Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate 3610773 Dshi_4159 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Dino:3610773 Length = 350 Score = 196 bits (499), Expect = 6e-55 Identities = 118/350 (33%), Positives = 179/350 (51%), Gaps = 12/350 (3%) Query: 9 MKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEK---- 64 MKAA H ++I++E + P EV IKV GICGSDLH + G I V E Sbjct: 1 MKAARWHGAKDIRVEDVDEPTPGAGEVKIKVAWTGICGSDLHEFLAGPIFVPVGEDHPLS 60 Query: 65 ----PFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFL 120 P +GHE GEI +G V VGDRVA+EP CG C AC++GRYNLC + F+ Sbjct: 61 HDKAPITMGHEYCGEITELGDGVTDLSVGDRVAIEPIFACGTCAACRDGRYNLCEKLGFV 120 Query: 121 ATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMG 180 G F Y + + +P+ LS E+ AL+EP +V +HA + + G A+ G Sbjct: 121 GLSGGHGGFAAYSVVPARMLHRMPEGLSMEQGALVEPAAVALHAVRVSAFKAGDRAAVFG 180 Query: 181 MGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDR 240 GP+GL+ V + + GA I+V + R A ++GAT ++ +DA+ ++ Sbjct: 181 AGPIGLLVVESLRIAGASKIVVVEPSETRRAKAMELGATTAVDPGAEDAVAAVQAAC-PG 239 Query: 241 GVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA 300 GV+VA+E G PA L A+ + R G+ +V + + E + E +I G Y Sbjct: 240 GVEVAFEVTGVPAVLAQAIDATRYEGETLVVSI-WETEASFQPNTVVLKERNIKGTIAYR 298 Query: 301 NTYPKGIEFLASGIVDTKHLVTDQYSLEQ-TQDAMERALQFKNECLKVMV 349 N YP ++ + G + LVT + L+ +D E + K++ +K++V Sbjct: 299 NVYPAVMDLMQQGYFQAERLVTRRIGLDDIVRDGFEALVAEKSQ-IKILV 347 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: 298 Number of extensions: 12 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: 350 Length adjustment: 29 Effective length of query: 324 Effective length of database: 321 Effective search space: 104004 Effective search space used: 104004 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