Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_084057804.1 B9A12_RS10300 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_900176285.1:WP_084057804.1 Length = 398 Score = 297 bits (760), Expect = 4e-85 Identities = 170/404 (42%), Positives = 240/404 (59%), Gaps = 21/404 (5%) Query: 3 EALIIDAVRTPIGRYA--GALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 + +++D +RT G+ G RADD+ ++ L+ R+PQ+ V++ ++G Q Sbjct: 5 DVVVVDGIRTAFGKAGERGIFWMTRADDMVVKVIRELMRRNPQVKPEMVEENVWGATTQE 64 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G+ + R A+LAGLPV+ G +++R+C G+ AV AA + G + +AGGVE M Sbjct: 65 GDQGLTMGRTTAILAGLPVATAGYSVDRMCAGGMTAVACAASEIAVGACDVAIAGGVEHM 124 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQF-NISRA 179 P MG + R KL+ Q + M +TAEN+ F I++ Sbjct: 125 GHHP--MGATADPNPRF-----------LTEKLVSQDALV--MGKTAENLHDMFPEITKE 169 Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLG 239 D ++L Q K A A G++ K IV + + + G K+ + DE PR +TT+E LA L Sbjct: 170 MADEYSLLCQKKTAKAYQEGKIQKMIVPMTVYTKNG-WKVADRDEQPRPETTMEGLANLR 228 Query: 240 TPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGP 299 TPFR G VT GNASG+NDGAC +LL S E A+ GLK + R+VG A AGV+P IMG GP Sbjct: 229 TPFRVKGKVTPGNASGLNDGACGVLLMSEEKAKELGLKPKMRLVGYAFAGVKPEIMGYGP 288 Query: 300 VPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLA-DDDERVNPNGGAIALGHP 358 +P+T+KVL TGL D+DV+ELNEAFA Q +A ++E G+ DD+R+NP GGAIA GHP Sbjct: 289 IPSTKKVLARTGLKFEDLDVVELNEAFAVQAIAYMKEFGMKFPDDKRLNPYGGAIAFGHP 348 Query: 359 LGMSGARLVTTALHELEER-QGRYALCTMCIGVGQGIALIIERI 401 L SG RLV +H EE + RY L TMC+G+GQG ++I E + Sbjct: 349 LASSGPRLVVHLMHYFEEHPEARYGLATMCVGLGQGGSIIWENV 392 Lambda K H 0.319 0.134 0.384 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: 441 Number of extensions: 26 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: 401 Length of database: 398 Length adjustment: 31 Effective length of query: 370 Effective length of database: 367 Effective search space: 135790 Effective search space used: 135790 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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