Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ac3H11_1916 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1916 Length = 399 Score = 282 bits (721), Expect = 1e-80 Identities = 172/393 (43%), Positives = 234/393 (59%), Gaps = 6/393 (1%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAG-IDPKEVEDVVMGAAMQQG 61 +A IV+ RTPIG++ RG T LL AI+ A+ + +DPK +ED ++G + +G Sbjct: 8 DAYIVAATRTPIGRSGRGYFKNTRPDDLLVAAIKSAMLQVPTLDPKAIEDAIIGCSFPEG 67 Query: 62 ATGGNIARKAL-LRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G N+AR A+ L PV G T++R CASG+ A+ +AA + ++ + GG ES+ Sbjct: 68 EQGMNMARIAVGLAFNHPV--GGVTVNRFCASGITALQMAADRIRVGEADVLIAGGAESM 125 Query: 121 SLV-QNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 SLV +F+A A + G Y L TAE VA+++ ISRE QD ++LES R Sbjct: 126 SLVPMGGNKPSFNAEVFARDEDVGIAYGMGL-TAEKVAQQWKISREAQDAFALESHLRAI 184 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGE 239 AQ+ G+F DEI P + ATG V K T+S DEGPRP+T+ EGLA LK V Sbjct: 185 KAQKAGEFTDEITPFEVVERSPNLATGEVVEKRRTVSLDEGPRPDTSLEGLAKLKPVFAA 244 Query: 240 GFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVP 299 ++TAGN+SQ SDGA A ++ S+K GL PL F + G P+ MGIGP+ A+P Sbjct: 245 RGSVTAGNSSQTSDGAGALIVASEKAVKQFGLTPLARFVSYAARGVPPEIMGIGPIEAIP 304 Query: 300 RLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARL 359 L+ GL DDIG +ELNEAFA Q L + LG++P +N GGAI++GHP G +GA Sbjct: 305 AALRYAGLKSDDIGWYELNEAFAAQSLAVINTLGLNPANVNPMGGAIALGHPLGATGAIR 364 Query: 360 AGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 A + RR K KY +VTMCVG G G+AG+ E Sbjct: 365 AATVVHALRRHKLKYGMVTMCVGTGQGAAGIIE 397 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: 440 Number of extensions: 19 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: 399 Length adjustment: 31 Effective length of query: 364 Effective length of database: 368 Effective search space: 133952 Effective search space used: 133952 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