Align BadH (characterized)
to candidate WP_035481637.1 B3C1_RS09380 acetoacetyl-CoA reductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000299915.1:WP_035481637.1 Length = 246 Score = 169 bits (428), Expect = 5e-47 Identities = 96/250 (38%), Positives = 140/250 (56%), Gaps = 6/250 (2%) Query: 5 QNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDI 64 + A++TG GGIG A CR A+EG ++A AE + G V DI Sbjct: 3 KGNVALVTGANGGIGTAICRALAKEGYQVAALCRCPSRAEPWLEQEKAQGYNPHLVIADI 62 Query: 65 ADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHA 124 D+ + +A++ LG ++++VNNAG K + + +W +I NLTGA H+ A Sbjct: 63 KDQDGIFSAVSVVEAELGAINLVVNNAGITRDKTLKRMQEDDWLEVIQTNLTGAYHLCRA 122 Query: 125 VLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVC 184 V+P M+ER++GRIVNI+S G G+ YAA K GL + +LA+E A GITVN + Sbjct: 123 VVPLMLERQYGRIVNISSINGEKGQMGQTNYAAAKAGLHGLTMSLAQEVASKGITVNTIS 182 Query: 185 PGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQV 244 PG T ++ V PE++ ++ IP+GRLG+P ++A + F S DAGFITG Sbjct: 183 PGYIATDMVMAV------PEEIRQSIINQIPVGRLGEPSEIARIVTFLASPDAGFITGSN 236 Query: 245 LSVSGGLTMN 254 LS +GG M+ Sbjct: 237 LSANGGQHMH 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: 171 Number of extensions: 6 Number of successful extensions: 2 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: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 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 24 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