Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate WP_011938498.1 GURA_RS08100 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-15952 (401 letters) >NCBI__GCF_000016745.1:WP_011938498.1 Length = 390 Score = 288 bits (736), Expect = 2e-82 Identities = 178/409 (43%), Positives = 235/409 (57%), Gaps = 27/409 (6%) Query: 1 MNEALIIDAVRTP-IGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQ 59 M A I+ A RTP G VR DDL A+ ++ L+ + +D AV+D+I GCA Sbjct: 1 MRNAYILAAFRTPGCKAKKGKFKDVRPDDLAAVAIRGLLEK-TGIDPLAVEDIIMGCAFP 59 Query: 60 AGEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVES 119 GE N+AR+AA+ AG+P VP T+NR C SGL ++ SAA + G + ++AGG ES Sbjct: 60 EGEQGMNMARVAAMKAGVPYQVPAQTVNRFCSSGLQSIASAAERIMAGFSDCIIAGGSES 119 Query: 120 MSRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRA 179 MS P K G A W + F SM TAE VA Q+ +SR Sbjct: 120 MSMVPMGGNKYSANPGLVAS-------W-------PESFA--SMGITAELVAEQYTVSRE 163 Query: 180 DQDAFALRSQHKAAAAIANGRLAKEIVAVEI-------AQRKGPAKIVEHDEHPRGDTTL 232 +QD FA S KAAAAIA G+ A+EI+ VE+ + K ++V D+ RG+TT Sbjct: 164 EQDFFAAESHRKAAAAIAQGKFAEEILPVEVESCALVNGKMKRSKELVTVDDGVRGETTR 223 Query: 233 EQLAKLGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEP 292 L KL F G+VTAGN+S + DGA A+L+ S E ++ G R V A GV P Sbjct: 224 HGLGKLKPAFSATGTVTAGNSSQMTDGAAAVLVVSEEFLKKCGKVPIGRFVSFAVRGVPP 283 Query: 293 RIMGIGPVPATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGA 352 IMGIGP+ A L+L GL L D+ + ELNEAFAAQ +A ++ LG+ D RVN NGGA Sbjct: 284 EIMGIGPIEAIPAALKLAGLKLEDIGLYELNEAFAAQSIACVKTLGI--DPARVNVNGGA 341 Query: 353 IALGHPLGMSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 IALGHPLG +GA+L T+ LHE++ RY + +MCIG G G A I E++ Sbjct: 342 IALGHPLGCTGAKLTTSLLHEMQRSNTRYGVVSMCIGGGMGAAGIFEKM 390 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: 388 Number of extensions: 19 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: 390 Length adjustment: 31 Effective length of query: 370 Effective length of database: 359 Effective search space: 132830 Effective search space used: 132830 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