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 Ac3H11_2994 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2994 Length = 397 Score = 486 bits (1250), Expect = e-142 Identities = 246/393 (62%), Positives = 300/393 (76%) Query: 2 TMSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVL 61 T DPIVIV A RTPMG QG+ SL+A LG AAI+AA+ERAGV+ DAV EVLFG L Sbjct: 3 TTIQDPIVIVGAARTPMGSLQGDFSSLAAHDLGGAAIKAAIERAGVSPDAVGEVLFGNCL 62 Query: 62 SAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMES 121 AG GQAPARQAA GL K TL+KMCGSGM+AA++AHDMLLAGS DV+VAGGMES Sbjct: 63 MAGQGQAPARQAAFKGGLPKGAGAVTLSKMCGSGMKAAMMAHDMLLAGSHDVMVAGGMES 122 Query: 122 MSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQD 181 M+NAPYLL + R GYR+GH ++ DHM LDGLEDAY+ GR MGTF EDCA FTRE QD Sbjct: 123 MTNAPYLLQKGRGGYRLGHDRIFDHMMLDGLEDAYEAGRSMGTFGEDCAAKYSFTREQQD 182 Query: 182 EFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRD 241 FA AS RA+ A + G+F AEIVP+ V + +++ DE P K KL+KIA+LKPAF+ Sbjct: 183 AFATASVQRAKAATESGAFAAEIVPVTVKTRAGETVVSVDEGPGKVKLEKIATLKPAFKK 242 Query: 242 GGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIK 301 GT+TAA+SSSI+DGAAAL++MR S A+K G KPLA I HA A P F AP+GA + Sbjct: 243 DGTITAASSSSINDGAAALVMMRESTAKKLGAKPLARIVSHATHAQEPEWFATAPLGATQ 302 Query: 302 KLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARI 361 K L K GW + +V+L+E+NEAFAVV + M +L++PH KVNV+GGACALGHPIGASGARI Sbjct: 303 KALAKAGWQVGDVQLWEINEAFAVVPMALMKELDLPHDKVNVNGGACALGHPIGASGARI 362 Query: 362 LVTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 +VTL+ AL+ +GL +G+A +CIGGGEATA+A+E Sbjct: 363 MVTLIHALKARGLTKGLATLCIGGGEATAVALE 395 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: 495 Number of extensions: 12 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: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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