Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_025331133.1 SALWKB2_RS07905 zinc-dependent alcohol dehydrogenase family protein
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_000600005.1:WP_025331133.1 Length = 356 Score = 134 bits (337), Expect = 4e-36 Identities = 105/357 (29%), Positives = 168/357 (47%), Gaps = 19/357 (5%) Query: 9 MKAAVMHNTREIKIETLPVPDI-NHDEVLIKVMAVGICGSDLHYYT--NGRIGNYVVEKP 65 MKA V + +I+ E P I + +I++ ICG+DL + N I ++K Sbjct: 1 MKAMVYYGAGDIRFEERTKPVIIEPTDAIIRLTRTTICGTDLGIWKGKNPEIEQTAIQKD 60 Query: 66 F-----ILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQ-F 119 ILGHE G I GS+V FK GD+V + CG CE C++ Y C + Sbjct: 61 GQFNGRILGHEGIGIIEETGSAVKNFKKGDKVIISCVSRCGTCENCQKQLYAHCQSGGGW 120 Query: 120 LATPPVDGAFVQYIK--MRQDFVFLIPDSLSYEEAALIEPFSVGIH--AAARTKLQPGST 175 + +DG +Y++ + ++ +P +L+ + A L+ H ++PG T Sbjct: 121 IMGYMIDGTQAEYVRTPFADNSLYRLPANLNEDVAVLLSDALPTAHEIGVQYGDVKPGDT 180 Query: 176 IAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKT 235 +AI+G GPVG+ + A+ + II+ D++ RL AK++GAT IIN +DA+ + Sbjct: 181 VAIVGAGPVGMSCLLTAQLYSPSQIIMIDMDDNRLHMAKELGATQIINSASEDAVARVLE 240 Query: 236 ITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYG 295 T RGVD A E G A V+ GG LA VG+ Q+ + + + + I Sbjct: 241 YTGGRGVDCAMEAVGLEATWNICQRVVKEGGHLANVGVHGQS-VNFELEKLWIKNLTITT 299 Query: 296 IFRYANTYPKGIEFLASGIVDTKHLVTDQY---SLEQTQDAMERALQFKNECLKVMV 349 ANT ++ SG + + L T + LE+ D + A K +KV++ Sbjct: 300 GLVNANTTGMLLKTCCSGKLPMEKLATHHFHFNELEKAYDVFKHAADEK--AMKVII 354 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: 296 Number of extensions: 19 Number of successful extensions: 2 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: 356 Length adjustment: 29 Effective length of query: 324 Effective length of database: 327 Effective search space: 105948 Effective search space used: 105948 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