Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate AO356_03560 AO356_03560 acetyl-CoA acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_03560 Length = 394 Score = 254 bits (649), Expect = 3e-72 Identities = 166/412 (40%), Positives = 233/412 (56%), Gaps = 33/412 (8%) Query: 3 REVYICDAVRTPIGR-FGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQA 61 REV I D+VRT + + F G R DD+AA V AL+ RN ++ + +++ +G + Sbjct: 2 REVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVNALLARN-DINPASVEDCIVGAGSNE 60 Query: 62 GEDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESM 121 G N+ R +L+ L G+TLNR C+SG+ A+ A IASG +++++AGGVES+ Sbjct: 61 GAQGYNIGRNVAVLSQLGIGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESI 120 Query: 122 SRAPYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMP--ETADNVADDYKVSR 179 S K +T INPL+K Q P +TA+ VA Y+VSR Sbjct: 121 SLT--------------MKSVNTD---NLINPLLKEQVPGIYFPMGQTAEIVARRYQVSR 163 Query: 180 ADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGET----------VVDADEHLRPD 229 +QD +AL+SQQ +AQAAG F +EI+P+ +K + + VVD D+ RPD Sbjct: 164 EEQDRYALQSQQRTAKAQAAGLFDDEIIPMAVKYRVEDKNTGVVQILDGVVDHDDCNRPD 223 Query: 230 TTLEALAKLKPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAG 289 TT E+LA LKPV D +VTAGN+S ++DG+ ++ S E GLK +A G AG Sbjct: 224 TTYESLAGLKPVFAEDGSVTAGNSSQLSDGASMTLVMSLEKALALGLKPKAFFRGFTVAG 283 Query: 290 VAPRVMGIGPVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPN 349 P MGIGPV +V KLL+ L +AD D+ ELNEAFA+Q L L I D + N N Sbjct: 284 CEPDEMGIGPVFSVPKLLKAKGLQIADIDLWELNEAFASQCLYSRDRLEI--DPQKYNVN 341 Query: 350 GGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401 GG+I++GHP G +G+R V V +L++ + G+ TMCVG G G E V Sbjct: 342 GGSISIGHPFGMTGSRQVGHLVRELQRRNLRYGIVTMCVGGGMGATGLFEAV 393 Lambda K H 0.317 0.134 0.379 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: 380 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: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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