Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ac3H11_2522 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2522 Length = 391 Score = 457 bits (1177), Expect = e-133 Identities = 234/393 (59%), Positives = 294/393 (74%), Gaps = 3/393 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MT AVIVSTARTP+ K+++G+ N T GATL GHA++HAV+RAGID +V+DV+MG A + Sbjct: 1 MTSAVIVSTARTPLAKSWKGSFNMTHGATLGGHAVQHAVQRAGIDGADVDDVIMGCATPE 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GATG NIAR+ L+AGLP+T +G T++R C+SGLQ IA+AA+ ++ ++ V GG ESI Sbjct: 61 GATGSNIARQIALKAGLPITASGVTVNRFCSSGLQTIAMAAQRIIAGEADVFVAGGVESI 120 Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180 S VQ + MN D AL K ++Y +ML TAE VAKRY I RE DEY SQ++ A Sbjct: 121 SCVQQE-MNLHMIQDLALAKQKPEIYWSMLQTAEQVAKRYNIGREAMDEYGAGSQQKACA 179 Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEG 240 AQ G F+ EIAPI+ GV DK G ++ K +T+S+DEG R TT E ++GL++ G Sbjct: 180 AQANGLFDAEIAPITVTAGVADKTLGLIT-KQVTVSKDEGTREGTTVEAISGLRSALPGG 238 Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300 I+AGNASQ SDGA A V+ S+ A+ KGLKPLG F G GCEPDEMGIGPVFAVP+ Sbjct: 239 L-ISAGNASQFSDGAGACVLTSEDYASKKGLKPLGRFLGFAVAGCEPDEMGIGPVFAVPK 297 Query: 301 LLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLA 360 +LK+ GL V+DI LWELNEAFAVQVLYCRDKLGI ++LNVNGGAI++GHPYG+SG RL Sbjct: 298 VLKKLGLKVEDIDLWELNEAFAVQVLYCRDKLGIPADRLNVNGGAIALGHPYGVSGQRLT 357 Query: 361 GHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393 GHALIEG+RR AK VTMC+GGGMG+AG+FE+ Sbjct: 358 GHALIEGKRRGAKRVCVTMCIGGGMGAAGIFEV 390 Lambda K H 0.316 0.134 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: 490 Number of extensions: 21 Number of successful extensions: 4 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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 (21.6 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