Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_011384976.1 AMB_RS13060 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000009985.1:WP_011384976.1 Length = 398 Score = 233 bits (595), Expect = 6e-66 Identities = 158/410 (38%), Positives = 220/410 (53%), Gaps = 28/410 (6%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M +A I R+PIG+ + G L L I V R+ P++VEDV++G Q Sbjct: 1 MLDAYIYDGLRSPIGR-HGGGLAPVRSDDLAAEVIRALVARSSFKPEDVEDVILGCTNQA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G N+AR A L AGLPV AG T++R CASGL A+ AARSV ++ + GG ES+ Sbjct: 60 GEDSRNVARHAALLAGLPVEVAGQTVNRLCASGLAAVLDAARSVTCGEGDLYLAGGVESM 119 Query: 121 S-----LVQNDKM---------NTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRER 166 + L + D T A + +K +M +TA+ +A G+SRE Sbjct: 120 TRAPFVLAKGDSAWSRDARIFDTTIGARFANPKVVKSFGGHSMPETADNIAHDLGLSREA 179 Query: 167 QDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETT 226 D ++ SQ + A A+ G + EI PI T A D +++DE PRP+T Sbjct: 180 SDAFAAASQAKYAKAKAEGFYEGEIHPI----------TIAGRKGDTIVAEDEHPRPQTD 229 Query: 227 AEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCE 286 L LK + EG +TAGNAS ++DGA+A I S G+ P+ + G Sbjct: 230 LAALTKLKPLF-EGGVVTAGNASGINDGAAALFIGSRAAGEKAGIAPIARIVAGAAAGVP 288 Query: 287 PDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNGG 344 P MG+GPV A+ + L R LS+ D+ L E+NEAFAVQVL C +LG+ D +LN NGG Sbjct: 289 PRVMGLGPVPAITKALARAKLSLKDLDLIEINEAFAVQVLGCVTQLGVAADDSRLNPNGG 348 Query: 345 AISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 AI++GHP G SGARLA A + +R ++AVV++C+G G G A + E V Sbjct: 349 AIAIGHPLGCSGARLALTAARQLQRTGGRHAVVSLCIGVGHGLAAVIERV 398 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: 454 Number of extensions: 24 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: 398 Length adjustment: 31 Effective length of query: 364 Effective length of database: 367 Effective search space: 133588 Effective search space used: 133588 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