Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_027456897.1 K420_RS0103905 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000519045.1:WP_027456897.1 Length = 396 Score = 240 bits (613), Expect = 5e-68 Identities = 153/399 (38%), Positives = 222/399 (55%), Gaps = 13/399 (3%) Query: 6 ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65 I A RT +G + G + A +LGA IKA I R G+D +++V+ GC QAG+ + Sbjct: 7 IVSAARTAMGSFQGGFSGLTAANLGAEAIKAAIAR-AGLDTHLIEEVLMGCVLQAGQ-GQ 64 Query: 66 NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125 AR +AL AGLP A ATI+++CGS M A I AG + GG+ESMT AP+ Sbjct: 65 APARQAALQAGLPLTAGCATIHKVCGSAMKATMLGHDGILAGSYGAAVVGGMESMTNAPY 124 Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDS----MPETAENVAEQFGISRADQ 181 ++ KA + H + F++ L + YG ++ M AE A +G +R Q Sbjct: 125 LLPKARGGYRLG---HGQLMDHMFLDGL-EDAYGKETRGRLMGTFAEECAAAYGFTREAQ 180 Query: 182 DAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVV 241 D FA+ S +A A +G+ A EI V +A +KGD + + DE P +++ + LK Sbjct: 181 DEFAVRSTTRAIEASNNGSFAWEITPVTVAGRKGDVV-IDKDEGPFAVNVDKIPTLKPAF 239 Query: 242 RPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPA 301 + DGTVTA N+S ++DGA A+++ + A + GL AR+VG T P P A Sbjct: 240 KKDGTVTAANSSSISDGAAAMVLMRESQAAKLGLSPVARIVGHTTHAGIPAQFPSAPVGA 299 Query: 302 TQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGAS 361 QKL + G T + +D+ E+NEAFA +A L L L D +VN +GGA ALGHP+GAS Sbjct: 300 MQKLFAKTGWTAESVDLYEINEAFAVVTMAALHDLKL--DPAKVNIHGGACALGHPIGAS 357 Query: 362 GARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 GAR+V T L L++ + + ++CIG G+ AL +E L Sbjct: 358 GARIVVTLLGALKKYGLKRGVASLCIGGGEATALAVEML 396 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: 393 Number of extensions: 24 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: 396 Length adjustment: 31 Effective length of query: 369 Effective length of database: 365 Effective search space: 134685 Effective search space used: 134685 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