Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate AO353_19865 AO353_19865 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19865 Length = 327 Score = 123 bits (309), Expect = 6e-33 Identities = 92/328 (28%), Positives = 137/328 (41%), Gaps = 17/328 (5%) Query: 27 PFKFSRRATGEKDVR---LKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEIVGVVTEVGS 83 P + RA D + +KVL CGVC +D H++ T P VPGHEIVG VT VG+ Sbjct: 12 PLQREERAIPTPDAQQLLIKVLACGVCRTDLHLVDGELPQATLPRVPGHEIVGEVTAVGA 71 Query: 84 KVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMV 143 V +G VG+ L +C CE C RE+ C+ F G GGY+D V Sbjct: 72 DVAPDWIGQRVGVPWLGSTCGRCEFCRSGRENLCDQA-------QFTGCNLDGGYADYTV 124 Query: 144 ADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMA 203 AD F R P L APLLCAG+ + L+ + K +G+ G G H+A+++A Sbjct: 125 ADARFCFRLPDTLSATEAAPLLCAGLIGFRALQ---MAKTARHLGLYGFGAAAHLAIQVA 181 Query: 204 KAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGIIDTVPVNHPLAP 263 G QV +A + ++ SDQ+ LD + PV + Sbjct: 182 LGRGQQVYAFTRPGDNEGQAYARTLGAAWAGPSDQK----PPHLLDASLIFAPVGALVPL 237 Query: 264 LFDLLKPNGKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITA 323 + G ++ G + LL G + + N ++ + + Sbjct: 238 ALEATVKGGCVICAGIHMSDIPAFPYRLLWGERSVRSVANLTREDGTAFFQEIRHTPVHS 297 Query: 324 DVEVIPMDYVNTAMERLVKSDVRYRFVI 351 DV +D N A+ +L V+ V+ Sbjct: 298 DVTCFALDDANQALAQLRSGQVKGAIVL 325 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: 265 Number of extensions: 11 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: 365 Length of database: 327 Length adjustment: 29 Effective length of query: 336 Effective length of database: 298 Effective search space: 100128 Effective search space used: 100128 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