Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_012709489.1 NGR_RS26100 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000018545.1:WP_012709489.1 Length = 393 Score = 253 bits (647), Expect = 5e-72 Identities = 155/395 (39%), Positives = 223/395 (56%), Gaps = 11/395 (2%) Query: 4 VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63 V I A RTP+G F G L + A +L A+ LKA ++ D VDEV G AG Sbjct: 7 VVIVSAARTPMGAFQGGLKDLTAPELGAIALKAALD---RAGLDAVDEVMMGNVLPAGL- 62 Query: 64 NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123 +N AR A L AGL + P T++++C SGM A+ A+ SG + GG+ESM+ A Sbjct: 63 GQNPARQAALGAGLGQQTPSTTVSKVCGSGMKALMLGHDALISGSASVVGVGGMESMTNA 122 Query: 124 PFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDA 183 P+++ KA G+ +L + ++ Y M A++ A YQ SRADQDA Sbjct: 123 PYLLPKARGGF----RLGHGEVKDHMFLDGLEDAYSGRLMGTYAEDTAQHYQFSRADQDA 178 Query: 184 FALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPVNGP 243 FALRS ++A A FA+EIV + K+G ++RDE + + KLKP Sbjct: 179 FALRSLERALKAAEDKSFADEIVAITDGGKRGTANLDRDEQPTKADPAK-IPKLKPAFRD 237 Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303 +VTA N+S ++DGAAAL+L A ++ GLTP A V G A P P+ A+ Sbjct: 238 GGSVTAANSSSISDGAAALVLMRASEAERRGLTPLAIVAGHAGHAQEPAWFTTAPIGAID 297 Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363 KL E+LG + E+NEAFA +A +R+LG++DD VN +GGA ALGHP+G SGA Sbjct: 298 KLIEKLGWEKGSVGLYEINEAFAIVAMAAIRDLGLSDDI--VNIHGGACALGHPIGASGA 355 Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIE 398 R+V+T LH + +G ++G+A++C+G G+ A+ +E Sbjct: 356 RIVVTLLHAMRANGVKRGIASLCIGGGEATAVGLE 390 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: 424 Number of extensions: 20 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: 393 Length adjustment: 31 Effective length of query: 369 Effective length of database: 362 Effective search space: 133578 Effective search space used: 133578 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 Apr 09 2024. 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