Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_041097741.1 SUTH_RS05630 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000828635.1:WP_041097741.1 Length = 392 Score = 477 bits (1228), Expect = e-139 Identities = 247/394 (62%), Positives = 300/394 (76%), Gaps = 2/394 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MT+AVIVSTART + K+++GA N T GATL H+++HAV RA IDP EVEDV+MG A + Sbjct: 1 MTDAVIVSTARTGLAKSWKGAFNMTHGATLGAHSVKHAVARAKIDPAEVEDVLMGCATPE 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GATG NIAR+ L AGLPVT G T++R C+SGLQ IA+AA+ ++ +I V GG ESI Sbjct: 61 GATGSNIARQIALAAGLPVTVPGATVNRFCSSGLQTIAMAAQRIIAGECDILVAGGVESI 120 Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180 S VQ + N DPAL IK +VY +ML TAE VAKRY I ++RQDEY + SQ R AA Sbjct: 121 SCVQQEA-NRHMITDPALLKIKPEVYWSMLQTAEQVAKRYKIGKDRQDEYGVNSQLRAAA 179 Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEG 240 Q GKF DEI P++ MGV DKATGA+S K++T++ DEG RP+TT EG++ +++ G Sbjct: 180 GQAAGKFADEIVPMTVTMGVADKATGALSTKEVTIAADEGIRPDTTLEGVSKIRSALPGG 239 Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300 ITAGNASQ SDG+SA+V+M+ A KGL PLGIFRG GCEPDEMGIGPVFAVP+ Sbjct: 240 -VITAGNASQFSDGSSASVVMNATVAERKGLTPLGIFRGFAVAGCEPDEMGIGPVFAVPK 298 Query: 301 LLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLA 360 LLK+ GL+V DI LWELNEAFAVQVLY D LGI ++LNVNGGAI+VGHPYG+SGARL Sbjct: 299 LLKKAGLTVADIDLWELNEAFAVQVLYSADTLGIPLDRLNVNGGAIAVGHPYGVSGARLV 358 Query: 361 GHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GHALIEG+RR AK VVTMC+GGG G+AGLFE+V Sbjct: 359 GHALIEGKRRGAKLVVVTMCIGGGQGAAGLFEVV 392 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: 478 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: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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 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