Align BadH (characterized)
to candidate 206645 3-oxoacyl-(acyl-carrier-protein) reductase
Query= metacyc::MONOMER-893 (255 letters) >MicrobesOnline__882:206645 Length = 259 Score = 168 bits (426), Expect = 9e-47 Identities = 98/245 (40%), Positives = 147/245 (60%), Gaps = 7/245 (2%) Query: 8 TAVITGGGGGIGGATCRRFAQEGAKIAVFDLNL-DAAEKVAGAIRDAGGTAEAVRCDIAD 66 TA++TGG GIG A A+ G ++ + ++ D AE VA IRDAGG+A A R D++D Sbjct: 19 TAIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAEAVAAGIRDAGGSATAFRLDVSD 78 Query: 67 RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126 +V A + +D+LVNNAG + + ++ER++ +NL GA Sbjct: 79 AAAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDEDFERVLDVNLCGAFTCLREAS 138 Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186 M +R GRI+NI S ++G++G+A Y A K GL+ +K+ A+E A +TVN V PG Sbjct: 139 KLMTRQRLGRIINITSVVGQMGNAGQANYCAAKAGLIGLTKSAAKELAARNVTVNAVAPG 198 Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246 +T D+T+G PE++ +A+ +AIPL RLG D+A A+AF S+ A +ITGQVL+ Sbjct: 199 FIET----DMTAGL--PEEVRKAYVEAIPLRRLGSAQDIADAVAFLASERASYITGQVLA 252 Query: 247 VSGGL 251 V+GG+ Sbjct: 253 VNGGM 257 Score = 23.1 bits (48), Expect = 0.006 Identities = 26/100 (26%), Positives = 37/100 (37%), Gaps = 10/100 (10%) Query: 156 AACKGGLVAFSKTLAREHARHGITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIP 215 A GG K +A AR G+ V + D A V +G + AF + Sbjct: 20 AIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEA--EAVAAGIRDAGGSATAFRLDV- 76 Query: 216 LGRLGKPDDLAGAIAFFGSDDAGFITGQVLSVSGGLTMNG 255 D A AFF S+ + VL + G+T +G Sbjct: 77 -------SDAAAVAAFFQSEIKDKVRLDVLVNNAGITKDG 109 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: 178 Number of extensions: 9 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: 2 Length of query: 255 Length of database: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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: 47 (22.7 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