Align BadH (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 135 bits (340), Expect = 9e-37 Identities = 83/249 (33%), Positives = 131/249 (52%), Gaps = 9/249 (3%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66 + ++TGG GIG A RRFA EGAK + D++ + +A + A VRCD+ D Sbjct: 21 RVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQALAAELG-----ALYVRCDVGD 75 Query: 67 RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126 + VDA +A G +D+LVNNAG F + +++ ++ +NL G+ + AV Sbjct: 76 KAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGSFLVGQAVA 135 Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186 MV G IVN++S + A Y KGG+ ++ +A A I VN V PG Sbjct: 136 RAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNAVAPG 195 Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246 T L A + ++ I + T P+ RLG+P ++A +A+ SD A ++TG++++ Sbjct: 196 TIATELAAKAVLTSDEAKRKIMSRT---PMKRLGQPSEIADVVAWLASDAASYVTGEIVT 252 Query: 247 VSGG-LTMN 254 V GG +T+N Sbjct: 253 VDGGRMTLN 261 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: 180 Number of extensions: 7 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: 267 Length adjustment: 25 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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