Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_013258115.1 DEBA_RS06455 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000143965.1:WP_013258115.1 Length = 392 Score = 275 bits (704), Expect = 1e-78 Identities = 167/405 (41%), Positives = 239/405 (59%), Gaps = 18/405 (4%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 MR+V I A RTP+G F GA A + A DL V L I + DQVDEV GC A Sbjct: 1 MREVVITSACRTPVGAFRGAFASLSALDLGVVVLNEAIA-RAGLAKDQVDEVIMGCVLPA 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G +N AR A L AGLP + +T+N++C SG+ A+ A +AIA G+ E+ +AGG+ESM Sbjct: 60 GL-GQNPARQACLRAGLPVEVGCITVNKVCGSGLKAVMLAAQAIACGDAEVIVAGGMESM 118 Query: 121 SRAPFVMGKAESGYSR-NMKLEDTTIG---WRFINPLMKSQYGVDSMPETADNVADDYQV 176 + AP+++ +A G N KL D+ + W +N M +A+ A+ Y V Sbjct: 119 TNAPYLVPQARGGMRMGNGKLVDSMVHDGLWDHLNDF--------HMGMSAELCAEKYGV 170 Query: 177 SRADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTK 236 SR DQD FA+ S K+ A A G F +I PV +A +KG T+VE DE L+ + EAL Sbjct: 171 SRQDQDQFAVESYAKSFEADAQGRFKAQIAPVSVAGRKGPTVVEHDEGLKLSSP-EALAA 229 Query: 237 LKPVNGPDK-TVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMG 295 L+P D TVTAGNAS +NDGAAA++L SAE G P RV A+ G+ P+ + Sbjct: 230 LRPAFKKDGGTVTAGNASTLNDGAAAVVLMSAEKAAALGARPLVRVGAQAAAGIDPKYVL 289 Query: 296 IGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALG 355 + P+ ++ K + G+ D D+ ELNEAFAS LAV R LG+ D ++N GG I++G Sbjct: 290 VAPMLSIPKACAKAGIDPKDIDLHELNEAFASSSLAVQRTLGL--DPARINIYGGGISIG 347 Query: 356 HPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 HP+G SGAR++ T ++ ++ G+A++C+G G+ ++L +E + Sbjct: 348 HPIGASGARVLTTLIYAMKDQDAATGMASLCLGGGEAVSLLVENI 392 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: 407 Number of extensions: 21 Number of successful extensions: 7 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: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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