Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_017549643.1 C792_RS0111725 aldo/keto reductase
Query= BRENDA::C5J3R6 (320 letters) >NCBI__GCF_000330705.1:WP_017549643.1 Length = 277 Score = 181 bits (459), Expect = 2e-50 Identities = 103/306 (33%), Positives = 159/306 (51%), Gaps = 43/306 (14%) Query: 5 TIKLNSGYDMPLVGFGLWKVNRETCADQVYEAIKAGYRLFDGACDYGNEVEAGQGVARAI 64 T +LN+G MP++GFG++K+ E A + A++AGYR FD A Y NE G + Sbjct: 8 TYELNNGVKMPVIGFGVYKIPEEQMAATIGTALEAGYRHFDTAAFYENERALGD----VL 63 Query: 65 KEGIVKREDLFIVSKLWNTFHEADKVEPIARKQLADWGLDYFDLYLIHFPIALKYVDPAE 124 K+ V RE+LFI +K+WN ++ L +DY DLYLIH+PI KY Sbjct: 64 KKSDVSREELFITTKVWNDDLGYEETLKAFETSLEKLQMDYLDLYLIHWPIEGKYT---- 119 Query: 125 IYPPGWTGTKKEVEFSNATIQETWQAMETLVDKKLTRSIGISNFSAQLIMDLLRYARIRP 184 E+W+A+E L R+IG+SNF +Q + ++ R+A + P Sbjct: 120 ---------------------ESWRALEKLYKDGRVRAIGVSNFHSQHLEEIFRFATVTP 158 Query: 185 ATLQIEHHPYLTQQALVEYVQKEGIAVTAYSSFGPLSFLELGHQVAKDTPLLFEHSTVKS 244 Q+E+HP L Q+ + + + GI + A++ +F F ++ Sbjct: 159 MVNQLEYHPQLAQKEMRAFCDEHGIQLEAWAPLKRGAF--------------FGDPVIRE 204 Query: 245 IAEKHGKTPAQVLLRWATQRNIAVIPKSNNPGRLAQNLDVTAWDLEPADIEALSALNKNL 304 +AEK+GKTPAQ++LRW Q ++ IPKS PGR+ QN+D+ ++L D+E L L+ + Sbjct: 205 LAEKYGKTPAQIVLRWDIQTGVSTIPKSVTPGRIRQNIDIFDFELTEGDMERLDTLDTHE 264 Query: 305 RFNNPP 310 R P Sbjct: 265 RLGKDP 270 Lambda K H 0.319 0.136 0.411 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: 263 Number of extensions: 15 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: 320 Length of database: 277 Length adjustment: 26 Effective length of query: 294 Effective length of database: 251 Effective search space: 73794 Effective search space used: 73794 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 (21.8 bits) S2: 48 (23.1 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