Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_068006577.1 PsAD2_RS13045 SDR family oxidoreductase
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_001623255.1:WP_068006577.1 Length = 263 Score = 159 bits (403), Expect = 4e-44 Identities = 102/269 (37%), Positives = 142/269 (52%), Gaps = 25/269 (9%) Query: 1 MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60 M +F L+TGAG IG ATA+RLA+EG A+AL+D+N LE+ AS+ +G AR Sbjct: 1 MEPRFANMTALITGAGSGIGRATAIRLADEGAALALVDLNETGLEET-ASMLPEGCRARI 59 Query: 61 YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGY--QGAFAPVQDYPSDDFARVLTINVT 118 YV DV E+AV V FG I L NNAG +G++ Q+ D+ +V +NV Sbjct: 60 YVVDVADEKAVETCAVDVENTFGGISVLCNNAGMICEGSWGRSQE-DFADWRKVYEVNVL 118 Query: 119 GAFHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPY 178 GA K Q+ G IVNTAS+AG++ AY SK A+I T+T+A D + Sbjct: 119 GAMLFTKYTREQLKASGVGSIVNTASVAGIRAGAGGNAYSASKAALINFTKTSACDFGEH 178 Query: 179 NIRVNAISPGYMGPG-----FMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGD 233 +RVNA+ PG + G F + R + K+GS+ +RR+GD Sbjct: 179 GVRVNAVCPGLIETGMTKPVFDYARHAGKEEKLGSR----------------AELRRHGD 222 Query: 234 INEIPGVVAFLLGDDSSFMTGVNLPIAGG 262 E+ +AFL D+SF+TG L + GG Sbjct: 223 PTEVAATIAFLASKDASFITGQALAVDGG 251 Lambda K H 0.318 0.135 0.384 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: 171 Number of extensions: 7 Number of successful extensions: 4 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: 262 Length of database: 263 Length adjustment: 25 Effective length of query: 237 Effective length of database: 238 Effective search space: 56406 Effective search space used: 56406 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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