Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate GFF3382 PGA1_c34350 acetyl-CoA acetyltransferase PhbA
Query= uniprot:B2SYZ2 (400 letters) >FitnessBrowser__Phaeo:GFF3382 Length = 391 Score = 326 bits (835), Expect = 8e-94 Identities = 185/401 (46%), Positives = 249/401 (62%), Gaps = 11/401 (2%) Query: 1 MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60 M D I D RT IG +GG+L DL V KA +ER+ GV + +V++G Sbjct: 1 MTDIVILDGARTAIGTFGGSLAGTTPIDLATVASKAAMERS-GVAPEQIGNVVFGHVINT 59 Query: 61 GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120 + ++R++A+ AG+P P +NRLCGSG A+ + +++ G+A + GG E+M Sbjct: 60 EPRDMYLSRVAAMQAGIPNGTPAMNVNRLCGSGAQAIVSGIQSLMLGDAEFALTGGAENM 119 Query: 121 TRAPFVMGKAT-SAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRA 179 +R+PF++ A A D +G + +G M TAENVA E ++RA Sbjct: 120 SRSPFIVPSARWGQKMGDARALDMMLG------ALNCPFGTGHMGVTAENVADEHDITRA 173 Query: 180 DQDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKG 239 D FALASQ +AA A + G A +I VE+ K+ D V +DEHP+ ++LE+LG LK Sbjct: 174 QMDEFALASQTRAAAAIEAGYFASQITPVEVKVKR-DMVPFDVDEHPKASTLETLGGLKA 232 Query: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299 V + DG VTAGNASG+NDGA A+++A AA Q GL+ +AR++G A AGV P +MGIGP Sbjct: 233 VFKKDGRVTAGNASGINDGAAAIVMATADAARQAGLKPKARILGYAHAGVRPEVMGIGPV 292 Query: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359 PA Q LLK+ G++ DV+E NEAFA+Q LAV + LGL D +VNPNGGAIALGHP+G Sbjct: 293 PAVQNLLKKTGLSASDFDVVESNEAFAAQALAVNKELGL--DPAKVNPNGGAIALGHPVG 350 Query: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400 A+GA + LY+LER G L TMCIG GQGIAL IERL Sbjct: 351 ATGAIITLKTLYELERIGGSKGLITMCIGGGQGIALAIERL 391 Lambda K H 0.318 0.135 0.386 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: 420 Number of extensions: 14 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: 400 Length of database: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 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 17 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