Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Dyella79:N515DRAFT_3009 Length = 427 Score = 178 bits (452), Expect = 2e-49 Identities = 140/435 (32%), Positives = 216/435 (49%), Gaps = 54/435 (12%) Query: 4 VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63 V + IR P R A A V ++ L AL+E + +++ EV G + + Sbjct: 8 VGVIGGIRIPFCRNNTAYADVGNFGMSVKVLGALVE-RFRLHGEELGEVAMGAVIKHSSE 66 Query: 64 NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123 N+AR A+L +GL + PG+T R C + +D IA+G++E IAGG ++ S Sbjct: 67 -WNLAREAVLSSGLAPTTPGITTARACGTSLDNAIIIANKIAAGQIEAGIAGGSDTTSDV 125 Query: 124 PFVMGKAESGYSRNMKLEDTTIGWR----------FINPLMKSQYGVD------SMPETA 167 P V+G+ + + + + GW+ + L S GV SM + Sbjct: 126 PIVLGER---FRKRLLAINRAKGWQDKMAAFTRGFSLKELKPSFPGVAEPRTGMSMGDHC 182 Query: 168 DNVADDYQVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRP 227 + +A ++ + R QD AL S QK AAA AGFF + +VP R ++RD LR Sbjct: 183 ERMAKEWHIGREAQDRLALESHQKLAAAYEAGFFEDLVVPFR--------GLKRDGFLRA 234 Query: 228 ETTLEALTKLKP----VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLG 283 ++++E L LKP ++G T+TAGN++G++DGAAA++L S E + GL +A L Sbjct: 235 DSSMEKLGTLKPAFDKISG-HGTLTAGNSTGLSDGAAAVLLGSDEWAARRGLKVQAYFLD 293 Query: 284 MASGGVAPRVMGIG----PVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLR----- 334 A V G G P AV ++ R G+ + DFD E++EAFA+Q L LR Sbjct: 294 -AEVAAVDFVHGEGLLMAPTVAVPRMLARHGLTLQDFDFYEIHEAFAAQVLCTLRAWESE 352 Query: 335 -----ELGVAD-----DAPQVNPNGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLAT 384 LG+ D ++N +G ++A GHP +GAR+V T LE+ G +GL + Sbjct: 353 TYCRNRLGLEQPLGSIDPAKLNVHGSSLAAGHPFAATGARIVATLAKMLEEKGSGRGLIS 412 Query: 385 MCVGVGQGLALAIER 399 +C G G+ +ER Sbjct: 413 ICTAGGMGVTAILER 427 Lambda K H 0.318 0.134 0.383 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: 396 Number of extensions: 17 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: 400 Length of database: 427 Length adjustment: 31 Effective length of query: 369 Effective length of database: 396 Effective search space: 146124 Effective search space used: 146124 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 (21.7 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