Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate Ac3H11_1916 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1916 Length = 399 Score = 295 bits (756), Expect = 1e-84 Identities = 184/413 (44%), Positives = 243/413 (58%), Gaps = 32/413 (7%) Query: 1 MNDAYICDAIRTPIGRYG-GALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQ 59 + DAYI A RTPIGR G G K+ R DDL IK+ + + P +D +A++D I GC+ Sbjct: 6 VQDAYIVAATRTPIGRSGRGYFKNTRPDDLLVAAIKSAMLQVPTLDPKAIEDAIIGCSFP 65 Query: 60 AGEDNRNVARMSALLAGLPADAP--GATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGV 117 GE N+AR++ GL + P G T+NR C SG+ A+ AA I+ GEA ++IAGG Sbjct: 66 EGEQGMNMARIAV---GLAFNHPVGGVTVNRFCASGITALQMAADRIRVGEADVLIAGGA 122 Query: 118 ESMTRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGIS 177 ESM+ P MG +F + D +G + M TAE VA+Q+ IS Sbjct: 123 ESMSLVP--MGGNKPSFNAEVFARDEDVGIAY------------GMGLTAEKVAQQWKIS 168 Query: 178 RADQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKK-----GDAIR----VTLDEHPR- 227 R QDAFAL S +A +AQ+ G EI E+ ++ G+ + V+LDE PR Sbjct: 169 REAQDAFALESHLRAIKAQKAGEFTDEITPFEVVERSPNLATGEVVEKRRTVSLDEGPRP 228 Query: 228 ETSLESLARLKGVVRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATA 287 +TSLE LA+LK V G+VTAGN+S +DGA AL++AS++A +Q+GL AR V A Sbjct: 229 DTSLEGLAKLKPVFAARGSVTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAAR 288 Query: 288 GVEPRIMGIGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNP 347 GV P IMGIGP A LR G+ D + ELNEAFA+Q LAV+ LGL + VNP Sbjct: 289 GVPPEIMGIGPIEAIPAALRYAGLKSDDIGWYELNEAFAAQSLAVINTLGL--NPANVNP 346 Query: 348 NGGAIALGHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 GGAIALGHPLGA+GA T +H L R ++ + TMC+G GQG A +IE L Sbjct: 347 MGGAIALGHPLGATGAIRAATVVHALRRHKLKYGMVTMCVGTGQGAAGIIEAL 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: 444 Number of extensions: 26 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: 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 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