Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000009985.1:WP_011383284.1 Length = 390 Score = 297 bits (761), Expect = 3e-85 Identities = 171/399 (42%), Positives = 244/399 (61%), Gaps = 9/399 (2%) Query: 1 MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60 M D I A RTP+G + G+L ++A LG + I+ ++R GV+ AVD+V+ G A Sbjct: 1 MTDIVIAAATRTPVGSFNGSLAGLQAAQLGEIVIREALKR-AGVEAEAVDEVLLGHILTA 59 Query: 61 GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120 G +N AR +A+ AG+P A IN+LCGSG+ AV +AIK G+A +++AGG ESM Sbjct: 60 G-CGQNTARQAAIKAGVPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESM 118 Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180 + A + A + DT I + G+ TAEN+AE+F I+R + Sbjct: 119 SNAQHAIYMRGGVKMGDASLVDTMIKDGLTDAFSPIHMGI-----TAENLAEKFQITREE 173 Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGV 240 QDAFAL SQ KA A + G +IV V I K+ + + T + +L+ +A+ K Sbjct: 174 QDAFALGSQNKAEAASKAGRFKDQIVPVTITVKREEKLFDTDEFIRMGCTLDQIAKPKPA 233 Query: 241 VRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAP 300 + DGTVTA NASG+NDG AL++ + + A++ G++ AR+ G ATAG +P MG GP P Sbjct: 234 FKKDGTVTAANASGINDGGAALVLMTAKEADKRGIKPLARIAGWATAGTDPNTMGYGPVP 293 Query: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360 ATQKLL +LG + LD+IE NEAFA+Q +AV + +G D +VN NGGAIA+GHP+GA Sbjct: 294 ATQKLLAKLGWKHEDLDLIEANEAFAAQAIAVNKGMGW--DTSKVNVNGGAIAIGHPIGA 351 Query: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIER 399 SGAR++ L+++ R + + L T+CIG G GIAL +ER Sbjct: 352 SGARILVDLLYEMGRRDAKKGLATLCIGGGMGIALCVER 390 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: 398 Number of extensions: 13 Number of successful extensions: 4 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: 390 Length adjustment: 31 Effective length of query: 369 Effective length of database: 359 Effective search space: 132471 Effective search space used: 132471 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 17 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