Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate Ac3H11_3920 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3920 Length = 403 Score = 593 bits (1529), Expect = e-174 Identities = 301/397 (75%), Positives = 337/397 (84%) Query: 4 AYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGED 63 A+ICDAIRTP GRYGGAL VR DDLGA+PIKAL+ RNPGVDW AV DV YGCANQAGED Sbjct: 7 AFICDAIRTPFGRYGGALSSVRTDDLGAIPIKALMDRNPGVDWAAVTDVFYGCANQAGED 66 Query: 64 NRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRA 123 NRNVA MS+LLAGLP + GATINRLCGSG+DAVGTAARAIKAGEA LMIAGGVESM+RA Sbjct: 67 NRNVAHMSSLLAGLPIEVAGATINRLCGSGLDAVGTAARAIKAGEAGLMIAGGVESMSRA 126 Query: 124 PFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDA 183 PFVM KA SAF+R + ++DTTIGWRFVN LMK +YGVDSMPETAENVA F I R QD Sbjct: 127 PFVMPKAESAFSRNSAVYDTTIGWRFVNKLMKEKYGVDSMPETAENVATDFKIEREAQDQ 186 Query: 184 FALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRP 243 AL SQ A A + G LA+EIV V I QKKGDAI V+ DEHPRETSLE+LA+LKGVVRP Sbjct: 187 MALRSQLNAVAAIKAGHLAREIVPVHIPQKKGDAIIVSQDEHPRETSLEALAKLKGVVRP 246 Query: 244 DGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQ 303 DGTVTAGNASGVNDGACALL+A + A +YGL+ RARVVGMA AGV PRIMG GP PATQ Sbjct: 247 DGTVTAGNASGVNDGACALLLADEANAAKYGLKPRARVVGMAVAGVAPRIMGFGPTPATQ 306 Query: 304 KLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGA 363 K+L Q G+T+D +DVIELNEAFA+QGLAVLR LGL+DDD RVN GGAIALGHPLGASGA Sbjct: 307 KVLAQTGLTIDHMDVIELNEAFAAQGLAVLRALGLKDDDGRVNAWGGAIALGHPLGASGA 366 Query: 364 RLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 RLVTTA+++L G++ALCTMCIGVGQGIA+++ER+ Sbjct: 367 RLVTTAVNRLHEHAGQYALCTMCIGVGQGIAVILERV 403 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: 529 Number of extensions: 8 Number of successful extensions: 1 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: 403 Length adjustment: 31 Effective length of query: 369 Effective length of database: 372 Effective search space: 137268 Effective search space used: 137268 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