Align D-sorbitol dehydrogenase (EC 1.1.1.14; EC 1.1.1.9) (characterized)
to candidate Ga0059261_1819 Ga0059261_1819 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= metacyc::MONOMER-13193 (363 letters) >FitnessBrowser__Korea:Ga0059261_1819 Length = 370 Score = 120 bits (301), Expect = 6e-32 Identities = 112/371 (30%), Positives = 166/371 (44%), Gaps = 37/371 (9%) Query: 14 LSFVLNKPGDVTFEERPKPTITDPNDVLVAVNYTGICGSDVHYWVHGAIGHFVVKDPMVL 73 ++F KP ++ + P P +VLV + TGIC +D Y + G + P VL Sbjct: 7 VAFEAKKPLEIVELDLEGPK---PGEVLVEIMATGICHTDA-YTLDGFDSEGIF--PSVL 60 Query: 74 GHESAGTVVEVGPAVKSLKPGDRVALEPGYPCRRCSFCRAGKYNLC------------PD 121 GHE AG V EVG V SLKPGD V CR+C C +GK NLC PD Sbjct: 61 GHEGAGVVREVGAGVTSLKPGDHVIPLYTPECRQCKSCLSGKTNLCTAIRATQGKGLMPD 120 Query: 122 ----MVFAATPPYH----GTLTGLWAAPADFCYKLPDGVSLQEGALIE-PLAVAVH-IVK 171 + P +H T + P K+ + Q I + V +V Sbjct: 121 GTTRFSYKGQPIFHYMGCSTFSNSTVLPEIALAKIREDAPFQTSCYIGCGVTTGVGAVVN 180 Query: 172 QARVQPGQSVVVMGAGPVGLLCAAVAKAYGASTIVSVDIVQSKLDFARGFCSTHTYVSQR 231 A+VQ G++VVV G G +GL AK GA IV VDI + ++ R F TH + Sbjct: 181 TAKVQVGETVVVFGLGGIGLNVIQGAKMVGADVIVGVDINPDREEWGRKFGMTHFINGKG 240 Query: 232 ISAEDNAKAIKELAGLPGGADVVIDASGAEPSIQTSIHVVRMG-GTYVQGGM---GKSDI 287 S ED + LA GGAD DA+G ++T++ G G + G+ GK Sbjct: 241 KSREDVIAEV--LALTDGGADYSFDATGNTEVMRTALECCHRGWGESIIIGVAEAGKEIA 298 Query: 288 TFPIMAMC--LKEVTVRGSFRYGAGDYELAVELVRTGRVDVKKLITGTVSFKQAEEAFQK 345 T P + + + T G + G D V+ G++ + +IT +S ++ + F Sbjct: 299 TRPFQLVTGRVWKGTAFGGAK-GRTDVPKIVDWYMNGKIAIDPMITHVLSLEEINKGFDL 357 Query: 346 VKSGEAIKILI 356 + +GE+I+ ++ Sbjct: 358 MHAGESIRSVV 368 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: 339 Number of extensions: 19 Number of successful extensions: 6 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: 370 Length adjustment: 30 Effective length of query: 333 Effective length of database: 340 Effective search space: 113220 Effective search space used: 113220 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