Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_013257091.1 DEBA_RS01270 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000143965.1:WP_013257091.1 Length = 400 Score = 303 bits (777), Expect = 4e-87 Identities = 181/405 (44%), Positives = 254/405 (62%), Gaps = 19/405 (4%) Query: 2 RDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEP---NPAVQWDQVDEVFFGCAN 58 RD I RT IG FGG+LAG+RA +LAA+ K L++ +PA+ D+V G Sbjct: 5 RDTVIVAMGRTAIGDFGGSLAGLRAHELAAIVTKNLLDKTGLDPAM----FDDVLMGDCC 60 Query: 59 QAGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVE 118 Q D N AR A L AG+P +P +T+ R C+S M A+ A I +GE E+ +AGGVE Sbjct: 61 QC-PDEANTARTAALKAGIPVDVPAMTIQRQCSSAMQALAQAEVYIRAGEAEVMLAGGVE 119 Query: 119 SMSRAPFVMGKAESGYS-RNMKLEDTTIGWRFINP---LMKSQYGVDSMPETADNVADDY 174 SMS AP+ + KA G ++ K+ D W ++ L++ + M +TA+N+A Y Sbjct: 120 SMSNAPYTLPKARWGARLQHAKMVDAL--WEMLHSGSTLLEPPGYI--MGQTAENLARKY 175 Query: 175 QVSRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGET-IVERDEHLRPETTLEA 233 VSR +QD ALRS A AA AG F +EIVPV + +KGE IV+ DEH+R T+ Sbjct: 176 DVSRQEQDIVALRSHNNAEAAIKAGKFKDEIVPVPVPQRKGEPKIVDTDEHVRMGLTMAD 235 Query: 234 LTKLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRV 293 L KL+P D TVTAGNASG+NDGAA I+ S E K GLTP A+++G A+ G P + Sbjct: 236 LDKLRPAFAKDGTVTAGNASGLNDGAALCIVMSREKAKDLGLTPIAKIVGHAAAGCPPEI 295 Query: 294 MGIGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIA 353 MG GPVP+ +K+ ++LG+ + D ++IELNEAFA+Q LA + LG+ D VN NG I Sbjct: 296 MGWGPVPSTQKVMKKLGMNLKDIELIELNEAFAAQYLACEKGLGLNRDI--VNVNGSGIG 353 Query: 354 LGHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIE 398 LGHP+G +GAR+V++ + ++++ G GLAT+CVG G G+++ +E Sbjct: 354 LGHPVGCTGARIVISLIGEMKRRGATVGLATLCVGGGMGMSMVVE 398 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: 398 Number of extensions: 15 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: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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