Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate GFF1320 PS417_06710 beta-ketoadipyl CoA thiolase
Query= uniprot:D8ITH5 (401 letters) >FitnessBrowser__WCS417:GFF1320 Length = 400 Score = 558 bits (1438), Expect = e-163 Identities = 276/399 (69%), Positives = 331/399 (82%), Gaps = 1/399 (0%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 + ICDAIRTP GR+GG L VRADDLAA PI++L+ERNP VDW+ V+++ GCANQAGE Sbjct: 3 DVFICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQAGE 62 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 DNRNVARMA LLAGLP ++PG T+NRLC S +DA+G A RAI SGE++L IAGGVESM+R Sbjct: 63 DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSR 122 Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181 APFVMGKA++AF+R+ + DTTIGWRF+NPLMKAQYG+D+MP+TA+NVA D+ ++RADQD Sbjct: 123 APFVMGKADAAFSRTMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYHVSRADQD 182 Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241 AFALRSQQR AAAQAAGFFA EI P+ + KKG+ VV DEHPR DTTL L KLK V Sbjct: 183 AFALRSQQRTAAAQAAGFFAEEIVPVRVAHKKGE-TVVEQDEHPRADTTLEALTKLKPVN 241 Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301 PD TVTAGNASGVNDGA AL+LAS +A + L RARVLGMA+AGVAPR+MG GP PA Sbjct: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPVPA 301 Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361 VRK++ ++GL + DVIELNEAFA+QGLAV+R+LG+ DDA VNPNGGAIA+GHPLG S Sbjct: 302 VRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNPNGGAIALGHPLGMS 361 Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 GARLV TA++QLE++GG L TMC+GVGQG+AL IER+ Sbjct: 362 GARLVLTALHQLEKTGGSKGLATMCVGVGQGLALAIERI 400 Lambda K H 0.320 0.135 0.394 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: 566 Number of extensions: 19 Number of successful extensions: 3 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: 400 Length adjustment: 31 Effective length of query: 370 Effective length of database: 369 Effective search space: 136530 Effective search space used: 136530 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 Apr 09 2024. 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