Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_085121636.1 B9O00_RS06430 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_900177295.1:WP_085121636.1 Length = 393 Score = 333 bits (854), Expect = 5e-96 Identities = 201/404 (49%), Positives = 259/404 (64%), Gaps = 14/404 (3%) Query: 1 MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60 M E + + AVR+ IG + GALA LGA ++ +AR ++ V V++G Q Sbjct: 1 MTEVVFVSAVRSAIGTFGGALAGESPCSLGAAVVREALAR-AGVEGEQVGHVVFGNVIQT 59 Query: 61 GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120 + +AR+AAL G+ + P TLNRLCGSG A+ SAA+++ G+A + +AGG E+M Sbjct: 60 EPRDAYLARVAALDGGVAKAAPAMTLNRLCGSGAQAIVSAAQSILLGDAEVAVAGGAEAM 119 Query: 121 SRAPFVM--GKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISR 178 SRAP ++ G+ Q G +A + D +G ++ FG M TAE VA ++ I R Sbjct: 120 SRAPHLLTTGRFGQRMGDTAAV-DALVG------ILTDPFGNGIMGLTAERVADKWGIGR 172 Query: 179 ADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKL 238 QDAFAL SQ +AA AI GR +I+ +E+ R A+ DEHP+ TT E LA L Sbjct: 173 ERQDAFALESQRRAARAIGEGRFESQILPLEVG-RGSRARSFAVDEHPKPQTTAEDLANL 231 Query: 239 GTPFRQ-GGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGI 297 FR+ GGSVTAGNASG+NDGA AL+L S+EAA+R G + R+VG A AGVEP MGI Sbjct: 232 KPAFRRDGGSVTAGNASGINDGAAALVLMSAEAAERGGHRPLGRLVGYAHAGVEPGEMGI 291 Query: 298 GPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGH 357 GPVPA R +L TGLA+ D D++E NEAFAAQ LAV ELGL D ERVNPNGGAIALGH Sbjct: 292 GPVPAVRGLLARTGLAVEDFDLVESNEAFAAQALAVSDELGL--DPERVNPNGGAIALGH 349 Query: 358 PLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 P+G +GA L AL+EL GR AL T+CIG GQGIAL +ER+ Sbjct: 350 PVGATGAILTVKALYELARSGGRRALVTLCIGGGQGIALALERL 393 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: 468 Number of extensions: 24 Number of successful extensions: 6 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: 393 Length adjustment: 31 Effective length of query: 370 Effective length of database: 362 Effective search space: 133940 Effective search space used: 133940 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