Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_025330258.1 SALWKB2_RS03265 zinc-dependent alcohol dehydrogenase family protein
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_000600005.1:WP_025330258.1 Length = 347 Score = 143 bits (360), Expect = 8e-39 Identities = 101/310 (32%), Positives = 147/310 (47%), Gaps = 21/310 (6%) Query: 9 MKAAVMHNTREIKIETLPVPDINHD-EVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67 MK AV R++ I + P I + +I+++ +CGSDL +Y G E I Sbjct: 1 MKVAVFVEPRKVAIREMEKPVIQKSTDAIIRIVRACVCGSDLWWYR----GISTCEPERI 56 Query: 68 LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQ--------- 118 +GHE G + A GS+V + GD V V CG C ACK G C + + Sbjct: 57 VGHEAIGVVEATGSAVTHVRNGDFVIVPFTHGCGHCAACKAGFDGNCQNKEDERNGGYQG 116 Query: 119 -FLATPPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTKLQPGSTIA 177 +L D A V+ QD+ + +SL L + + G HAAA +++PG T+ Sbjct: 117 EYLRFTNADWALVKIPGQPQDYSDAVLNSL----LTLADVMATGYHAAASAEVKPGDTVV 172 Query: 178 IMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTIT 237 +MG G VGL AV AAK GA II P R + A++ GAT I+ R +A+E++ ++T Sbjct: 173 VMGDGAVGLCAVIAAKLRGAERIIAMSRHPDRAKLAEEFGATDIVPERGDEAVEKVLSLT 232 Query: 238 NDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIF 297 G D E G +LQ+A+A R G + VG+ EI + F I + G Sbjct: 233 RQAGADAVLECVGTQQSLQTAVAVARPGAIVGCVGIQHDTEIKTSDVFW--RNIGLRGGI 290 Query: 298 RYANTYPKGI 307 TY K + Sbjct: 291 ASVTTYDKNL 300 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: 284 Number of extensions: 13 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: 347 Length adjustment: 29 Effective length of query: 324 Effective length of database: 318 Effective search space: 103032 Effective search space used: 103032 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