Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate Pf6N2E2_1145 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1145 Length = 396 Score = 697 bits (1798), Expect = 0.0 Identities = 351/395 (88%), Positives = 376/395 (95%) Query: 3 MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLS 62 MS+DPIVIVSAVRTPMGGFQGELKSL+APQLGAAAI+AAVERAG+A VEEVLFGCVL+ Sbjct: 2 MSNDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGIAPGVVEEVLFGCVLA 61 Query: 63 AGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESM 122 AG GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEA ILAHDML+AGSA+VVVAGGMESM Sbjct: 62 AGQGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEATILAHDMLIAGSAEVVVAGGMESM 121 Query: 123 SNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDE 182 SNAPYLLDRAR GYRMGHG+VLDHMFLDGLEDAYDKGRLMGTFAEDCAEANG +REAQD Sbjct: 122 SNAPYLLDRARGGYRMGHGRVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGLSREAQDA 181 Query: 183 FAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDG 242 FAIASTTRAQQAIKDGSF+AEIVPLQV+VGKEQ I DEQPPKA++DKIASLKPAFR+G Sbjct: 182 FAIASTTRAQQAIKDGSFDAEIVPLQVMVGKEQVTIRHDEQPPKARIDKIASLKPAFREG 241 Query: 243 GTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKK 302 GTVTAAN+SSISDGAAAL+LMR+S+A +RGLKPLAVIHGHAAFADTP LFP AP+GA+KK Sbjct: 242 GTVTAANASSISDGAAALVLMRQSQAAQRGLKPLAVIHGHAAFADTPSLFPTAPIGAVKK 301 Query: 303 LLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARIL 362 L++KTGWSLD+V+LFEVNEAFAVV LVTM KLEI H KVNVHGGACALGHPIGASGARIL Sbjct: 302 LMQKTGWSLDQVDLFEVNEAFAVVGLVTMDKLEIAHDKVNVHGGACALGHPIGASGARIL 361 Query: 363 VTLLSALRQKGLKRGVAAICIGGGEATAMAVECLY 397 VTLLSALRQKGLKRGVAAICIGGGEATAMAVECLY Sbjct: 362 VTLLSALRQKGLKRGVAAICIGGGEATAMAVECLY 396 Lambda K H 0.318 0.133 0.378 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: 613 Number of extensions: 11 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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