Align 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Endoplasmic reticulum-associated amyloid beta-peptide-binding protein; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate WP_012589851.1 MSIL_RS04185 3-hydroxybutyrate dehydrogenase
Query= SwissProt::O08756 (261 letters) >NCBI__GCF_000021745.1:WP_012589851.1 Length = 261 Score = 89.4 bits (220), Expect = 7e-23 Identities = 65/205 (31%), Positives = 105/205 (51%), Gaps = 17/205 (8%) Query: 7 SVKGLVAVVTGGASGPWLATAKRLVGQGATAVLLDVPDSEG-ESQAKKL----GESCIFA 61 ++K A+VTG SG LA A+ GA + + D+ E++ K+ G ++ Sbjct: 2 TLKSRNAIVTGSTSGIGLAIAREFAKDGANVTINGLGDAAAIEAERAKIEADFGVKAAYS 61 Query: 62 PANVTSEKEIQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHQKKNKIHTLEDFQRVINVN 121 PAN+T +EI+A +T A++ FG +D+ VN AGI H + ++ + +I +N Sbjct: 62 PANMTKPEEIRAMVTDAEKAFGSVDILVNNAGIQ------HVAPIEDFPIDTWNLIIAIN 115 Query: 122 LIGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIDGMTLP 181 L F+ I M + + G II+TAS + ++AY ++K GIDG+T Sbjct: 116 LSAAFHAIAAAIPGM------KARKWGRIISTASAHSKVASPFKSAYVSAKHGIDGLTKT 169 Query: 182 IARDLAPTGIRVVTIAPGLFATPLL 206 A +LA G+ V I+PG TPL+ Sbjct: 170 AALELATFGVTVNCISPGYVWTPLV 194 Lambda K H 0.317 0.134 0.380 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: 160 Number of extensions: 12 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: 261 Length of database: 261 Length adjustment: 25 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 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