDELAAETIQHMMNELPDFDKKRIDDVMVGNAMPEAEQG 65 Query: 98 AIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLAD 157 R+ + VP TVNR C+SGL+ + I++G D +A G ESMS Sbjct: 66 LNFGRLISLMGLEINDVPGVTVNRYCASGLETIGMATARIQSGMADCIIAGGAESMSFIP 125 Query: 158 RGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKG 217 G + K D MG+T+E VA++F ISRE QD FA S QKA +AQ++G Sbjct: 126 MGGYKPTPDYALAKAGHEDYYWGMGLTAEAVAKQFNISREDQDLFAYNSHQKALKAQAEG 185 Query: 218 CFQAEIVPVTT--TVHDDKGTKR--SITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAG 273 F ++IVP+T T + KG K S TV +DEG R T++E LAKL+P F DGS TAG Sbjct: 186 KFDSQIVPITVEQTFINAKGKKETTSYTVNKDEGPRADTSLEALAKLRPVFAADGSVTAG 245 Query: 274 NSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAG 333 SSQ+SDGAA +L+ +EL L + L +YA GV P IMGIGP AIP AL++AG Sbjct: 246 TSSQMSDGAAFVLIMSEELVKELNLTPIARLVNYASAGVEPRIMGIGPVKAIPKALKQAG 305 Query: 334 LTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNE 393 L + D+D+ E+NEAFASQ+ + +L L P+ VN GGA+ALGHPLGCTGA+ + L NE Sbjct: 306 LQLKDIDLIELNEAFASQSLAVIRELGLNPDIVNVNGGAIALGHPLGCTGAKLSVQLFNE 365 Query: 394 LKRRGKRAYGVVSMCIGTGMGAAAVFE 420 +KRRG + YG+V+MC+GTG GAA +FE Sbjct: 366 MKRRGNK-YGMVTMCVGTGQGAAGIFE 391 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: 414 Number of extensions: 16 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: 424 Length of database: 393 Length adjustment: 31 Effective length of query: 393 Effective length of database: 362 Effective search space: 142266 Effective search space used: 142266 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