Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_043530869.1 JH15_RS12340 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_000759345.1:WP_043530869.1 Length = 393 Score = 331 bits (849), Expect = 2e-95 Identities = 187/406 (46%), Positives = 259/406 (63%), Gaps = 20/406 (4%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M + +I+ A RT IG + G+LA + A DLGA+ +K L+AR + VD+V+ G A Sbjct: 1 MQDVVIVAARRTAIGTFGGSLAGIPASDLGALVIKDLLAR-TGVSGDQVDEVLLGQVLTA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G +N AR AA+ AGLP +VP T+N++CGSGL A+ A +A+RCG+A L++AGG E+M Sbjct: 60 GV-GQNPARQAAIKAGLPDAVPAMTINKVCGSGLKALHLATQAIRCGDADLIIAGGQENM 118 Query: 121 SRAPFVMGKSE--QAFGRSAEIFDTTIGWRFVNKLMQQG----FGIDSMPETAENVAAQF 174 S +P V+ S Q G W+ ++ ++ G F M TAEN+A ++ Sbjct: 119 SMSPHVLPNSRNGQRMG----------DWKAIDTMVHDGLWDAFNNYHMGITAENLAEKY 168 Query: 175 NISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQ 234 I+R + D F+ SQ KAAAAI +GR ++V VEI QRKG + + DE PR T E+ Sbjct: 169 GITRDEMDEFSAASQQKAAAAIDSGRFDSQVVPVEIPQRKGDPIVFDKDEGPRAGVTAEK 228 Query: 235 LAKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRI 294 L + F++ G++TAGNAS +NDGA A+++ S+E A+ GL+ A + A AGV+P I Sbjct: 229 LGGMKPAFKKDGTITAGNASSINDGAAAVMICSAEKAKALGLEPLAYIKAYANAGVDPSI 288 Query: 295 MGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIA 354 MGIGP PATR+ LE G +L ++D++E NEAFAAQ LAV +ELG D ++N NGGAIA Sbjct: 289 MGIGPAPATRRCLEKAGWSLDELDLVEANEAFAAQALAVNKELGW--DTSKINVNGGAIA 346 Query: 355 LGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 LGHP+G SG R+ T LHE+ R L T+CIG GQG+AL IER Sbjct: 347 LGHPIGASGCRVFVTLLHEMIARDVHKGLATLCIGGGQGVALAIER 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: 429 Number of extensions: 20 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: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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