Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Pedo557:CA265_RS17585 Length = 391 Score = 290 bits (743), Expect = 4e-83 Identities = 177/406 (43%), Positives = 236/406 (58%), Gaps = 27/406 (6%) Query: 3 EALIIDAVRTPIGRYA-GALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAG 61 EA II RT +G+ G RADDL A ++AL+A P LD +DDVI G A Sbjct: 2 EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61 Query: 62 EDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMS 121 E N+ RM +L+ VPG T+NR C SGLD + +A ++ G A ++AGGVE MS Sbjct: 62 EQGLNIGRMISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMS 121 Query: 122 RAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQ 181 PF K +AE+ W + G G+ TAE VA ++N+SR DQ Sbjct: 122 GMPFGGWKLVP----NAEVAKNNPDWYW-------GMGL-----TAEAVAKEYNVSREDQ 165 Query: 182 DAFALRSQHKAAAAIANGRLAKEIVAVEIAQ--------RKGPAKIVEHDEHPRGDTTLE 233 DAF+L+S KA AI NG L I+ + + + +K + +V+ DE PR DTTL+ Sbjct: 166 DAFSLKSHEKAIHAIKNGHLKDGILPITVNENYLDANLKKKTRSYVVDTDEGPRADTTLD 225 Query: 234 QLAKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPR 293 +LAKL F GSVTAGN+S +DGA +L+ S + + + AR+V AGV PR Sbjct: 226 KLAKLKPVFDAVGSVTAGNSSQTSDGAAFVLVVSEKKMKELNAEPIARLVSYGIAGVPPR 285 Query: 294 IMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAI 353 IMGIGP+ A K L+ GL D+D+IELNEAFA+Q LAV+R L L D +N NGGAI Sbjct: 286 IMGIGPIEAIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLDLNPD--VINVNGGAI 343 Query: 354 ALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIE 399 ALGHPLG +GA+L ++EL+ + +Y + TMC+G GQG A I E Sbjct: 344 ALGHPLGCTGAKLTVQIMNELKRQNKKYGMVTMCVGTGQGAAGIFE 389 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: 411 Number of extensions: 15 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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