Align Sorbitol dehydrogenase; SDH; EC 1.1.1.-; Glucitol dehydrogenase; L-iditol 2-dehydrogenase; EC 1.1.1.14; Polyol dehydrogenase; Xylitol dehydrogenase; EC 1.1.1.9 (uncharacterized)
to candidate Echvi_0507 Echvi_0507 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= curated2:Q9Z9U1 (343 letters) >FitnessBrowser__Cola:Echvi_0507 Length = 337 Score = 179 bits (454), Expect = 9e-50 Identities = 109/322 (33%), Positives = 173/322 (53%), Gaps = 9/322 (2%) Query: 1 MKALVKTQHGTGHFAVQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYPVAA-PVTLG 59 MK L T+ G ++ EKP +PG+ IK+K G+CG+D+H YEG P P LG Sbjct: 1 MKILTCTEPGNFEYSEGEKPTLSPGR--AIIKIKRIGICGTDLHAYEGTQPFFNYPRVLG 58 Query: 60 HEFSGEIVELGEGVTGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLGNQQDGSF 119 HE SGE+VE+ +G GF GD VT Y CG+C C +G N C+ G +DG Sbjct: 59 HELSGELVEV-DGAEGFVPGDLVTI-IPYFNCGECVACKAGKPNCCATISVFGVHEDGGM 116 Query: 120 AKYVIARQESLHHLPAGVDDRSAAMTEPLACTHHAIAKTSINKGDLVVVTGPGPIGLLAA 179 +++ SL G+ A+ EPLA H + + + G+ VVV G GPIGL Sbjct: 117 KEFISVPSSSLVK-QEGLSLEQLALAEPLAIGAHGVRRAGVQPGEFVVVMGAGPIGLGVM 175 Query: 180 QVAKSHGGTVIITGLSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSELTDGYGADVVLEC 239 + A+ GG VI ++ D++ + + +G++Y ++ + D K ++++T G A+ V++ Sbjct: 176 EFARIAGGKVIAMDINEDRLAFCR-ETLGVEYTVNAKG-DFKAAIADITGGSFAESVIDA 233 Query: 240 SGAVPAAKQGIDLLRKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVGSRSQKPADWEPAL 299 +G+ A G L+ G+Y VGL P I+FN + ++E +++ SR+ D++ L Sbjct: 234 TGSSVAIHHGFGLMAHGGRYVLVGLQKGP-IEFNHPEFHKRESTLMSSRNATREDFDTVL 292 Query: 300 SLLNEKKVNAKTLVTHEYTISE 321 L E+KV A + +THE + Sbjct: 293 KALKEQKVKAASYITHEVAFDQ 314 Lambda K H 0.315 0.133 0.388 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: 351 Number of extensions: 21 Number of successful extensions: 7 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: 343 Length of database: 337 Length adjustment: 28 Effective length of query: 315 Effective length of database: 309 Effective search space: 97335 Effective search space used: 97335 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: 42 (22.0 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