Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate H281DRAFT_03586 H281DRAFT_03586 L-threonine 3-dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Burk376:H281DRAFT_03586 Length = 343 Score = 182 bits (462), Expect = 1e-50 Identities = 110/333 (33%), Positives = 174/333 (52%), Gaps = 7/333 (2%) Query: 9 MKA-AVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67 MKA A + + + + VP++ H++V+I++ ICG+D+H + + P Sbjct: 1 MKALAKLERAPGLTLTDVKVPEVGHNDVMIRIKRTAICGTDIHIWKWDDWAQKTIPVPMH 60 Query: 68 LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDG 127 +GHE GEI +G+ V F +GDRV+ E +TCG C C+ GR +LC + + +G Sbjct: 61 VGHEYVGEIVEMGAEVRGFSIGDRVSGEGHITCGFCRNCRAGRRHLCRNTVGVGVNR-EG 119 Query: 128 AFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLM 187 AF +Y+ + F IP +S + AA+ +PF H A L G + I G GP+G+M Sbjct: 120 AFAEYLVIPAFNAFKIPPEISDDLAAIFDPFGNATHTALSFNLV-GEDVLITGAGPIGIM 178 Query: 188 AVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVAWE 247 AVA AK GA +++TD+ RL A+KMGAT +N+ + + + + G DV E Sbjct: 179 AVAIAKHVGARNVVITDINDYRLGLARKMGATRAVNVSRESLRDVMADLHMAEGFDVGLE 238 Query: 248 TAGNPAALQSALASVRRGGKLAIVGL-PSQNEIPLNVPFIADNEI-DIYGIFRYANTYPK 305 +G P A L ++ GGK+A++G+ P+Q I N EI IYG + T+ K Sbjct: 239 MSGVPGAFTGMLEAMNHGGKIALLGIPPAQTAIDWNQVIFKGLEIKGIYGREMF-ETWYK 297 Query: 306 GIEFLASGIVDTKHLVTDQYSLEQTQDAMERAL 338 + L SG+ D ++T + ++ Q A L Sbjct: 298 MVAMLQSGL-DLSPILTHHFKVDDYQQAFATML 329 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: 283 Number of extensions: 16 Number of successful extensions: 3 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: 343 Length adjustment: 29 Effective length of query: 324 Effective length of database: 314 Effective search space: 101736 Effective search space used: 101736 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