Align L-iditol 2-dehydrogenase (EC 1.1.1.14); D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate N515DRAFT_0211 N515DRAFT_0211 Threonine dehydrogenase
Query= reanno::HerbieS:HSERO_RS17015 (345 letters) >FitnessBrowser__Dyella79:N515DRAFT_0211 Length = 338 Score = 85.5 bits (210), Expect = 2e-21 Identities = 93/333 (27%), Positives = 129/333 (38%), Gaps = 15/333 (4%) Query: 1 MQALVLEATRELKLREIDLPQQMGAQDVRIRIHTVGICGSDLHYYTHGSIGPFKVEAPMV 60 M+ VL +++ E+ P+ D IRI +CGSDL Y S G P Sbjct: 1 MKGTVLHGPNDIRFEEVPEPKIEKPTDAIIRIAVTCVCGSDLWPYRGISPG----SGPTR 56 Query: 61 LGHEASGTVIEVGSAVSHLKVGDRVCMEPGIPRLDSPATLRGMYNLDPAVRFWATPPIHG 120 +GHE G V EVGSAV +K G V P G Y R + + Sbjct: 57 MGHEYCGYVEEVGSAVMAIKKGQFVVGSFATSDNTCPTCNIG-YQSSCVQREFVSQAQSP 115 Query: 121 CLTGSVVHPAAFTYRLPDNVSFAEGAIV--EPLSIGLQAATKARMKPGDTAVVIGAGTIG 178 L + R + S G + + L G AA AR++PG TAVV+G G +G Sbjct: 116 YLRVAHADGTLVATREAPDASMVPGLLASSDVLGTGWYAADAARVRPGVTAVVVGDGAVG 175 Query: 179 AMTALAALAGGAARVILADVVAEKLAHFADNPAVITVDVTRETLTDVVRQATDGWGADVV 238 + L+A GA R+I+ + D A V E + + T G GAD V Sbjct: 176 LLAVLSAKQMGAERIIVMSRHPARQKLALDFGATDIVAERGEEGVARIMELTRGLGADSV 235 Query: 239 FEASGHAGVYQTLLDLVCPGGCAVLVGMPPAPVALDVVAMQTKEVRLES----VFRYANI 294 E G Q + + GG VG+P V ++ A+ + LE V RY Sbjct: 236 LECVGTGESMQQAMRVTRKGGHMSFVGVPHG-VEIEGQALFFSHIHLEGGPAPVRRY--- 291 Query: 295 FPRALALISSGMIDVKPFISRKFPFSQSIRAFE 327 P + LI ID P Q ++ Sbjct: 292 LPDLIDLILDQKIDPSAVFDLVLPLDQVAEGYK 324 Lambda K H 0.321 0.137 0.403 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: 268 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 345 Length of database: 338 Length adjustment: 29 Effective length of query: 316 Effective length of database: 309 Effective search space: 97644 Effective search space used: 97644 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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