Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate RR42_RS10260 RR42_RS10260 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS10260 Length = 391 Score = 475 bits (1222), Expect = e-138 Identities = 238/394 (60%), Positives = 300/394 (76%), Gaps = 3/394 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EAVIVSTART + K+++GA N T GATL HA+ HAV R+G+DP E+ED +MG + Sbjct: 1 MNEAVIVSTARTGLAKSWKGAFNMTHGATLGAHAVYHAVARSGLDPSELEDCIMGGTFGE 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G TGGNIAR LRAGLPVTT G +++R C+SGLQ IA+AA+ V+ +G V GG ESI Sbjct: 61 GTTGGNIARAIALRAGLPVTTGGVSVNRFCSSGLQTIAMAAQRVILEGAPAIVAGGVESI 120 Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180 S VQN + NT DP L K ++Y M+ TAETVA+RYGI RE QD Y + SQ+R AA Sbjct: 121 SCVQN-QANTHMGCDPWLVEHKPELYWGMVQTAETVARRYGIPREIQDAYGVRSQQRAAA 179 Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEG 240 A+ GKF+DEI P++T MGVVD+A G V+ + + +S+DEG RP+TT E ++ ++ G Sbjct: 180 ARAAGKFDDEIVPMTTTMGVVDEA-GRVTTRQVVISEDEGIRPDTTLEAVSRIRPALPGG 238 Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300 +TAGNASQ SDG+SA V+M+ K A +G++PLG+FRG GCEPDEMGIGPVFAVPR Sbjct: 239 -VVTAGNASQFSDGSSACVVMNAKLAERRGIEPLGLFRGFAIAGCEPDEMGIGPVFAVPR 297 Query: 301 LLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLA 360 LL R G+ ++D+GLWELNEAFA QVLYCRDKLGI ++LNVNGGAI+VGHPYG+SG+RL Sbjct: 298 LLDRAGVKLEDVGLWELNEAFACQVLYCRDKLGIPDDRLNVNGGAIAVGHPYGVSGSRLT 357 Query: 361 GHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GHALIEG+RR KY VVTMC+GGG G+AGLFE++ Sbjct: 358 GHALIEGKRRGVKYVVVTMCIGGGQGAAGLFEVL 391 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: 552 Number of extensions: 23 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: 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 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