Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate 1937156 b3845 acetyl-CoA acetyltransferase (NCBI)
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__Keio:1937156 Length = 387 Score = 294 bits (752), Expect = 3e-84 Identities = 177/406 (43%), Positives = 239/406 (58%), Gaps = 25/406 (6%) Query: 1 MNDAYICDAIRTPIGRY-GGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQ 59 M I DAIRTP+GR GGA ++VRA+DL A +++L+ RNP ++ A+DD+ +GC Q Sbjct: 1 MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60 Query: 60 AGEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVES 119 E N+AR +ALLA +P P T+NRLCGS M A+ AAR I G+AQ + GGVE Sbjct: 61 TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120 Query: 120 MTRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQY--GVDSMPETAENVAEQFGIS 177 M P G + H P + R M TAE +A GIS Sbjct: 121 MGHVPMSHG---------VDFH----------PGLSRNVAKAAGMMGLTAEMLARMHGIS 161 Query: 178 RADQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLAR 236 R QDAFA S +A A + EI+ G + DE R ET++E+LA Sbjct: 162 REMQDAFAARSHARAWAATQSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALAT 221 Query: 237 LKGVVRP-DGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMG 295 L+ P +G VTAG +S ++DGA A+L+ S+ A + GL+ RARV MA G +P IMG Sbjct: 222 LRPAFDPVNGMVTAGTSSALSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMG 281 Query: 296 IGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDD-DPRVNPNGGAIAL 354 GP PA++ L++ G++ + V E+NEAFA+Q L ++ LGL + D ++N NGGAIAL Sbjct: 282 YGPVPASKLALKKAGLSASDIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIAL 341 Query: 355 GHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 GHPLG SGAR+ TT L+ +ER + +F L TMCIG+GQGIA V ER+ Sbjct: 342 GHPLGCSGARISTTLLNLMERKDVQFGLATMCIGLGQGIATVFERV 387 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: 382 Number of extensions: 19 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: 387 Length adjustment: 31 Effective length of query: 369 Effective length of database: 356 Effective search space: 131364 Effective search space used: 131364 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