Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate GFF401 PGA1_c04120 3-ketoacyl-CoA thiolase FadA
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__Phaeo:GFF401 Length = 391 Score = 266 bits (679), Expect = 1e-75 Identities = 163/388 (42%), Positives = 227/388 (58%), Gaps = 9/388 (2%) Query: 39 VVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA-G 97 V+V RT + ++ RG F T L + A ++ +L + D +G GA G Sbjct: 5 VIVSAARTGLAKSFRGSFNQTHGATLGGHAVAAAVERASLEGGVIEDCIIGCGFPEGATG 64 Query: 98 AIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLAD 157 + R + +P+T TVNR C+SGLQ +A A I +A GVES+S+ Sbjct: 65 HNIGRQIALRAGLPQTAAGMTVNRFCASGLQTIALAAQQITAEGAGPMVAGGVESISMV- 123 Query: 158 RGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKG 217 + N + +++ D + M T++ VAER+GISRE QD + L SQQK A AQ G Sbjct: 124 QPNVTQVQDPWLQEHNP-DVYMAMIDTADVVAERYGISREAQDAYGLRSQQKIAAAQDAG 182 Query: 218 CFQAEIVPVTTTVH-DDKGT----KRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTA 272 F EIVP+ T + D+ T R +TV +DE RP TT++GLA L+P TA Sbjct: 183 IFDDEIVPMQTVMAVKDRDTGEISHREVTVNRDECNRPQTTLDGLAGLEPVRGAGKFITA 242 Query: 273 GNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKA 332 GN+SQ+SDGAAA+++ +A GL +G R + V G PD MGIGP +A+P L++ Sbjct: 243 GNASQLSDGAAAVVMMEADEASRRGLDPMGAFRGFCVAGCAPDEMGIGPVHAVPRLLERH 302 Query: 333 GLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLN 392 G+TV+D+D++E+NEAFASQA +C + L +P E N GG++A+GHP G TGAR V LL Sbjct: 303 GVTVADIDLWELNEAFASQALFCRDNLGIPDEICNVNGGSIAIGHPFGMTGARMVGHLLR 362 Query: 393 ELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 E RRG + GVV+MCIG GMGAA +FE Sbjct: 363 EGHRRGAK-LGVVTMCIGGGMGAAGLFE 389 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: 480 Number of extensions: 27 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 17 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