Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011799880.1 PNAP_RS02270 acetyl-CoA C-acyltransferase
Query= reanno::acidovorax_3H11:Ac3H11_2994 (397 letters) >NCBI__GCF_000015505.1:WP_011799880.1 Length = 393 Score = 624 bits (1608), Expect = 0.0 Identities = 311/393 (79%), Positives = 344/393 (87%) Query: 5 IQDPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCLMA 64 + + IVI+GAARTPMG+ QGDF+SL+A+DLGGAAI+AA+ER+GVSP V EVLFGNCLMA Sbjct: 1 MSESIVILGAARTPMGAFQGDFASLSANDLGGAAIRAAVERSGVSPAQVDEVLFGNCLMA 60 Query: 65 GQGQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMESMT 124 GQGQAPARQA FKGGLP GAVTLSKMCGSGM+A M+AHD LLAGS DV+VAGGMESMT Sbjct: 61 GQGQAPARQAGFKGGLPASTGAVTLSKMCGSGMEATMLAHDQLLAGSRDVVVAGGMESMT 120 Query: 125 NAPYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQDAF 184 NAPYLL K R G R+GHDR+ DHMMLDGLEDAYEAGRSMGTFGEDCAAKY FTRE QDAF Sbjct: 121 NAPYLLPKARAGMRIGHDRVMDHMMLDGLEDAYEAGRSMGTFGEDCAAKYGFTREAQDAF 180 Query: 185 ATASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKKDG 244 ATASVQRAKAA+ESGAF EI PVTVK RAG+TV+S+DEGPGKVKLEKI L+PAFKKDG Sbjct: 181 ATASVQRAKAASESGAFKDEITPVTVKGRAGDTVISIDEGPGKVKLEKIPALRPAFKKDG 240 Query: 245 TITAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQKA 304 TITAASSSSINDGAAALV+ R STA +LG PLARIV HAT AQ PEWF+TAP+GA K Sbjct: 241 TITAASSSSINDGAAALVLARASTATELGLTPLARIVGHATFAQAPEWFSTAPVGAVNKL 300 Query: 305 LAKAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARIMV 364 L K GW+V DV LWEINEAFAVVPMA M +L L HD VNVNGGACALGHPIG SGARI+V Sbjct: 301 LKKIGWEVKDVDLWEINEAFAVVPMAAMADLGLSHDIVNVNGGACALGHPIGCSGARIIV 360 Query: 365 TLIHALKARGLTKGLATLCIGGGEATAVALELV 397 TL+HALKARGL KG+ATLCIGGGE TA+A+E++ Sbjct: 361 TLMHALKARGLKKGVATLCIGGGEGTALAIEVL 393 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: 604 Number of extensions: 14 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: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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 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