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 H281DRAFT_06377 H281DRAFT_06377 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= SwissProt::O18404 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_06377 Length = 249 Score = 105 bits (263), Expect = 7e-28 Identities = 80/258 (31%), Positives = 135/258 (52%), Gaps = 20/258 (7%) Query: 1 MIKNAVSLVTGGAS--GLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVD 58 +++N V +VTG AS G+G+ATA+ LA QGA V++ DL A +LG + + D Sbjct: 2 LLENKVVIVTGAASPRGIGKATAKALAAQGARVVILDLREEDAKAAAADLGAAHLGLACD 61 Query: 59 VTSEKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVG 118 VT++ A +++GR+D VN AG V+T + + E F ++++N G Sbjct: 62 VTNKAACVQAATATLERYGRIDGLVNNAGITQPVRTLDIS------AEGFDAIVDVNLRG 115 Query: 119 TFNVIRLSAGLMGANEPNQDGQRGVIVNTASVAA--FDGQIGQAAYSASKAAVVGMTLPI 176 T + +S ++ A ++ +RG IV +SV+A G G YSA+KA V+G+ + Sbjct: 116 T---LYMSQAVLPA---MKEQKRGSIVCMSSVSAQRGGGIFGGPHYSAAKAGVLGLARAM 169 Query: 177 ARDLSTQGIRICTIAPGLFNTPMLA-ALPEKVRTFLAKSIPFPQRLGEPSEYAHLVQAIY 235 AR+ IR+ +I PGL T + L ++R + K IP RLG+ ++ A+ + Sbjct: 170 AREFGPDSIRVNSITPGLIQTDITGDKLTAEMRVDIIKGIPL-GRLGDAADVANACLFLV 228 Query: 236 E--NPLLNGEVIRIDGAL 251 + L G + ++G + Sbjct: 229 SDLSTYLTGVTLDVNGGM 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: 152 Number of extensions: 10 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: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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 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