Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_047213848.1 PATSB16_RS09090 zinc-dependent alcohol dehydrogenase family protein
Query= CharProtDB::CH_000596 (353 letters) >NCBI__GCF_001931675.1:WP_047213848.1 Length = 345 Score = 151 bits (381), Expect = 3e-41 Identities = 105/352 (29%), Positives = 176/352 (50%), Gaps = 16/352 (4%) Query: 9 MKAAVMHNTREIKIETLPVPDINH-DEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFI 67 MKA + E+ +E P P++ + ++KV ICG+DLH G + + I Sbjct: 1 MKALIYRGPGELALEERPHPELYAATDAIVKVTKTTICGTDLHIL-KGDVPTCAPGR--I 57 Query: 68 LGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDG 127 LGHE G + VG+ V F GD V + +CG+C AC++G Y+ C ++ +DG Sbjct: 58 LGHEGVGIVEQVGTGVTAFMPGDPVLISCISSCGKCAACRKGMYSHCETGGWILGNRIDG 117 Query: 128 AFVQYIKM--RQDFVFLIPDSLSYEEAALIEP-----FSVGIHAAARTKLQPGSTIAIMG 180 +Y+++ ++ IP + E ++ F G+ K+QPG+T+AI+G Sbjct: 118 TQAEYVRIPHADTSLYRIPPNADEEALVMLSDILPTGFECGV---LNGKVQPGNTVAIVG 174 Query: 181 MGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDR 240 GP+GL A+ A+ + +IV D + RLE A++ GA+ I+ + D L+EI+ +T Sbjct: 175 AGPIGLAALLTAQFYSPAQLIVIDRDTSRLEVARRFGASATIDPDQTDPLKEIQRLTGGA 234 Query: 241 GVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA 300 GVD A E G PA Q V GG +A VG+ + L++ + D I I Sbjct: 235 GVDTAIEAVGVPATFQLCEEIVAAGGVIANVGVHGV-KADLHLEKLWDRNIAITTRLVDT 293 Query: 301 NTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQ-FKNECLKVMVYP 351 + P ++ + +G +D L+T ++ L++ +A Q + LKV++ P Sbjct: 294 ASTPMLLKTVQAGKLDPLKLITHRFKLDEALEAYRTFGQAAATQALKVIITP 345 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: 288 Number of extensions: 14 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: 345 Length adjustment: 29 Effective length of query: 324 Effective length of database: 316 Effective search space: 102384 Effective search space used: 102384 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