Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_073037060.1 BUB04_RS03720 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_900129305.1:WP_073037060.1 Length = 392 Score = 335 bits (858), Expect = 2e-96 Identities = 196/405 (48%), Positives = 261/405 (64%), Gaps = 18/405 (4%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M A+I+ AVRTP+G + +LA++ A LG ++ + R L VD+VI G QA Sbjct: 1 MQRAVIVSAVRTPVGSFGKSLAAIPAVALGVTAVREALKRIA-LSPDQVDEVILGNVLQA 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 + +N AR A+ AG+P VP T+N++C SGL +V AA+A+ G+A +++AGG+E+M Sbjct: 60 AQ-GQNPARQVAVHAGIPHEVPAFTINKVCASGLKSVVLAAQAVLAGDAEVVVAGGIENM 118 Query: 121 SRAPFVMGKSE--QAFGRSAEIFDTTIG---WRFVNKLMQQGFGIDSMPETAENVAAQFN 175 S AP+ + K+ Q G E+ D I W N G+ M TAENVA +F Sbjct: 119 SAAPYALPKARWGQRMGHG-ELVDLMILDGLWDIFN-----GY---HMGITAENVAERFG 169 Query: 176 ISRADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQL 235 ISR +QDAFAL SQ KA AI GR EIV VEI QRKG + + DEHPR TTLE L Sbjct: 170 ISREEQDAFALASQQKAETAIKEGRFKDEIVPVEIPQRKGDPVLFDTDEHPRFGTTLEAL 229 Query: 236 AKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIM 295 AKL F++ G+VTAGNASG+NDGA L++ S + AQ GL A + A+AGV+P IM Sbjct: 230 AKLKPAFKKDGTVTAGNASGINDGAAILVVMSEKKAQELGLTPLAAIRSYASAGVDPAIM 289 Query: 296 GIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIAL 355 G GP+PA+RK LE G + D+D++E NEAFAAQ +AV +ELG D +VN NGGAIA+ Sbjct: 290 GTGPIPASRKALEKAGWTVDDLDLVEANEAFAAQAIAVNKELGW--DTAKVNVNGGAIAI 347 Query: 356 GHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIER 400 GHP+G SGAR++TT L+E++ R + L T+CIG GQG AL +ER Sbjct: 348 GHPIGASGARILTTLLYEMKRRDAKKGLATLCIGGGQGTALTVER 392 Lambda K H 0.319 0.134 0.384 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: 404 Number of extensions: 15 Number of successful extensions: 4 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: 401 Length of database: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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