Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_099619682.1 CLH62_RS18535 acetyl-CoA C-acyltransferase FadA
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_002744735.1:WP_099619682.1 Length = 391 Score = 246 bits (629), Expect = 6e-70 Identities = 160/395 (40%), Positives = 216/395 (54%), Gaps = 17/395 (4%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61 + V+V RTP+G+A G TL IE +R +DPKEVEDV+ G Q Sbjct: 7 DVVVVDCVRTPMGRAKNGCFRNVRAETLSAALIEALFERNPKLDPKEVEDVIWGCVNQTK 66 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 G N+AR+ L +P +A T++R C S + AI AA++++ ++ V GG E + Sbjct: 67 EQGFNVARQISLLTRIPHESAAQTVNRLCGSSMSAIHTAAQAIMTGNGDVFVVGGVEHMG 126 Query: 122 LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAA 181 V M +PA M TAE +AK +GI+R++QDE+ S R A Sbjct: 127 HVP---MTEGFDHNPAASKYTAKASNMMGLTAEMLAKMHGITRKQQDEFGARSHRLAHEA 183 Query: 182 QQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AVRGEG 240 G+FN+EI PI G V + +DE RP+TT E L LK A + Sbjct: 184 TLEGRFNNEIVPIEGH-----DENGFVKL----IEEDETIRPDTTVESLGQLKPAFDPKN 234 Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300 T+TAG +SQL+DGA+A V+MS + A A GLKP+ R M GC+P MG GPV A + Sbjct: 235 GTVTAGTSSQLTDGAAAMVLMSAERAEALGLKPIARVRSMAVAGCDPAIMGYGPVPATKK 294 Query: 301 LLKRHGLSVDDIGLWELNEAFAVQ---VLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGA 357 LKR GL V+DI WELNEAFA Q VL LG+ EK+N+NGGAI++GHP G SGA Sbjct: 295 ALKRAGLKVEDIDFWELNEAFAGQSLPVLKDLKLLGVMAEKVNLNGGAIALGHPLGCSGA 354 Query: 358 RLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 R++ L + + K V TMC+G G G A ++E Sbjct: 355 RISTTLLNVMQAKGGKLGVSTMCIGLGQGIATVWE 389 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: 397 Number of extensions: 17 Number of successful extensions: 6 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 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