Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_010442540.1 G7G_RS0116445 acetyl-CoA C-acyltransferase family protein
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000192475.1:WP_010442540.1 Length = 391 Score = 349 bits (895), Expect = e-101 Identities = 195/400 (48%), Positives = 265/400 (66%), Gaps = 9/400 (2%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M D+ I D RT IG FGGALA DLA V +A +E + V+ Q+ V FG Sbjct: 1 MTDIVILDGARTAIGTFGGALASTAPIDLATVATEAALERS-GVEGGQIGHVVFGHVINT 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 + ++R+A + AG+P P + +NRLC SG AI +A +++ G+ + A+AGG ESM Sbjct: 60 EPRDMYLSRVAAMQAGIPNGTPAMNVNRLCGSGAQAIVSAVQSLMLGDADFAVAGGAESM 119 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SR+P+++ +A G K+ D T + L +G M TA+NVAD++Q+SR Sbjct: 120 SRSPYIVPQARWG----AKMGDVTSLDMMLGAL-NCPFGTGHMGVTAENVADEHQISREQ 174 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 DAFAL SQ +AA A AG+F +I PV++ K+ + DEH + TT EAL L+PV Sbjct: 175 MDAFALTSQSRAATAIDAGYFESQITPVQVKVKREMVDFKVDEHPKA-TTAEALAGLRPV 233 Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 + VTAGNASG+NDGAAA++LA+++A +K GL P+AR+LG A GV P VMGIGPVP Sbjct: 234 FKKEGRVTAGNASGINDGAAAMVLATSDAAEKAGLKPKARILGYAHAGVRPEVMGIGPVP 293 Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 AV+ L ++ G++ DFDVIE NEAFA+Q LAV +ELG+ DA +VNPNGGAIALGHP+G Sbjct: 294 AVQNLFKKTGLSAVDFDVIESNEAFAAQALAVNQELGL--DAAKVNPNGGAIALGHPVGA 351 Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 +GA + L AL++LE+ GG K L TMC+G GQG+ALAIER+ Sbjct: 352 TGAIITLKALYELERVGGSKALITMCIGGGQGIALAIERL 391 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: 408 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: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 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