Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate AO353_25145 AO353_25145 butanediol dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25145 Length = 364 Score = 194 bits (493), Expect = 3e-54 Identities = 117/357 (32%), Positives = 183/357 (51%), Gaps = 12/357 (3%) Query: 7 QNMKAAVMHNTREIKIETLPVPDINHDE-VLIKVMAVGICGSDLHYYTNGRIGNYV---- 61 ++M+AAV H +I++E +P+P V I+V GICGSDLH Y G + V Sbjct: 9 RSMRAAVWHGRHDIRVEDVPLPIAPPAGWVQIRVQWCGICGSDLHEYVAGPVFIPVDAPH 68 Query: 62 ----VEKPFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDV 117 ++ ILGHE GEI +G+ V F VG+ VA + CG C C G YN+C ++ Sbjct: 69 PLTGIKGQCILGHEFCGEIVELGAGVQGFSVGEPVAADACQHCGTCYYCTHGLYNICENL 128 Query: 118 QFLATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIA 177 F +GAF + + + + ++ +P + E ALIEP +VG+HA + G + Sbjct: 129 AFTGLMN-NGAFAELVNVPANLLYKLPANFPAEAGALIEPLAVGMHAVKKAGSLLGQNVV 187 Query: 178 IMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTIT 237 ++G G +GL + AKA GA +I ++ R A ++GATH+++ E DAL E++ +T Sbjct: 188 VVGAGTIGLCTIMCAKAAGAAQVITLEMSGARKAKALEVGATHVLDPNECDALAEVRRLT 247 Query: 238 NDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF 297 G DV++E GN + A+ +R+ GK +VG+ + N + E + G Sbjct: 248 GGLGADVSFECIGNKHTAKLAIDLIRKAGKCVLVGI-FEEPSEFNFFELVATEKQVLGAL 306 Query: 298 RYANTYPKGIEFLASGIVDTKHLVTDQYSLEQ-TQDAMERALQFKNECLKVMVYPNR 353 Y + I F+A G +D LVT + LEQ E + K +K++V P R Sbjct: 307 AYNGEFADVIAFIADGRLDITPLVTGRIQLEQIVGQGFEELVNNKEHNVKIIVSPAR 363 Lambda K H 0.320 0.137 0.401 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: 319 Number of extensions: 16 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: 353 Length of database: 364 Length adjustment: 29 Effective length of query: 324 Effective length of database: 335 Effective search space: 108540 Effective search space used: 108540 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 (21.8 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