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; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized)
to candidate HSERO_RS19055 HSERO_RS19055 oxidoreductase
Query= SwissProt::O18404 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS19055 Length = 256 Score = 116 bits (290), Expect = 5e-31 Identities = 82/250 (32%), Positives = 138/250 (55%), Gaps = 19/250 (7%) Query: 6 VSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKEL---GDKVVFVPVDVTSE 62 V+LVTGGA G+G + +++LA +G +V++AD+ ++ A L G + + +D+ S Sbjct: 10 VALVTGGAMGIGASISQQLAAKGHTVLVADINLDAASKTADALVAAGHRAAPLQMDLGSP 69 Query: 63 KDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFNV 122 + ++AA + +GR D+ VN AG A +T++F + + LE++ + +N+N G Sbjct: 70 ESIAAAFAHIEKDYGRCDVLVNNAGVA---RTYSF---LDYPLENWLQTMNVNVTGVLLA 123 Query: 123 IRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLST 182 + +A LM Q G IVN +S++ G+ AY SKAAV+G+T +A +L+ Sbjct: 124 GQHAARLMVKQ------QWGRIVNISSISGIRAGAGRTAYGTSKAAVIGLTRQMAIELAQ 177 Query: 183 QGIRICTIAPGLFNTPMLAAL-PEKVRTFLAKSIPFPQRLGEPSEYAHLV--QAIYENPL 239 GI + ++APG +TPM A+ E+ R + +P +R G E A V A E+ Sbjct: 178 YGITVNSVAPGPVDTPMTQAMHSEQTRESYYRLVPM-RRYGTTDEIASAVCYLAAEESAY 236 Query: 240 LNGEVIRIDG 249 + G VI +DG Sbjct: 237 ITGHVIPVDG 246 Lambda K H 0.317 0.133 0.369 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: 129 Number of extensions: 7 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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