Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_058929093.1 AU252_RS00785 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_001484605.1:WP_058929093.1 Length = 405 Score = 244 bits (622), Expect = 4e-69 Identities = 154/416 (37%), Positives = 219/416 (52%), Gaps = 38/416 (9%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQ 59 MTEAVIVS AR+PIG+A +G+L L + A+ + +DP ++ D+++G + Sbjct: 1 MTEAVIVSIARSPIGRAMKGSLVDMRPDDLAAQMVRAALDKVPALDPTDINDLLLGCGLP 60 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G G N+ R ++ G GTTI R C+S LQ +A ++ ++ + G E+ Sbjct: 61 GGEQGYNMGRNVAVQLGYDFMP-GTTITRYCSSSLQTTRMALHAIKAGEGDVFISAGVET 119 Query: 120 ISLVQN-------DKMNTFHA----------------VDPALEAIKGDVYMAMLDTAETV 156 +S D N +A DP + D Y+AM TAE V Sbjct: 120 VSRFVKGNSDSLPDTHNPLYADAQTRTEKLAQGGQTWEDPRKVGLVADTYIAMGQTAENV 179 Query: 157 AKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLS 216 A+ GISRE QD +++ SQ R A G + EI P++ G V +S Sbjct: 180 AQMTGISREEQDRWAVRSQNRAEKAIINGFYEREITPVTLPDGTV-------------VS 226 Query: 217 QDEGPRPETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGI 276 D+GPR TT E ++ LK + T+TAGNA L+DGA+A VIMSD A GL P+ Sbjct: 227 TDDGPRAGTTYEAVSQLKPIFRPDGTVTAGNACPLNDGAAALVIMSDTKAKELGLTPIAR 286 Query: 277 FRGMVSYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDP 336 G P+ MG+GP+ A R L G+ + DI L+E+NEAFAVQVL +LGID Sbjct: 287 IVSTGVSGLSPEIMGLGPIEASKRALAIAGMGIGDIDLFEINEAFAVQVLGSARELGIDE 346 Query: 337 EKLNVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 +KLNV+GG I++GHP+GM+GAR+ L + ++ + TMCVGGG G A + E Sbjct: 347 DKLNVSGGGIALGHPFGMTGARITATLLNNLQTYDKQFGLETMCVGGGQGMAMVLE 402 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: 439 Number of extensions: 22 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: 405 Length adjustment: 31 Effective length of query: 364 Effective length of database: 374 Effective search space: 136136 Effective search space used: 136136 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 Apr 09 2024. 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