Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 199217 SO0020 fatty oxidation complex, beta subunit (NCBI ptt file)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__MR1:199217 Length = 387 Score = 231 bits (590), Expect = 2e-65 Identities = 158/399 (39%), Positives = 215/399 (53%), Gaps = 17/399 (4%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59 M +AVIV RTP+G++ G TL ++ + R +DP +EDV+ G Q Sbjct: 1 MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G NIAR A L AG+P T T++R C S ++AI AAR+++ + + GG E Sbjct: 61 TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120 Query: 120 ISLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 + V + FH P L M TAE + K +GI+RE+QD +++ S +R Sbjct: 121 MGHVPMNHGVDFH---PGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRAY 177 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239 AA G+F EI I ATGA+ I + QDE RPETT E LA L+ V Sbjct: 178 AATIEGRFAKEIYGIEGH-----DATGAL----IKVLQDEVIRPETTMESLAVLRPVFDP 228 Query: 240 -GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAV 298 T+TAG +S LSDGASA +IM + A A GL R M GC+ MG GPV A Sbjct: 229 VNGTVTAGTSSALSDGASAMLIMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPAT 288 Query: 299 PRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLG---IDPEKLNVNGGAISVGHPYGMS 355 + L R G++V+D+ + ELNEAFA Q L C LG + EK+N+NGGAI++GHP G S Sbjct: 289 QKALARAGITVNDLDVIELNEAFAAQSLPCVKDLGLLDVVDEKINLNGGAIALGHPLGCS 348 Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 GAR++ + + A + TMC+G G G A +FE V Sbjct: 349 GARISTTLINLMEHKDATLGLATMCIGLGQGIATVFERV 387 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: 381 Number of extensions: 22 Number of successful extensions: 6 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: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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