Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF1551 HP15_1513 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Marino:GFF1551 Length = 374 Score = 239 bits (610), Expect = 1e-67 Identities = 156/384 (40%), Positives = 212/384 (55%), Gaps = 17/384 (4%) Query: 14 IGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQGATGGNIARKAL 72 +G+A G TL + IE +R +DPKEVEDV+ G Q G N+AR+ Sbjct: 1 MGRAKNGCFRNVRAETLSANLIEALFERNPKLDPKEVEDVIWGCVNQTKEQGFNVARQIS 60 Query: 73 LRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQNDKMNTFH 132 L +P +A T++R C S + AI AA++++ ++ GG E + V M Sbjct: 61 LLTRIPHESAAQTVNRLCGSAMSAIHTAAQAIMTGNGDVFFVGGVEHMGHVP---MTEGF 117 Query: 133 AVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEIA 192 +PA M TAE +AK +GI+RE+QDE+ S R A G+F +EI Sbjct: 118 DHNPAASKYSAKASNMMGLTAEMLAKMHGITREQQDEFGARSHRLAHEATLEGRFKNEIV 177 Query: 193 PISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLK-AVRGEGFTITAGNASQL 251 PI + FK + + +DE RPETTAE L+ LK A + T+TAG +SQL Sbjct: 178 PI--------EGHDENGFK-VLIEEDETIRPETTAESLSQLKPAFDPKNGTVTAGTSSQL 228 Query: 252 SDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPRLLKRHGLSVDD 311 +DGA+A V+MS + A A GLKP+ R M GC+P MG GPV A + LKR GL V+D Sbjct: 229 TDGAAAMVLMSAERAEALGLKPIAKIRSMAVAGCDPAIMGYGPVPATKKALKRAGLKVED 288 Query: 312 IGLWELNEAFAVQ---VLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLAGHALIEGR 368 I WELNEAFA Q VL LG+ EK+N+NGGAI++GHP G SGAR++ L + Sbjct: 289 IDFWELNEAFAGQSLPVLKDLKLLGVMEEKVNLNGGAIALGHPLGCSGARISTTLLNVMQ 348 Query: 369 RRKAKYAVVTMCVGGGMGSAGLFE 392 + K V TMC+G G G A ++E Sbjct: 349 AKGGKLGVSTMCIGLGQGIATVWE 372 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: 386 Number of extensions: 17 Number of successful extensions: 5 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: 374 Length adjustment: 30 Effective length of query: 365 Effective length of database: 344 Effective search space: 125560 Effective search space used: 125560 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