Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_017600331.1 D471_RS0120380 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000341125.1:WP_017600331.1 Length = 395 Score = 267 bits (682), Expect = 5e-76 Identities = 157/392 (40%), Positives = 236/392 (60%), Gaps = 11/392 (2%) Query: 6 ICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGEDNR 65 I RTP GR G+LAG A DL +KA +E + +QV V G QAG + Sbjct: 6 IVGGARTPTGRLLGSLAGFSAADLGGFAIKAALE-RAGISGEQVGYVVMGQVLQAGA-GQ 63 Query: 66 NVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPF 125 +R A + AG+P S+P VT+N++C SG+DAI A + + +GE ++ +AGG+ESM+ AP Sbjct: 64 IPSRQAAVKAGIPMSVPSVTINKVCLSGLDAIALADQLVTAGEFDVVVAGGMESMTNAPH 123 Query: 126 VMGKAESGYS-RNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDAF 184 ++ K+ G+ ++++ D T + + + +SM + + + RA+QDAF Sbjct: 124 LLPKSRKGFKYGSVEVLDAT-----AHDGLTDAFDNESMGASTERHNAKLGIGRAEQDAF 178 Query: 185 ALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALTKLKPVNGP 243 A RS Q+AAAA A G FA+EIVPV+I +KG+ +V DE +RP+TT+E+L KL+P Sbjct: 179 AARSHQRAAAAAAEGRFADEIVPVQIPQRKGDPVVFGTDEGVRPDTTVESLAKLRPAFDG 238 Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303 D T+TAG +S ++DGAAA+++ S ++ G A + + + P A++ Sbjct: 239 DGTITAGTSSQISDGAAAVVVMSRAKAEELGAPVLAEIGAHGNVAGPDNSLHSQPSNAIQ 298 Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363 + G AV D D+IE+NEAFA+ G+ ++LGV++D VN NGGAIA+GHP+G SGA Sbjct: 299 HALTKAGRAVEDLDLIEINEAFAAVGIQSTKDLGVSEDI--VNVNGGAIAIGHPIGASGA 356 Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLAL 395 R+ L +H+L + GG G A +C G GQG AL Sbjct: 357 RIALHLVHELRRRGGGLGAAALCGGGGQGDAL 388 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: 431 Number of extensions: 21 Number of successful extensions: 6 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: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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 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