Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AO356_14000 AO356_14000 aldehyde dismutase
Query= BRENDA::P35497 (357 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_14000 Length = 399 Score = 98.6 bits (244), Expect = 3e-25 Identities = 91/273 (33%), Positives = 123/273 (45%), Gaps = 32/273 (11%) Query: 4 NSNPAVVLEKVGDIAIEQRPIPTIKDP------HYVKLAIKATGICGSDIHYYRSGGIGK 57 + N VV G + +++ P ++DP H V L + +T ICGSD H R G+ Sbjct: 2 SGNRGVVYLGNGKVEVQKIDYPKMQDPRGRKIEHGVILRVVSTNICGSDQHMVR----GR 57 Query: 58 YILKAPMVLGHESSGQVVEVGDAVTRVKVGDRVAIEPGVPSRYSDETKEGRYNLC----P 113 + +VLGHE +G+V+E G V +K+GD V++ V KE +C P Sbjct: 58 TTAQTGLVLGHEITGEVIEKGSDVENLKIGDLVSVPFNVACGRCRSCKEQHTGVCLTVNP 117 Query: 114 HMAFAATPPID-----GTLVKYYLSP-EDF-LVKLPEGVSYEEG----ACVEP-LSVGVH 161 A A +D G +Y L P DF L+KLP+ E C+ L G H Sbjct: 118 ARAGGAYGYVDMGDWTGGQAEYVLVPYADFNLLKLPDRDKAMEKIRDLTCLSDILPTGYH 177 Query: 162 SNKLAGVRFGTKVVVFGAGPVGLLTGAVARAFGATDVIFVDVFDNKLQRAKDFGATNTFN 221 AGV G+ V + GAGPVGL A AR GA VI DV +L AK G F Sbjct: 178 GAVTAGVGPGSTVYIAGAGPVGLAAAASARLLGAAVVIIGDVNPVRLAHAKAQG----FE 233 Query: 222 SSQFSTDKAQDLADGVQKLLGGNHADVVFECSG 254 + STD L + + LLG D + G Sbjct: 234 IADLSTD--TPLHEQIAALLGEPEVDCAVDAVG 264 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: 371 Number of extensions: 21 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: 357 Length of database: 399 Length adjustment: 30 Effective length of query: 327 Effective length of database: 369 Effective search space: 120663 Effective search space used: 120663 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 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