Align D-sorbitol dehydrogenase (EC 1.1.1.14; EC 1.1.1.9) (characterized)
to candidate GFF875 Psest_0895 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= metacyc::MONOMER-13193 (363 letters) >FitnessBrowser__psRCH2:GFF875 Length = 379 Score = 114 bits (285), Expect = 4e-30 Identities = 101/331 (30%), Positives = 137/331 (41%), Gaps = 25/331 (7%) Query: 15 SFVLNKPGDVTFEERPKPTITDPNDVLVAVNYTGICGSDVHYWVHGAIGHFVVKDPMVLG 74 + V N P DV+ + P I P D LV V T ICGSD+H + G + V G Sbjct: 3 AIVYNGPRDVSVQNVPDAKIERPTDALVRVTSTNICGSDLHMYE----GRTTFETGRVFG 58 Query: 75 HESAGTVVEVGPAVKSLKPGDRVALEPGYPCRRCSFCRAGKYNLC----PDMV-----FA 125 HE+ G VVEVG V+ +K GD V L C C C G C P FA Sbjct: 59 HENLGEVVEVGAGVERVKVGDMVCLPFNIGCGFCENCEKGLTGYCLTANPGSAGAAYGFA 118 Query: 126 ATPPYHGTLTGLWAAP-ADF-CYKLPDGVSLQEG---ALIEPLAVAVHIVKQARVQPGQS 180 Y G L P ADF C LP+ +E L + H + A +QPG+S Sbjct: 119 EMGTYDGGQAELLRVPFADFNCLVLPEDAKEREDDYVMLSDIFPTGWHATRLAGLQPGES 178 Query: 181 VVVMGAGPVGLLCAAVAKAYGASTIVSVDIVQSKLDFARGFCSTHTYVSQRISAEDNAKA 240 + + GAGPVGL+ A A GAS + +D +L A +T S A D Sbjct: 179 IAIYGAGPVGLMAAHSALIQGASQVFVIDDQPDRLKLAAQMGAT-PINSVEQKAVDEILN 237 Query: 241 IKELAGLPGGADVV----IDASGAEPSIQTSIHVVRMGGTYVQGGMGKSDITFPIMAMCL 296 + G G + V D G E + T ++V T GG+G + P Sbjct: 238 YTDGKGTDRGCECVGYQCCDKHGHEVNHLTMNNLV--ASTKATGGIGVVGLFVPQDPGAK 295 Query: 297 KEVTVRGSFRYGAGDYELAVELVRTGRVDVK 327 E+ G + G + + + TG+ +VK Sbjct: 296 NELAKEGKMAFDFGSFWFKGQKIGTGQANVK 326 Lambda K H 0.319 0.136 0.406 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: 366 Number of extensions: 21 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: 363 Length of database: 379 Length adjustment: 30 Effective length of query: 333 Effective length of database: 349 Effective search space: 116217 Effective search space used: 116217 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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