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_035235479.1 Q366_RS00870 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >NCBI__GCF_000745975.1:WP_035235479.1 Length = 392 Score = 304 bits (778), Expect = 4e-87 Identities = 182/393 (46%), Positives = 242/393 (61%), Gaps = 14/393 (3%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMT-AVLKDVNLRPEQLGDICVGNVL-QP 94 D +V RT C+ +G F T P+EL+S +M AV + VNL+PE + D+ +G + Sbjct: 3 DAYIVQSVRTPGCKQKKGLFNQTRPEELISFIMKEAVERTVNLKPEDIDDVMLGCAFPEA 62 Query: 95 GAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMS 154 G + RIA ++ P+ V +TVNR C+SGL+A+A + + G DI + G ESM+ Sbjct: 63 EQGLNLGRIAAKMAGFPDEVSGATVNRFCASGLEAIALASVRVSAGWSDICVGAGCESMT 122 Query: 155 LADRGNPGNITSRLMEKEKAR-DCLIPMGITSENVAERFGISREKQDTFALASQQKAARA 213 G GN+ E K + + MGIT+ENVA R+ +SRE QD FA ASQ KA A Sbjct: 123 FVPMG--GNVPRPHPEYSKTYPEMYVSMGITAENVASRYKVSREDQDIFAAASQAKATAA 180 Query: 214 QSKGCFQAEIVPVTTTVH----DDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGS 269 + G F EI+P + D K + V D+GIR ST EGLAKL FK +GS Sbjct: 181 RDNGKF-TEIIPTPAYKYVVQPDGTYKKETFIVEHDDGIRLSTP-EGLAKLGAVFKVNGS 238 Query: 270 TTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVAL 329 TAGNSSQ +DGAAA ++A + K +ELGL + L Y VG D MG+GP YAIP L Sbjct: 239 VTAGNSSQTTDGAAASIIASKEKCKELGLTPIARLVGYTTVGCKADEMGVGPKYAIPKVL 298 Query: 330 QKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPP--EKVNPLGGAVALGHPLGCTGARQV 387 ++ G+T+ D+DI+EINEAFASQA +C+ +L + +K+N GGA+ALGHPLGCTGA+ Sbjct: 299 KQVGMTIDDIDIYEINEAFASQALHCIRELGIEKYMDKINIHGGAIALGHPLGCTGAKLT 358 Query: 388 ITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 T + L+ G + YGVVSMCIG GMGAAAVFE Sbjct: 359 ATCIANLREVGGK-YGVVSMCIGGGMGAAAVFE 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: 473 Number of extensions: 35 Number of successful extensions: 7 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: 392 Length adjustment: 31 Effective length of query: 393 Effective length of database: 361 Effective search space: 141873 Effective search space used: 141873 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