Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate BPHYT_RS28135 BPHYT_RS28135 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__BFirm:BPHYT_RS28135 Length = 339 Score = 170 bits (430), Expect = 6e-47 Identities = 109/320 (34%), Positives = 160/320 (50%), Gaps = 13/320 (4%) Query: 36 GEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEIVGVVTEVGSKVEKVKVGDNVG 95 G V +K+ CG+CHSD W YP VPGHEI GV+ VG+ VE G VG Sbjct: 27 GAGQVLIKIQACGICHSDVLTKEGQWPGLEYPRVPGHEIAGVIDTVGAGVEGWAAGQRVG 86 Query: 96 IGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPKN 155 +G G C CE C C+ + G GGY++ MVA + R P + Sbjct: 87 VGWHGGHCGRCEHCRRGDFVLCQRAL-------VPGISYDGGYAEFMVAPVEALARIPDD 139 Query: 156 LPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVIDI 215 L APLLCAGITT++ L+ G + G + V+G+GGLGH+ V+ A+ G I Sbjct: 140 LSDVDAAPLLCAGITTFNALRNSGA-RAGDVVAVLGIGGLGHLGVQFARKMGFVTVAIAR 198 Query: 216 SESKRKEALEKLGADSFLLNSDQEQMKGARSSLDG---IIDTVPVNHPLAPLFDLLKPNG 272 + K A E LGA + ++S + A +L G I+ TV ++ + L NG Sbjct: 199 GQDKASLAKE-LGAHHY-IDSTTANVAQALQALGGARVILATVTSGKAMSAVVGGLGLNG 256 Query: 273 KLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVIPMDY 332 KL+MVG E+P E+P+ + GR + G +G ++Q+ L F+A I +E P+ Sbjct: 257 KLIMVGLSEEPVEVPIAQFIMGRNSVQGWPSGTSADSQDTLAFSALSGIKPMIEEFPLTK 316 Query: 333 VNTAMERLVKSDVRYRFVID 352 A +R++ R+R V++ Sbjct: 317 AAEAYDRMMSGAARFRVVLN 336 Lambda K H 0.319 0.137 0.415 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: 305 Number of extensions: 11 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: 365 Length of database: 339 Length adjustment: 29 Effective length of query: 336 Effective length of database: 310 Effective search space: 104160 Effective search space used: 104160 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 (21.7 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