Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate CA265_RS08610 CA265_RS08610 alcohol dehydrogenase
Query= CharProtDB::CH_000596 (353 letters) >FitnessBrowser__Pedo557:CA265_RS08610 Length = 339 Score = 159 bits (403), Expect = 8e-44 Identities = 98/325 (30%), Positives = 162/325 (49%), Gaps = 12/325 (3%) Query: 28 PDINHDEVLIKVMAVGICGSDLHYYTNGR-IGNYVVEKPFILGHECAGEIAAVGSSVDQF 86 P++ D +IK+ +GICG+DLH + + NY P +LGHE +GE+ + D F Sbjct: 20 PELKKDHAIIKIKRIGICGTDLHAFEGTQPFFNY----PRVLGHELSGELVEADGA-DGF 74 Query: 87 KVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGAFVQYIKMRQDFVFLIPDS 146 K+G+ V P CG C AC+ + N C +Q VDG +Y+++ L + Sbjct: 75 KIGEAVTFIPYFNCGECIACRMNKPNCCVKMQVCGVH-VDGGMREYLQVPSR-TLLHGEG 132 Query: 147 LSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLE 206 LSY+E AL+EP ++G H R +QPG + ++G GP+GL + A+ GA +I D+ Sbjct: 133 LSYDELALVEPLAIGAHGVRRADVQPGEFVLVIGAGPIGLGTMEFARIAGA-NVIALDIN 191 Query: 207 PLRLEAAK-KMGATHIINIREQDALEEIKTITNDRGVDVAWETAGNPAALQSALASVRRG 265 RL K K+ H++N D ++++ ITN V + GN A+ +A+ + G Sbjct: 192 EDRLAFCKDKLKVAHVVNALSPDVVQQLSDITNGDMPTVVIDATGNQKAINNAINYMAHG 251 Query: 266 GKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA-NTYPKGIEFLASGIVDTKHLVTDQ 324 + ++GL + ++ N P E + + I+ + +G+V+ + +T Q Sbjct: 252 ARFVLIGL-QKGDLIFNHPEFHKRESTLMSSRNATIEDFEHVIKSMKAGLVNPTNYITHQ 310 Query: 325 YSLEQTQDAMERALQFKNECLKVMV 349 E +D E L KN +K MV Sbjct: 311 VQFEAVKDEFESWLDPKNGVIKAMV 335 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: 285 Number of extensions: 13 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: 339 Length adjustment: 29 Effective length of query: 324 Effective length of database: 310 Effective search space: 100440 Effective search space used: 100440 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