Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PP_4636 PP_4636 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Putida:PP_4636 Length = 392 Score = 345 bits (886), Expect = 1e-99 Identities = 202/402 (50%), Positives = 263/402 (65%), Gaps = 12/402 (2%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 MN+ +I+ A RT IG + GALA+V A DLGA +K L+ + LD + VD+VI G A Sbjct: 1 MNDVVIVAATRTAIGSFQGALATVPAVDLGAAVIKQLL-KQTGLDPAQVDEVILGQVLTA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 G +N AR AA+ AGLP SVP TLN++CGSGL A+ AA+A+RCG+A +++AGG E+M Sbjct: 60 GA-GQNPARQAAIKAGLPFSVPALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENM 118 Query: 121 SRAPFVM--GKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178 S AP+VM ++ Q G ++ D+ I + GI TAEN+ ++ +SR Sbjct: 119 SLAPYVMPSARTGQRMGHG-QLIDSMITDGLWDAFNDYHMGI-----TAENLVDKYGLSR 172 Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238 QDAFA SQ KA AAI GR EI + + Q+KG K+ DE PR DTT E LAKL Sbjct: 173 EQQDAFAAESQRKAVAAIEAGRFDAEITPIVLPQKKGEPKVFARDEQPRPDTTAESLAKL 232 Query: 239 GTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIG 298 F++ GSVTAGNAS +NDGA A+LL S+ A+ GL A++ A+AGV+P IMGIG Sbjct: 233 RPAFKKDGSVTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIG 292 Query: 299 PVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHP 358 PV AT++ L+ G LA++D+IE NEAFAAQ LAV LA D RVN NGGAIALGHP Sbjct: 293 PVSATQRCLDKAGWQLAELDLIEANEAFAAQALAVGN--ALAWDAARVNVNGGAIALGHP 350 Query: 359 LGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 +G SG R++ T LHE+ +R + L T+CIG GQG+AL IER Sbjct: 351 IGASGCRVLVTLLHEMIKRDVKKGLATLCIGGGQGVALAIER 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: 398 Number of extensions: 16 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: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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