Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate Ga0059261_1483 Ga0059261_1483 acetyl-CoA acetyltransferases
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__Korea:Ga0059261_1483 Length = 395 Score = 240 bits (613), Expect = 5e-68 Identities = 150/389 (38%), Positives = 211/389 (54%), Gaps = 10/389 (2%) Query: 11 RTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNRNVARM 70 RTP+G G L D A +LGA + A ++R G+ AV+ + GC AG + AR Sbjct: 13 RTPMGSMQGVLSDATATELGAAAVGAAVER-AGLKGEAVERIYMGCVLPAGL-GQAPARQ 70 Query: 71 SALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKA 130 +A AGLP T+N++CGSGM A A A+ AG L++AGG+ESMT AP++ K Sbjct: 71 AARKAGLPDHVEATTVNKMCGSGMQAAIMGAEALAAGSVDLLVAGGLESMTNAPYLSMKH 130 Query: 131 ASAFTRQAEI-HDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQ 189 S A I HD F++ L +M AE +A ++ +R QD FA+AS Sbjct: 131 RSG----ARIGHDRLFDHMFLDGLEDAYEPGRAMGTFAEEIATEYQFTREAQDEFAIASL 186 Query: 190 QKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGVVRPDGTVTA 249 +A +AQ+ G +EI VEI +KG + V DE P + + LK DGT+TA Sbjct: 187 MRAQKAQQTGGFDREITPVEIKTRKG-VVTVDKDEQPAKADPSKIPTLKPAFAKDGTITA 245 Query: 250 GNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQL 309 NAS ++DGA AL++ AE+ GL AR+V A P P A QK L + Sbjct: 246 ANASSISDGAAALVLTRASVAERLGLDPVARIVSHAAHAHLPARFTTAPVFAMQKALGKA 305 Query: 310 GMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTA 369 G + +D+ E+NEAFA + +R L + D +N NGGA ALGHP+GASGAR++ T Sbjct: 306 GWGIGDVDLFEVNEAFAVVAMIAMRDLSISHD--VLNVNGGACALGHPVGASGARILATL 363 Query: 370 LHQLERSNGRFALCTMCIGVGQGIALVIE 398 L L+ S + L ++CIG G+ A+ +E Sbjct: 364 LAALQNSGQKRGLASLCIGGGEATAMAVE 392 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: 364 Number of extensions: 16 Number of successful extensions: 5 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: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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