Align D-threo-aldose 1-dehydrogenase; L-fucose dehydrogenase; EC 1.1.1.122 (characterized)
to candidate H281DRAFT_02575 H281DRAFT_02575 D-threo-aldose 1-dehydrogenase
Query= SwissProt::Q52472 (329 letters) >FitnessBrowser__Burk376:H281DRAFT_02575 Length = 325 Score = 168 bits (426), Expect = 1e-46 Identities = 109/315 (34%), Positives = 166/315 (52%), Gaps = 26/315 (8%) Query: 15 IPALGYGAANVGNLFRALSDDEAWAVLEAAWDAGIRYYDTAPHYGLGLSEKRLGAFLQTK 74 +P +G GA G+L A + + ++ AAW +G+RY+DT+ Y G SE+RLGA L Sbjct: 14 LPRVGVGA---GSLANAAGEQAFFNMIHAAWASGVRYFDTSAAYLGGESEQRLGAALAAC 70 Query: 75 PRDEFVVSTKAGRLL-RPNPERRPSGLDTDNDFHVPDDLRREWDFTEQGIRASIAESQER 133 PR+E VSTK GR L +P P G ++F++ D+T S+ S R Sbjct: 71 PREELYVSTKLGRYLSQPGASSLPGG----SNFYL--------DYTYDTTLRSVERSLSR 118 Query: 134 LGLDRIDLLYLHDPE--------RHDLDLALASAFPALEKVRAEGVVKAIGIGSMVSDAL 185 L +DR+D +++HD + R +L A+ AFPAL++++ E VV AIG+ SM A Sbjct: 119 LKVDRLDAVFIHDLDPGFAQAAYREELKTAVEGAFPALQRLKDEKVVGAIGVASMDWQAC 178 Query: 186 TRAVREADLDLIMVAGRYTLLEQPAATEVLPACAENATGIVAASVFNSGLLAQSEPKRDG 245 AD+D++M AG Y+LL + +T +L C E +AAS FNSG+LA + D Sbjct: 179 LDFAEMADVDVVMPAGEYSLL-RTRSTALLEHCVEKGIAWIAASPFNSGILATGS-RPDA 236 Query: 246 RYEYGQLPDELWDRLVRIAAICRNHDVPLPAAAIQFPLQSALVRSVVVGGSRPAQLTQNA 305 Y ++ + + ICR HDVPL AA+ FPL+ V ++V G + ++ Sbjct: 237 FYNMRPATRQVLSQTEGLECICRRHDVPLATAALLFPLRHPAVSTIVFGAKTSDEFNESF 296 Query: 306 EYAALEIPAGLWAEL 320 + +P W E+ Sbjct: 297 ARLSGNLPDQFWHEM 311 Lambda K H 0.318 0.135 0.395 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: 271 Number of extensions: 16 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: 329 Length of database: 325 Length adjustment: 28 Effective length of query: 301 Effective length of database: 297 Effective search space: 89397 Effective search space used: 89397 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: 48 (23.1 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