Align BadH (characterized)
to candidate 8502394 DvMF_3100 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Miya:8502394 Length = 247 Score = 165 bits (418), Expect = 7e-46 Identities = 94/245 (38%), Positives = 146/245 (59%), Gaps = 7/245 (2%) Query: 8 TAVITGGGGGIGGATCRRFAQEGAKIAVFDLNL-DAAEKVAGAIRDAGGTAEAVRCDIAD 66 TA++TGG GIG A A+EG ++ + ++ + AE VA I AGG+A A R D++D Sbjct: 7 TALVTGGSRGIGKAVAETLAREGFQVYLTYVSKPEEAEAVAAGINAAGGSARAFRLDVSD 66 Query: 67 RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126 +V A +D+LVNNAG + + +++R++ +NL+GA Sbjct: 67 AAAVAAFFQEEIREKVTLDVLVNNAGITKDGLILRMKDDDFDRVLDVNLSGAFTCLREAA 126 Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186 M +R GRIVNI S ++G++G+ Y+A K GL+ +K+ A+E A +TVN V PG Sbjct: 127 KLMTRQRKGRIVNITSVVGQMGNAGQVNYSAAKAGLIGMTKSAAKELAGRNVTVNAVAPG 186 Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246 +T + A +T +++ A+ +AIPL RLG+P D+A A+AF SD AG+ITGQV++ Sbjct: 187 FIETDMTAKLT------DEVRAAYIEAIPLRRLGQPQDIADAVAFLASDKAGYITGQVIA 240 Query: 247 VSGGL 251 V+GG+ Sbjct: 241 VNGGM 245 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: 185 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 255 Length of database: 247 Length adjustment: 24 Effective length of query: 231 Effective length of database: 223 Effective search space: 51513 Effective search space used: 51513 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