Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PfGW456L13_2498 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2498 Length = 400 Score = 462 bits (1188), Expect = e-134 Identities = 229/400 (57%), Positives = 299/400 (74%), Gaps = 6/400 (1%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EAVIVSTARTPIGKA+RGA N TE L GH + AV+RAGI+P EV+DV++GAA QQ Sbjct: 1 MKEAVIVSTARTPIGKAFRGAFNDTEAPQLGGHVVREAVRRAGIEPGEVDDVIIGAAAQQ 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G N+ R + GLP + AG ++RQC+SGL +IA+AA+ ++ D ++IAV GG ESI Sbjct: 61 GTQSYNLGRLCAIAGGLPASVAGMAVERQCSSGLMSIAMAAKGIMCDEIDIAVAGGLESI 120 Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180 SLVQN N + ++ + Y+ M++TAE V+ RYGISR+ QDEYS +SQ RTA Sbjct: 121 SLVQNKHKNLYRNQSGSVIELDPHAYIPMIETAEIVSARYGISRDEQDEYSYQSQLRTAQ 180 Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAV---- 236 AQ G+F+ E+AP++++ + DKATG S++ +TL +DE R +TT + L L+ V Sbjct: 181 AQSAGRFDRELAPLTSRKALFDKATGETSYETVTLLRDECNRIDTTLQSLKALEPVWPGG 240 Query: 237 --RGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGP 294 +G ITAGNASQLSDGASA+V+MS K A +GL+PLGI+RGM GC DEMGIGP Sbjct: 241 QWSDKGGFITAGNASQLSDGASASVLMSAKMAEKRGLEPLGIYRGMAVAGCNSDEMGIGP 300 Query: 295 VFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGM 354 ++A+P+LLKRHGL++D IGLWELNEAFA QVL+CRD LGI E+LNVNGGAI++GHP+GM Sbjct: 301 IYAIPKLLKRHGLTMDHIGLWELNEAFACQVLHCRDTLGIPAERLNVNGGAIAIGHPFGM 360 Query: 355 SGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 SGAR+ GHAL+EG+RR +Y VV+MC+GGGMG+A LFE+V Sbjct: 361 SGARMVGHALVEGQRRGLRYVVVSMCIGGGMGAAALFEVV 400 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: 511 Number of extensions: 17 Number of successful extensions: 2 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: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 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