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 GFF2479 HP15_2423 acyl-CoA thiolase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >FitnessBrowser__Marino:GFF2479 Length = 379 Score = 447 bits (1149), Expect = e-130 Identities = 231/380 (60%), Positives = 290/380 (76%), Gaps = 2/380 (0%) Query: 18 MGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQAPARQAALGA 77 MGGFQG L S+SA LGA I AV RAG+ V+EV+ G VL AGL Q PARQA A Sbjct: 1 MGGFQGSLASVSATDLGAITIAEAVRRAGLQPADVQEVIMGNVLPAGLKQGPARQAMRKA 60 Query: 78 GLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPYLLDRARSGYR 137 GL T TT+NK+CGSGM+AA+ AHD++ AGS D++VAGGMESMSNAPY+L RSGYR Sbjct: 61 GLPDHTGATTINKLCGSGMKAAMFAHDLIKAGSNDIMVAGGMESMSNAPYILQGVRSGYR 120 Query: 138 MGHGKV-LDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIASTTRAQQAIK 196 MG G+ DHMFLDGLEDA + GRLMG FA++ A+ G+TRE DE+AI S TRA++AI+ Sbjct: 121 MGPGQAPQDHMFLDGLEDA-ETGRLMGAFAQEMADKKGYTREEMDEYAITSLTRAKKAIE 179 Query: 197 DGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTAANSSSISDG 256 +G EI+P+ V K + ++ DDEQP A +DKI SL+PAF GTVTAAN+SSISDG Sbjct: 180 EGLLKDEIIPVTVKSRKGEVVVEDDEQPHNANIDKIPSLRPAFAKDGTVTAANASSISDG 239 Query: 257 AAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKTGWSLDEVEL 316 A+ALLLMR SEAEKRGLKPLA I GH+ + P F APVGAI+ L KTGWS D+V+L Sbjct: 240 ASALLLMRESEAEKRGLKPLARIVGHSTQSQHPSEFTCAPVGAIETLFGKTGWSKDDVDL 299 Query: 317 FEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLSALRQKGLKR 376 FE+NEAFA+V+++ + +L + KVN+HGGACA GHP+G++G+R+LVTL+ AL++ G K+ Sbjct: 300 FEINEAFAMVAMMPIRELGLDPEKVNIHGGACAQGHPVGSTGSRLLVTLMYALQRYGKKK 359 Query: 377 GVAAICIGGGEATAMAVECL 396 G+AA+CIGGGEATAMA+E L Sbjct: 360 GIAALCIGGGEATAMAIEML 379 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: 437 Number of extensions: 13 Number of successful extensions: 3 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: 379 Length adjustment: 30 Effective length of query: 367 Effective length of database: 349 Effective search space: 128083 Effective search space used: 128083 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