Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_092484149.1 BM299_RS11340 acetyl-CoA C-acetyltransferase
Query= uniprot:B2SYZ2 (400 letters) >NCBI__GCF_900115975.1:WP_092484149.1 Length = 393 Score = 279 bits (713), Expect = 1e-79 Identities = 164/398 (41%), Positives = 240/398 (60%), Gaps = 9/398 (2%) Query: 1 MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60 M + I A RTP G+ GGALK+++A LG + I + R G+D TVD+VI+G Q Sbjct: 1 MRQSVIVSAARTPFGKLGGALKNLKATQLGGIAIAEAVRR-AGIDGATVDNVIFGQVLQG 59 Query: 61 GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120 G + +R +A AGLP E P TIN++C SG+ AV + I+AG+A +++AGG+ESM Sbjct: 60 G-CGQIPSRQAAREAGLPWETPSETINKVCASGLRAVTMGDQIIRAGDADVIVAGGMESM 118 Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180 + AP+ + A +++T ++ + + M VA E+++SR + Sbjct: 119 SNAPYFVPGARWGLR----MFNTQFTDLMVHDGLWCSFYDRHMAIHGGEVAVEYNISREE 174 Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPR-ETSLESLGKLKG 239 QD +AL S Q A A G L +EI+ V I +KKGDPV DE PR ETS+E+L KL Sbjct: 175 QDEWALRSHQLAISAIDGGRLKEEIIPVTIPRKKGDPVVVDTDEGPRRETSMEALRKLPP 234 Query: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299 V P+ +VTAGNA GVNDGA AL++ + + A + G++ A V+G A+ E + + P Sbjct: 235 VFDPNNTVTAGNAPGVNDGAGALVIMSNEKAGELGIKPMATVLGHASVSQEAKYIATVPG 294 Query: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359 + KLLKQ GMT++Q+D++E+NEAFA+ L + G D +VN NGGAIA GHP+G Sbjct: 295 LSINKLLKQKGMTIDQVDLLEVNEAFAAVALVSGKIAGWNPD--KVNVNGGAIAFGHPIG 352 Query: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVI 397 ASGAR++ T +Y+L R G + +C G QG A+++ Sbjct: 353 ASGARILMTLIYELRRRGGGIGVAAICSGAAQGDAVMV 390 Lambda K H 0.318 0.135 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: 410 Number of extensions: 20 Number of successful extensions: 6 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: 393 Length adjustment: 31 Effective length of query: 369 Effective length of database: 362 Effective search space: 133578 Effective search space used: 133578 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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