Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_084544078.1 GY23_RS09030 alcohol dehydrogenase catalytic domain-containing protein
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_001939075.1:WP_084544078.1 Length = 349 Score = 194 bits (494), Expect = 2e-54 Identities = 114/350 (32%), Positives = 186/350 (53%), Gaps = 16/350 (4%) Query: 7 QNMKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPF 66 + M+A + +++K+ +P+P IN DE+L++V G+CG+D Y G ++E P Sbjct: 3 KTMRALTFYAPKDLKVVEVPIPVINEDELLVRVSYAGVCGTDNRIYQ----GTKIIEGPR 58 Query: 67 ILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVD 126 I+GHE +G I VG++V F VGD V V P ++CG C CK GR N+C + + + +D Sbjct: 59 IIGHEFSGVIEKVGTNVQSFSVGDHVTVYPMISCGDCYTCKTGRKNICVNRKTIGYE-ID 117 Query: 127 GAFVQYIKM-----RQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGM 181 G F QYIK+ VF + +L + A+ EP + ++ R +Q G + I+G Sbjct: 118 GGFAQYIKIPKIAINMGNVFKVSSNLDQKVVAITEPIAAALNGIKRANIQQGDCVVIIGA 177 Query: 182 GPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRG 241 GP+GL V AK G ++V + + + E A K+GATH IN +++ +K +T+ G Sbjct: 178 GPIGLFHVQLAKLKEPGILVVIEPDHAKREIALKLGATHTINPFDENPEIRLKELTDGEG 237 Query: 242 VDVAWETAGNPAALQSALASVRRGGKLAI-VGLPSQNEIPLNVPFIADNEIDIYGIFRYA 300 DV G P ++ ++ V++GG I G P ++I L+ I EI++ G Sbjct: 238 ADVVIIDVGIPKIIEESIEYVKKGGTYVIFAGAPHGSKISLDPNLIHYKEINLTGSSAAT 297 Query: 301 -NTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVMV 349 + + ++ + SG VD L+++ L D ERAL+ KN K+ V Sbjct: 298 PELHQEVLDLVESGQVDVTLLISEVVGL----DEWERALEMKNSFQKIKV 343 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: 290 Number of extensions: 14 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: 349 Length adjustment: 29 Effective length of query: 324 Effective length of database: 320 Effective search space: 103680 Effective search space used: 103680 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 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