Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate AZOBR_RS28180 AZOBR_RS28180 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__azobra:AZOBR_RS28180 Length = 397 Score = 254 bits (649), Expect = 3e-72 Identities = 156/405 (38%), Positives = 233/405 (57%), Gaps = 19/405 (4%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 ++ +I+ A RTP+GR+ G L+++ A LGA ++A ++R L VD+V+ GC A Sbjct: 5 LDPVVIVSAARTPLGRFQGELSALPAHALGAHAVRAALSR-AGLAPERVDEVLLGCVLPA 63 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G+ + AR AA AGLP + TT+N++CGSG+ A A +R G A L++AGG+ESM Sbjct: 64 GQ-GQAPARQAARGAGLPDATGATTVNKVCGSGMKATMLAHDLIRAGSADLVVAGGMESM 122 Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGF-----GIDSMPETAENVAAQFN 175 S AP+++ K+ + + R ++ LM G G M + E A + Sbjct: 123 SNAPYLLAKARGGYRIGHD--------RILDHLMLDGLEDAYEGGRPMGDFGEATADLYG 174 Query: 176 ISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQL 235 +RA+QDA+A+ + +A AAIA+G EI V +A KG + V DE+P E++ Sbjct: 175 FTRAEQDAYAVETLTRARAAIASGAFTAEIAPVTLAV-KGGERTVADDENPL-KVAPEKI 232 Query: 236 AKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIM 295 L FR+ G++TA ++S DGA ALLL A+R GL A ++G AT +P Sbjct: 233 PALKPAFRRDGTITAASSSANADGAAALLLTRRSLAEREGLPVLATILGHATHSQDPAWF 292 Query: 296 GIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIAL 355 P+PA RK+L+ G + D+D+ E+NEAFA +A R+LG+ D +N NGGA AL Sbjct: 293 TTAPIPAIRKLLDRVGWGIGDVDLFEINEAFAVVAMAAQRDLGIPRD--ALNVNGGACAL 350 Query: 356 GHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 GHP+G +GARL+ T LH L R R + ++CIG G+ A+ +ER Sbjct: 351 GHPIGATGARLIVTLLHALAARGLRRGVASLCIGGGEATAIAVER 395 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: 425 Number of extensions: 33 Number of successful extensions: 6 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: 397 Length adjustment: 31 Effective length of query: 370 Effective length of database: 366 Effective search space: 135420 Effective search space used: 135420 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 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