Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate CA265_RS12005 CA265_RS12005 glutathione-dependent formaldehyde dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Pedo557:CA265_RS12005 Length = 385 Score = 133 bits (334), Expect = 9e-36 Identities = 112/389 (28%), Positives = 169/389 (43%), Gaps = 50/389 (12%) Query: 9 MKAAVMHNTREIKIETLPVPDI-NHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67 MKAAV H +I+++ +P P I + +V++KV + ICGSDLH + G + P I Sbjct: 1 MKAAVFHKPGDIRVDYVPDPKILDPRDVILKVTSTAICGSDLHILS----GAVPQKDPLI 56 Query: 68 LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPP--- 124 +GHE G + VG+S+ K GDRV V ++CG+C C C F P Sbjct: 57 MGHEFMGIVEEVGASITNLKRGDRVVVPFPISCGKCFFCTHEASPACETSNFKNYGPNGD 116 Query: 125 ------------------VDGAFVQYIKMRQDFVF--LIPDSLSYEEAA-LIEPFSVGIH 163 G QY+++ + ++P+ LS E+A L + F G Sbjct: 117 MMSQKGAALFGYTDLYGGYSGGQAQYVRVPYADISPRIVPEHLSDEQALFLTDIFPTGWS 176 Query: 164 AAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIIN 223 A +L+ G +AI G GPVGLMA AA GA +I D RLE AK + I+N Sbjct: 177 AIDWAQLKGGEVVAIFGSGPVGLMAQKAAWINGASRVIAIDPLDYRLEKAKAVNNVDILN 236 Query: 224 IREQDALEEIKTITNDRGVDVAWETA--------------------GNPAALQSALASVR 263 + D +E I+ +T RG D+ + G+ L+ +VR Sbjct: 237 PHKVDVVEAIREMTGGRGADLCVDAVGFEPERSFFDKVKATVHFEKGSIKVLEMCFEAVR 296 Query: 264 RGGKLAIVGLPSQNEIPLNVPFIADNEIDI-YGIFRYANTYPKGIEFLASGIVDTKHLVT 322 R G ++I+G+ + I D I I G N K I + G V ++T Sbjct: 297 RMGTVSIMGVYGSPYDNFPLFRIFDKGITIKQGQAPVLNYIDKLIGLVNEGKVVLDDIIT 356 Query: 323 DQYSLEQTQDAMERALQFKNECLKVMVYP 351 LE + + +C+KV++ P Sbjct: 357 HTLPLEDAAHGYKIFDNKEEDCVKVVLKP 385 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: 332 Number of extensions: 18 Number of successful extensions: 4 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: 385 Length adjustment: 30 Effective length of query: 323 Effective length of database: 355 Effective search space: 114665 Effective search space used: 114665 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