Align NAD(P)H-dependent D-xylose reductase XYR1; XR; EC 1.1.1.307 (characterized)
to candidate 7026457 Shewana3_3599 aldo/keto reductase (RefSeq)
Query= SwissProt::G4N708 (324 letters) >FitnessBrowser__ANA3:7026457 Length = 280 Score = 133 bits (335), Expect = 4e-36 Identities = 91/299 (30%), Positives = 143/299 (47%), Gaps = 43/299 (14%) Query: 14 MPQVGFGLWKVENSVCADVVYNAIKAGYRLFDGACDYGNEVECGQGVKRAIDEGLVKREE 73 MP +G G ++++++ D V A++ G R D A YGNE Q V AI+ + REE Sbjct: 17 MPMLGTGTFRLKDNAAFDAVLMALEEGSRHIDTAQIYGNE----QAVGDAINTSGIPREE 72 Query: 74 LFIVSKLWNTFHDGERVEPIVKKQLADWGIEYFDLYLIHFPVALEYVDPSVRYPPGWHYD 133 LFI +K+W ER E V L +Y DL LIH+P Sbjct: 73 LFITTKVWTENLTKERFETSVIDSLTALQTKYLDLLLIHWP------------------- 113 Query: 134 DAGTEIRPSKASIQETWTAMEKLVDAGLSKAIGVSNF-QAQLLYDMLRYARIRPATLQIE 192 + + S+ E + ++ ++D GL++ IGVSNF AQL + T Q+E Sbjct: 114 -----LNSDEPSMVEYLSELKAVLDKGLTRRIGVSNFTNAQLAQAIAILGEGVIYTNQVE 168 Query: 193 HHPYLVQQRLIEACKTEGIVVTAYSSFGPASFKEFNMEHAEALTPLLEEPTIVKLAEKYG 252 HPYL+ +++ + C+ ++VT Y F A +L++ TIV LA + Sbjct: 169 VHPYLINRKVTDFCRQHNVLVTGYMPF--------------AYGAVLQDETIVNLASVHQ 214 Query: 253 KDPGQVLLRWATQRGLAVIPKSSREKTMKSNFEAVGWDMEDSDIKTISALDKGIRFNQP 311 P Q++L W Q G A IP S++ ++SN A ++ ++I+ I+ LD+ R P Sbjct: 215 ATPAQIVLAWLRQLGFATIPSSTKRDNVRSNLAAASINLTPAEIEQINQLDRNHRVANP 273 Lambda K H 0.319 0.136 0.418 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: 177 Number of extensions: 10 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: 324 Length of database: 280 Length adjustment: 27 Effective length of query: 297 Effective length of database: 253 Effective search space: 75141 Effective search space used: 75141 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: 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