Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011842153.1 RSPH17029_RS16020 3-oxoadipyl-CoA thiolase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000015985.1:WP_011842153.1 Length = 399 Score = 539 bits (1389), Expect = e-158 Identities = 277/400 (69%), Positives = 321/400 (80%), Gaps = 1/400 (0%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M +ICD IRTPIGRYGGAL VRADDLGAVP+KAL+ RN GVDW AVDDVI+GCANQA Sbjct: 1 MTQVFICDYIRTPIGRYGGALSPVRADDLGAVPLKALMARNGGVDWEAVDDVIFGCANQA 60 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 GEDNRNVARMSALLAGLP G TINRLCGSGMDAV TAAR I AGEA L+IAGGVESM Sbjct: 61 GEDNRNVARMSALLAGLPVGVTGTTINRLCGSGMDAVLTAARQIAAGEADLVIAGGVESM 120 Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180 +RAPFV+ KA +AFTR AEIHDTTIGWRFVNP M+ YGVD MP+T +NVA FGISR Sbjct: 121 SRAPFVLPKAGTAFTRSAEIHDTTIGWRFVNPAMEAAYGVDPMPQTGQNVACDFGISREA 180 Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGV 240 QDA ALASQ KAA AQ +G LAQEI V + Q++G+ +RV DEHPR T+ E+LA+LK + Sbjct: 181 QDAMALASQTKAAAAQANGRLAQEITPVLVPQRRGEPVRVEQDEHPRATTPEALAKLKPL 240 Query: 241 VRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAP 300 G+VTAGN+SGVNDGA AL++AS+ A ++GL ARV+G ATAGV PRIMGIGP P Sbjct: 241 F-AGGSVTAGNSSGVNDGAAALILASEAAVRRHGLTPIARVLGGATAGVPPRIMGIGPVP 299 Query: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360 A KL+ +LG+T + DVIELNEAFA+QG+A LR LG+ ++D RVNPNGGAIALGHPLG Sbjct: 300 AALKLMARLGLTTEAFDVIELNEAFAAQGVATLRQLGIAEEDARVNPNGGAIALGHPLGM 359 Query: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 SGAR+ TA QL+R+ GR AL MCIGVGQGIA+ +ER+ Sbjct: 360 SGARITGTAALQLQRTGGRRALSAMCIGVGQGIAIALERV 399 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: 515 Number of extensions: 11 Number of successful extensions: 2 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: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 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 10 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