Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase
Query= SwissProt::Q8VPF1 (401 letters) >FitnessBrowser__Dyella79:N515DRAFT_3009 Length = 427 Score = 177 bits (450), Expect = 4e-49 Identities = 143/434 (32%), Positives = 215/434 (49%), Gaps = 48/434 (11%) Query: 3 REVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAG 62 + V + +R P R + A V ++ + ALVER ++ +L EV +G + Sbjct: 6 KRVGVIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVERF-RLHGEELGEVAMGAVIKHS 64 Query: 63 EDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMS 122 + N+AR A+L +GL + PG+T R C + +D IA+G+ E IAGG ++ S Sbjct: 65 SE-WNLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTS 123 Query: 123 RAPYVMG----KADSAFGRGQKIEDTTIGWR--FINPLMKAQYGVDAMPETA-------D 169 P V+G K A R + +D + F +K + A P T + Sbjct: 124 DVPIVLGERFRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGDHCE 183 Query: 170 NVADDYKVSRADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPD 229 +A ++ + R QD AL S Q A AG+F + +VP +G K D LR D Sbjct: 184 RMAKEWHIGREAQDRLALESHQKLAAAYEAGFFEDLVVP--FRGLK------RDGFLRAD 235 Query: 230 TTLEALAKLKP----VNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGM 285 +++E L LKP ++G T+TAGN++G++DG+ A++L S E + GLK +A L Sbjct: 236 SSMEKLGTLKPAFDKISGHG-TLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLDA 294 Query: 286 ASAGVAPRVMGIG----PVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTR------ 335 A V V G G P AV ++L R L++ DFD E++EAFAAQ L R Sbjct: 295 EVAAV-DFVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESET 353 Query: 336 ----ELGIAD-----DDARVNPNGGAIALGHPLGASGARLVLTAVHQLEKSGGQRGLCTM 386 LG+ D A++N +G ++A GHP A+GAR+V T LE+ G RGL ++ Sbjct: 354 YCRNRLGLEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLISI 413 Query: 387 CVGVGQGVALAVER 400 C G GV +ER Sbjct: 414 CTAGGMGVTAILER 427 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: 385 Number of extensions: 18 Number of successful extensions: 5 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: 427 Length adjustment: 31 Effective length of query: 370 Effective length of database: 396 Effective search space: 146520 Effective search space used: 146520 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