Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase
Query= BRENDA::Q8KQG6 (338 letters) >FitnessBrowser__HerbieS:HSERO_RS04830 Length = 341 Score = 126 bits (316), Expect = 9e-34 Identities = 95/311 (30%), Positives = 148/311 (47%), Gaps = 23/311 (7%) Query: 3 ALVLTGTKKLEVKDIDRPKVLPNEVLIHTAFAGICGTD-HALYAGLPGSADAVPPIVLGH 61 A+V K L ++ + P P ++L+ +G+C TD HA + P PP + GH Sbjct: 8 AVVREFGKPLSIEQVPVPTPAPGQILVKFEASGVCHTDLHAAHGDWP--VKPTPPFIPGH 65 Query: 62 ENSGVVAEIGSAVTNVKVGDRVTVD-PNIYCGQCKYCRTARPELCENLSAVGVTRDGGFE 120 E +G VA +G+ V +VK GDRV V + CG C CRT LC G + +G F Sbjct: 66 EGTGYVAAVGAGVKHVKEGDRVGVPWLHTACGCCSPCRTGWETLCAEQQNTGYSVNGSFA 125 Query: 121 EFFTAPASVVYPIPDNVSLKSAAVVEPISCA----VHGIQLLKVTPYQKALVIGDGFMGE 176 E+ A V +PDN+ AA P+ CA G++ +V P + ++ G G +G Sbjct: 126 EYGLADPKFVGHLPDNLDFGPAA---PVLCAGVTVYKGLKETEVRPGEWVVISGIGGLGH 182 Query: 177 LFVQILQAYGIHQVDLAGIVDEKLAMNKEKFGVKNTYNTMKGDKIPE------GEYDVII 230 + VQ +A G+H V A I ++KLA+ K K G T + + + E G + ++ Sbjct: 183 MAVQYAKAMGMHVV-AADIHEDKLALAK-KLGADLTVDGRNHNAVAEVQRIIGGAHGALV 240 Query: 231 EAVGLPQTQEAAIEASARGAQVLMFGVGGPDAKFQMNTYEVFQKQLTIQGSFINPNA-FE 289 AV ++A ARG L VG P + + K++T++GS + E Sbjct: 241 TAVSPKAMEQAFGFLRARGTMAL---VGLPPGDISLPVFNTVLKRITVRGSIVGTRQDLE 297 Query: 290 DSLALLSSGKL 300 +SL + GK+ Sbjct: 298 ESLVFAAEGKV 308 Lambda K H 0.317 0.136 0.390 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: 264 Number of extensions: 20 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: 338 Length of database: 341 Length adjustment: 28 Effective length of query: 310 Effective length of database: 313 Effective search space: 97030 Effective search space used: 97030 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 (21.6 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