Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_086509112.1 BZY95_RS06260 formaldehyde dehydrogenase, glutathione-independent
Query= BRENDA::P35497 (357 letters) >NCBI__GCF_002151265.1:WP_086509112.1 Length = 397 Score = 107 bits (267), Expect = 5e-28 Identities = 100/312 (32%), Positives = 143/312 (45%), Gaps = 49/312 (15%) Query: 1 MSQNSNPAVVLEKVGDIAIEQRPIPTI-----KDPHYVKLAIKATGICGSDIHYYRSGGI 55 MSQ +N VV + G + +E P P + K H V L + T ICGSD H R Sbjct: 1 MSQ-ANRGVVYKGPGKVDVESIPYPELALGNRKCDHGVILKVVTTNICGSDQHMVR---- 55 Query: 56 GKYILKAPMVLGHESSGQVVEVGDAVTRVKVGDRVAIEPGVPSRYSDETKEGRYNLC--- 112 G+ A +VLGHE +G VVE G V +K GD V++ + KEGR +C Sbjct: 56 GRTTAPAGLVLGHEITGLVVECGRDVEFIKPGDLVSVPFNIACGRCRNCKEGRTGICLNV 115 Query: 113 -PHMAFAATPPID-----GTLVKYYLSP-EDF-LVKLPEGVSYEEGA-----CVEPLSVG 159 P AA +D G +Y + P DF L+K P+ E + G Sbjct: 116 NPARPGAAYGYVDMGGWVGGQTEYVMVPYADFNLLKFPDSDQAMEKIRDLTLLSDIFPTG 175 Query: 160 VHSNKLAGVRFGTKVVVFGAGPVGLLTGAVARAFGATDVIFVDVFDNKLQRAKDFGATNT 219 H AGV G+ V + GAGPVGL A A+ GA VI D+ + +L +A+ FG T Sbjct: 176 FHGCVTAGVGPGSTVYIAGAGPVGLAAAASAQLLGAACVIVGDMIEERLAQARSFGC-ET 234 Query: 220 FNSSQFSTDKAQDLADGVQKLLGGNHADVVFECSG--ADVC------------IDAAVKT 265 + +Q D+AD ++ +LG D +C G A C +++A++ Sbjct: 235 IDLTQ-----EGDMADKLEAILGEREVDCFVDCVGFEAHACGCNHDKEAPATVLNSAMQM 289 Query: 266 TKVGGTMVQVGM 277 T+ GG Q+G+ Sbjct: 290 TRAGG---QIGI 298 Lambda K H 0.318 0.137 0.403 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: 373 Number of extensions: 22 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: 357 Length of database: 397 Length adjustment: 30 Effective length of query: 327 Effective length of database: 367 Effective search space: 120009 Effective search space used: 120009 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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