Align L-iditol 2-dehydrogenase (EC 1.1.1.14); D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_037458740.1 N825_RS26665 2,3-butanediol dehydrogenase
Query= reanno::HerbieS:HSERO_RS17015 (345 letters) >NCBI__GCF_000576635.1:WP_037458740.1 Length = 355 Score = 163 bits (412), Expect = 7e-45 Identities = 107/355 (30%), Positives = 178/355 (50%), Gaps = 12/355 (3%) Query: 1 MQALVLEATRELKLREIDLPQQMGAQ-DVRIRIHTVGICGSDLHYYTHGSI------GPF 53 M+++ A R++++ + P A V +R GICG+DLH Y G I P+ Sbjct: 1 MKSVRFHAARDVRVDSVAAPPDRPAPGQVLVRNRFCGICGTDLHEYVAGPIFIPREPHPY 60 Query: 54 K-VEAPMVLGHEASGTVIEVGSAVSHLKVGDRVCMEPGIPRLDSPATLRGMYNLDPAVRF 112 P +LGHE GTV+ VG V+ +K GDRV ++P I D RG+Y L + Sbjct: 61 TGASGPQILGHEFGGTVVAVGDGVTIVKPGDRVSIQPLIAPRDDHFGRRGLYQLSDQLGL 120 Query: 113 WATPPIHGCLTGSVVHPAAFTYRLPDNVSFAEGAIVEPLSIGLQAATKARMKPGDTAVVI 172 G + V +R+PD VS + A++EP ++ + A ++ ++ G++A++ Sbjct: 121 VGLSWAWGGMAEYSVLNDYNVFRMPDAVSDEQSALIEPAAVAVYAIDRSGLRAGESALIT 180 Query: 173 GAGTIGAMTALAALAGGAARVILADVVAEKLAHFAD-NPAVITVDVTRETLTDVVRQATD 231 GAG IGA+T LAA A GA+++ ++D +L D P IT++ E L + VR T+ Sbjct: 181 GAGPIGALTMLAARAAGASKIFISDTNDNRLRMMRDILPDCITINPGTENLVEAVRDRTE 240 Query: 232 GW-GADVVFEASGHAGVYQTLLDLVCPGGCAVLVGMPPAPVALDVVAMQTKEVRLESVFR 290 G GADV E GH G ++ V G V VG+ P +D A+ K++ L + Sbjct: 241 GQVGADVALECVGHGGALADCVNAVRRQGTVVQVGLHVKPATVDGFAITFKDIDLRGSWT 300 Query: 291 Y-ANIFPRALALISSGMIDVKPFISRKFPFSQSI-RAFEEAASGRPQDVKIQIEM 343 Y +PR +++ +G+ V+ ++++ + + FE +KI I++ Sbjct: 301 YPTQSWPRVASMVEAGIFPVEKVVTKRIALDDVVSQGFEALLDPAASQLKILIDI 355 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: 312 Number of extensions: 17 Number of successful extensions: 5 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: 345 Length of database: 355 Length adjustment: 29 Effective length of query: 316 Effective length of database: 326 Effective search space: 103016 Effective search space used: 103016 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 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