Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate N515DRAFT_0878 N515DRAFT_0878 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Dyella79:N515DRAFT_0878 Length = 345 Score = 154 bits (388), Expect = 4e-42 Identities = 99/325 (30%), Positives = 164/325 (50%), Gaps = 16/325 (4%) Query: 39 DVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHEIVGVVTEVGSKVEKV-KVGDNVGIG 97 +V ++V CG+C +D I T P VPGHE+VG + +G K+G VG+G Sbjct: 30 EVLIEVEACGICGADAADIERANPATRPPRVPGHEVVGRIAALGPGTPSTWKLGQRVGVG 89 Query: 98 CLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPKNLP 157 L G C C+ C + C + G GGY++ MVA ++ P L Sbjct: 90 RLGGHCNQCDECRRGQFQLCRDQPVL-------GATCDGGYAEMMVARSTGLVSIPDELR 142 Query: 158 LDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVIDISE 217 + AP+LCAGI T++ LK G + G + VVG+GGLGH+A++ A+ G +V I + Sbjct: 143 AEEAAPILCAGIATFNALKKCGAEA-GDLVAVVGVGGLGHMALQYARRMGFKVAAIGRGQ 201 Query: 218 SKRKEALEKLGADSFLLNSDQEQMKGAR----SSLDGIIDTVPVNHPLAPLFDLLKPNGK 273 +AL LGA ++ ++Q+ GAR II T+ ++ L L P G+ Sbjct: 202 DIAGDALA-LGAHVYIDTNEQDA--GARLKDLGGAQAIITTIAHAATVSALVAGLAPQGR 258 Query: 274 LVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVIPMDYV 333 LV++G +P +P+ L+ G + + G+I G E ++ L+F+ + A +E +P++ Sbjct: 259 LVVLGVGAEPLSIPLGQLVAGERSILGSITGTPYENEKTLEFSVLAGVRAMIETMPLERA 318 Query: 334 NTAMERLVKSDVRYRFVIDIANTMR 358 A R+ + + ++R V+ + R Sbjct: 319 PDAYRRMKRGEAKFRMVLTMEQANR 343 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: 268 Number of extensions: 11 Number of successful extensions: 5 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: 345 Length adjustment: 29 Effective length of query: 336 Effective length of database: 316 Effective search space: 106176 Effective search space used: 106176 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