Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate 3609950 Dshi_3331 acetyl-CoA acetyltransferase (RefSeq)
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__Dino:3609950 Length = 394 Score = 328 bits (842), Expect = 1e-94 Identities = 189/399 (47%), Positives = 250/399 (62%), Gaps = 11/399 (2%) Query: 3 DAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGE 62 D I D RT IG +GG+L LGA KA ++R+ GV+ + V++G Sbjct: 6 DIVILDGARTAIGTFGGSLAGTAPITLGATVAKAALERS-GVEGAQIGHVVFGHVINTEP 64 Query: 63 DNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTR 122 + ++R++A+ AG+P P +NRLCGSG A+ + +++ G+AQ +AGG ESM+R Sbjct: 65 RDMYLSRVAAMEAGIPDTTPAMNVNRLCGSGAQALVSVIQSLMLGDAQFGLAGGAESMSR 124 Query: 123 APFVMGKAA-SAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQ 181 +P+ M A A D +G + +G M TAENVA + GI RADQ Sbjct: 125 SPYAMPVARWGQKMGDATAMDMMLG------ALNCPFGTGHMGVTAENVAAEHGIGRADQ 178 Query: 182 DAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVV 241 DAFAL SQ +AARAQ G +IV V + K+ D + DEHP+ T+ E+LA L+ V Sbjct: 179 DAFALESQARAARAQEAGHFNSQIVPVPVKVKR-DMVDFVRDEHPKPTTAEALAGLRTVF 237 Query: 242 RPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPA 301 + DGTVTAGNASG+NDGA AL++A AAE GL+ RAR++G A AGV P +MGIGP PA Sbjct: 238 QKDGTVTAGNASGINDGAAALVLARASAAESAGLKPRARILGYAHAGVRPEVMGIGPVPA 297 Query: 302 TQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGAS 361 Q LL + +++ DVIE NEAFA+Q LAV + LGL D +VNPNGGAIALGHP+GA+ Sbjct: 298 VQALLAKTDLSVSDFDVIESNEAFAAQALAVNKGLGL--DPAKVNPNGGAIALGHPVGAT 355 Query: 362 GARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 GA + AL++LER G+ AL TMCIG GQGIAL E L Sbjct: 356 GAIIALKALYELERIGGKRALVTMCIGGGQGIALAFEAL 394 Lambda K H 0.319 0.134 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: 444 Number of extensions: 21 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: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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 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