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 Ac3H11_2732 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::O18404 (255 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2732 Length = 278 Score = 124 bits (310), Expect = 3e-33 Identities = 84/251 (33%), Positives = 126/251 (50%), Gaps = 9/251 (3%) Query: 3 KNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVTSE 62 K+ V++VTGGASG+G AT RL +GA+V++AD+ + + +A ELG + D Sbjct: 15 KDQVAIVTGGASGIGEATCRRLVAEGATVVVADVNAERAAALASELGPRASAQVFDAADV 74 Query: 63 KDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTFNV 122 + + +Q ++FGRLD+ N A ++ + E + +V+ +N G Sbjct: 75 RSIERLVQGTVERFGRLDVLHNNAALSSPAIHAKDKNAIDIEFEVWDQVMAVNLRGYLAG 134 Query: 123 IRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDLST 182 + + M A Q G G IVNTAS F G I + AYS SKAA++G+T IA Sbjct: 135 CKYALPTMIA----QGG--GAIVNTASTGGFSGDITRMAYSVSKAAIIGLTRQIATHHGA 188 Query: 183 QGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFPQRLGEPSEYAHLV--QAIYENPLL 240 QG+R +APGL TP V + + + P+ GEP + A LV A E + Sbjct: 189 QGVRCNAVAPGLVLTPGTRGAAASVIDVMQRHLLVPE-FGEPEDIAALVCFLASGEARYI 247 Query: 241 NGEVIRIDGAL 251 NG+ DG + Sbjct: 248 NGQTYIADGGM 258 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: 176 Number of extensions: 9 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: 278 Length adjustment: 25 Effective length of query: 230 Effective length of database: 253 Effective search space: 58190 Effective search space used: 58190 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