Align BadH (characterized)
to candidate RR42_RS25125 RR42_RS25125 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS25125 Length = 249 Score = 176 bits (446), Expect = 4e-49 Identities = 98/248 (39%), Positives = 146/248 (58%), Gaps = 5/248 (2%) Query: 3 RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62 +++++ A++TG G+G AT RR A+EGA++ V D+ + AE+ A+R G A V Sbjct: 4 QIKDRVAIVTGSARGLGAATARRLAEEGARVVVTDVLRERAEETVAALRADGLQAHCVIA 63 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122 DI V + T G V ILVNNAG+ K K +W+ +IA+ L GA Sbjct: 64 DITKAEDVSRLVEETVAQFGGVHILVNNAGFPRDKYLVKMSEEDWDLVIAVMLKGAFLAT 123 Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182 AV+P +E+ GR++NI+S A +G+ +A Y+A K GL+ +K LA E R+G+TVN Sbjct: 124 RAVMPHFIEQGWGRVINISS-RAHLGNPTQANYSAAKAGLIGVAKALAIEEGRYGVTVNC 182 Query: 183 VCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITG 242 V PG +T ++ + S E + E + P+ R+G+P D+A A+AF S+ AGFITG Sbjct: 183 VAPGFIETEMVQALPS----YETIKERAVQMQPIKRVGRPGDIADAVAFLASERAGFITG 238 Query: 243 QVLSVSGG 250 +VL VSGG Sbjct: 239 EVLHVSGG 246 Lambda K H 0.318 0.135 0.398 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: 157 Number of extensions: 5 Number of successful extensions: 3 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: 255 Length of database: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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 (21.7 bits) S2: 46 (22.3 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