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 WP_013091686.1 BC1002_RS19415 KR domain-containing protein
Query= SwissProt::O18404 (255 letters) >NCBI__GCF_000092885.1:WP_013091686.1 Length = 242 Score = 119 bits (297), Expect = 8e-32 Identities = 90/252 (35%), Positives = 129/252 (51%), Gaps = 24/252 (9%) Query: 1 MIKNAVSLVTGGASGLGRATAERLAKQGASVILADLPSSKGNEVAKELGDKVVFVPVDVT 60 +++ +LVTGG SG+G A A LA+ GA + A LP +G + L ++ V +DV Sbjct: 7 LLEGKTALVTGGLSGIGAAIANALAQLGAHTVAAGLPLPEG--APETLDREIPRVALDVR 64 Query: 61 SEKDVSAALQTAKDKFGRLDLTVNCAGTATAVKTFNFNKNVAHRLEDFQRVININTVGTF 120 S VSAA+ F RLD+ VNCAG + V+ HRL+ F+RV++IN GT Sbjct: 65 SGDAVSAAVNA----FERLDIVVNCAGVISRVEE--------HRLDVFERVMDINLNGTM 112 Query: 121 NVIRLSAGLMGANEPNQDGQRGVIVNTASVAAFDGQIGQAAYSASKAAVVGMTLPIARDL 180 V + L+ A+ G IVNTAS+ +F G AYSASK AV +T +A Sbjct: 113 RVCAAARDLLKASA-------GCIVNTASMLSFFGGGLVPAYSASKGAVAQLTKSLAIAY 165 Query: 181 STQGIRICTIAPGLFNTPMLAALPEKVRTFLAKSIPFP-QRLGEPSEYAHLVQAIY--EN 237 + GIR+ +APG TP+ AL + R A P +R G P E A + + Sbjct: 166 AADGIRVNAVAPGWIATPLTQALQDDDRRSQAILERTPLRRWGTPQEVAQVAVFLCTPAA 225 Query: 238 PLLNGEVIRIDG 249 + G ++ +DG Sbjct: 226 SFMTGAIVPVDG 237 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: 159 Number of extensions: 9 Number of successful extensions: 4 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: 242 Length adjustment: 24 Effective length of query: 231 Effective length of database: 218 Effective search space: 50358 Effective search space used: 50358 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