Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PfGW456L13_2157 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2157 Length = 394 Score = 387 bits (994), Expect = e-112 Identities = 202/394 (51%), Positives = 261/394 (66%), Gaps = 1/394 (0%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M E VIV + RT + K++RG N T + H ++ + R GIDP VED ++GA + Sbjct: 1 MREVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVDALLARTGIDPASVEDCIVGAGSNE 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GA G NI R + + L + TAG T++R C+SGLQAIA+AA + +I V GG ESI Sbjct: 61 GAQGFNIGRNVAVLSRLGIGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESI 120 Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180 SL +NT + ++P L+ +Y M TAE VA+RY +SR+ QD Y+L+SQ+RTA Sbjct: 121 SLTMKS-VNTDNLINPLLKEQVPGIYFPMGQTAEIVARRYNVSRQEQDLYALQSQQRTAE 179 Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEG 240 AQ G F DEI P+S K V DKATG D + +D+ RP+TT E L GLK V E Sbjct: 180 AQAAGLFTDEIVPMSVKYRVEDKATGQAQILDGIVDRDDCNRPDTTLESLTGLKPVFAED 239 Query: 241 FTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPR 300 ++TAGN+SQLSDGAS T++MS + A GLKP FRG GC PDEMGIGPVF+VP+ Sbjct: 240 GSVTAGNSSQLSDGASMTLVMSLEKALELGLKPKAFFRGFTVAGCAPDEMGIGPVFSVPK 299 Query: 301 LLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLA 360 LLK GL + DI LWELNEAFA Q LY R++L ID + NVNGG+IS+GHP+GM+G+R Sbjct: 300 LLKAKGLRIADIDLWELNEAFASQCLYSRNRLEIDNARYNVNGGSISIGHPFGMTGSRQV 359 Query: 361 GHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GH + E +RR +Y +VTMCVGGGMG+ GLFE V Sbjct: 360 GHLVRELQRRNLRYGIVTMCVGGGMGATGLFEAV 393 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: 437 Number of extensions: 13 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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