Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate 200842 SO1677 acetyl-CoA acetyltransferase (NCBI ptt file)
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__MR1:200842 Length = 396 Score = 253 bits (645), Expect = 9e-72 Identities = 153/393 (38%), Positives = 225/393 (57%), Gaps = 9/393 (2%) Query: 6 ICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNR 65 I A RTP+G + G+L + + L A IKAL+ + V VD+V+ GC AG + Sbjct: 12 IVAAKRTPMGSFQGSLSGITSLSLAATAIKALLA-DTQVAPDKVDEVLMGCVLPAGL-GQ 69 Query: 66 NVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPF 125 AR + L AGLP T+N++CGSGM V A IKAG A+++IAGG+ESM++AP+ Sbjct: 70 APARQATLGAGLPLSVGATTVNKVCGSGMKTVMLAHDLIKAGSAKVVIAGGMESMSQAPY 129 Query: 126 VMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFA 185 ++ KA + H + F++ L + Y +M A+ A++FGI+R DAFA Sbjct: 130 LLDKARAGIRMG---HGKVLDHMFLDGL-EDAYTGGAMGTFAQKTADEFGITREQMDAFA 185 Query: 186 LASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDG 245 L+S +KA A G EIV V ++ ++GD + + DE P E + L+ DG Sbjct: 186 LSSLEKANAAINSGAFKTEIVPVTVSDRRGD-VTIDTDEQPGNARPEKIPTLRPAFAKDG 244 Query: 246 TVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKL 305 T+TA N+S ++DGA AL++ ++ AEQ GL A + G T EP + P A KL Sbjct: 245 TITAANSSSISDGAAALMLTTRANAEQLGLTVLATIKGHTTHAQEPALFTTAPVGAMAKL 304 Query: 306 LRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARL 365 L +G + D++D+ E+NEAFA + + LGL D +VN NGGA ALGHP+G SGARL Sbjct: 305 LSNVGWSKDEVDLFEINEAFAMVTMLAVSELGL--DMTKVNVNGGACALGHPIGCSGARL 362 Query: 366 VTTALHQLERSNGRFALCTMCIGVGQGIALVIE 398 + T +H L+ + + ++CIG G+ A+ IE Sbjct: 363 LVTLIHALKARGLKRGVASLCIGGGEATAMAIE 395 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: 374 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: 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 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