Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_013074586.1 BTUS_RS02645 thiolase family protein
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000092905.1:WP_013074586.1 Length = 395 Score = 305 bits (782), Expect = 1e-87 Identities = 179/403 (44%), Positives = 238/403 (59%), Gaps = 12/403 (2%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 MREA I D IRTPIGR G+L+ V DL A L+EL +R LDA +DDVI+GC +Q Sbjct: 1 MREAVIVDAIRTPIGRRRGSLAQVHPVDLLAGVLKEL-IRRSGLDAAVVDDVIVGCVDQV 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 GE + N+ R A L AGLP+SV TI+R CGS L AL FAA+ + AG D+ IA GVESM Sbjct: 60 GEQSVNIGRNAWLSAGLPESVPAVTIDRQCGSSLQALHFAAQGVMAGVYDIAIAAGVESM 119 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 +R P + ++ + R+ Q G AE +A+ +RED Sbjct: 120 TRVPMMSTIGVHGVPMTRDLQERYRMDRWNRQFFDQALG-------AEMIAKQWGFTRED 172 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLK--NKKGVVTEIQHDEHLRPETTLEQLRGL 238 D F LRS + KA+ G A EIVPV + + G DE +RP+T+LE++ L Sbjct: 173 LDRFGLRSHELATKARQKGCFAREIVPVQVPVPDAPGEYRTFAEDEGIRPDTSLEKMLAL 232 Query: 239 KAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLG 298 F +ITAGNAS ++DGA+A ++ S + A GL PRAR VA A GV+P M G Sbjct: 233 PPAFEDLELITAGNASQISDGASAALVMSRETAERLGLRPRARFVAFAAVGVDPVTMLTG 292 Query: 299 PVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHP 358 P+PAT++VLERAGL + D+D+ E+NEAFA+ L +E+G P D VN +GGA+A+GHP Sbjct: 293 PIPATQKVLERAGLKVEDIDLFEVNEAFASVVLAWQKEIGAPWD--KVNVHGGAVAIGHP 350 Query: 359 LGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 LG +G R+ + L R GRY L +C G G A I+ER+ Sbjct: 351 LGATGTRITATLLNGLEERKGRYGLMAICEGGGMANATIIERI 393 Lambda K H 0.319 0.135 0.384 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: 440 Number of extensions: 20 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: 401 Length of database: 395 Length adjustment: 31 Effective length of query: 370 Effective length of database: 364 Effective search space: 134680 Effective search space used: 134680 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 24 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