Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate 3606642 Dshi_0074 acetyl-CoA acetyltransferase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2994 (397 letters) >FitnessBrowser__Dino:3606642 Length = 392 Score = 468 bits (1204), Expect = e-136 Identities = 238/387 (61%), Positives = 287/387 (74%) Query: 9 IVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLMAGQGQ 68 + I GAARTPMG QG FS ++A LGGAAI A+ AGV+P V E+L G L AGQGQ Sbjct: 4 VAICGAARTPMGGFQGVFSDVSAAQLGGAAIAGALADAGVAPAQVNELLMGCVLPAGQGQ 63 Query: 69 APARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESMTNAPY 128 APARQA + GL A TL+KMCGSGMKAAM+A D + G D++VAGGMESMTNAPY Sbjct: 64 APARQAGYAAGLGDAVPATTLNKMCGSGMKAAMIACDQIALGQSDLVVAGGMESMTNAPY 123 Query: 129 LLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQDAFATAS 188 LL K RGG R+GH ++ DHM LDGLEDAY+ GR MGTF EDCA + FTR QD +A S Sbjct: 124 LLDKMRGGARIGHGQVIDHMFLDGLEDAYDKGRLMGTFAEDCAEAFQFTRAAQDTYALGS 183 Query: 189 VQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKKDGTITA 248 ++ A AA S AFA E+VPVTV R GETVV DE P + EKI LKPAF+KDGT+TA Sbjct: 184 LENALAAEASEAFAMELVPVTVSGRKGETVVIRDEQPAAARPEKIPHLKPAFRKDGTVTA 243 Query: 249 ASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQKALAKA 308 A+SSSI+DGAAALV+ A+ G AR++ HA+HAQ+P F TAP+ A +K L + Sbjct: 244 ANSSSISDGAAALVLADAGQAEAHGLPVRARVLGHASHAQKPALFPTAPVPAARKLLDRL 303 Query: 309 GWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARIMVTLIH 368 GW V DV LWE+NEAFAVVPMA M E+ +P +K+NVNGGACALGHPIGASGARI+VTL++ Sbjct: 304 GWCVADVDLWEVNEAFAVVPMAFMHEMGVPREKMNVNGGACALGHPIGASGARILVTLLN 363 Query: 369 ALKARGLTKGLATLCIGGGEATAVALE 395 A++AR L +G+A +CIGGGE TA+ALE Sbjct: 364 AMEARDLKRGVAAICIGGGEGTAIALE 390 Lambda K H 0.317 0.131 0.376 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: 511 Number of extensions: 19 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: 397 Length of database: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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