Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000185905.1:YP_004140539.1 Length = 392 Score = 251 bits (642), Expect = 2e-71 Identities = 151/393 (38%), Positives = 219/393 (55%), Gaps = 21/393 (5%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64 VI S ARTP+G ++ GA AT L I + RAG++P EV++V++G + A G Sbjct: 6 VIASAARTPVG-SFNGAFAATPAHELGAVVIRELLSRAGVEPGEVDEVILGQVLT-AAQG 63 Query: 65 GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124 N AR+A + AGLP T +++ C SGL+AIAL + + + + GG ES+SL Sbjct: 64 QNPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQESMSLST 123 Query: 125 ND-------KMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSLESQ 175 + KM F +D ++ D + M +TAE VA+++ I+RE QD+++L SQ Sbjct: 124 HAQHLRAGVKMGDFKLIDTMIKDGLWDAFNGYHMGNTAENVARQFQITREDQDQFALASQ 183 Query: 176 RRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKA 235 + AAQ+ GKF DEI ++ K D + QDE R T + + LK Sbjct: 184 NKAEAAQKAGKFKDEIVAVTIKG----------KKGDTIVDQDEYIRHGATIDAMTKLKP 233 Query: 236 VRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPV 295 + T+TA NAS ++DGA+ ++MS+ A +G+ PL + G +P MG GP+ Sbjct: 234 AFDKDGTVTAANASGINDGAAGALLMSEAEAVRRGITPLARIVSWATAGVDPQIMGTGPI 293 Query: 296 FAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMS 355 A + L++ G SV D+ L E NEAFA Q +G DP +NVNGGAI++GHP G S Sbjct: 294 PASRKALEKAGWSVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGAS 353 Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 GAR+ + E RRR AK + T+C+GGGMG A Sbjct: 354 GARVFNTLVFEMRRRGAKKGLATLCIGGGMGVA 386 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: 418 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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