Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_047212839.1 PATSB16_RS04610 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >NCBI__GCF_001931675.1:WP_047212839.1 Length = 328 Score = 165 bits (417), Expect = 2e-45 Identities = 107/312 (34%), Positives = 165/312 (52%), Gaps = 7/312 (2%) Query: 27 ALGTWAIG-GWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRD 85 ALG +G + G D+ SI TIHRA++LG+N DTA YG E +VGKA+KG R+ Sbjct: 15 ALGLGCMGMSEFYSGRDEAESIATIHRALELGVNFFDTADMYGPFTNELLVGKALKGLRN 74 Query: 86 NLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIE 145 +I+ATK G + + R A +K+ + SL+RLG D+IDLY H DP VPIE Sbjct: 75 EVILATKFGNERGANGEFLGIRGDDAY-VKRACDASLQRLGVDHIDLYYQHRVDPKVPIE 133 Query: 146 ETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAK 205 ET + L K GK+R +G+S + Q + + Q+ Y+L+ R+++ +ILP + Sbjct: 134 ETVGAMADLVKAGKVRYLGLSEAAAQTVRRAHAVHPITALQTEYSLWSRDVESEILPTLR 193 Query: 206 KNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKE 265 + + + Y L RG L+G++ DD R+ P+FQ F+ L E++++A E Sbjct: 194 ELGIGFVAYSPLGRGFLTGQIKRIDDLAADDYRRNSPRFQGDNFQRNLDLFAEIERMAAE 253 Query: 266 HYNKSVLALAIRWMLEQGPTLA-LWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAKNI 324 + LA+ W+L QG + + G + +++ +SD DL++ID IL Sbjct: 254 K-GCTPAQLALAWVLAQGEDIVPIPGTKRRAKLEDNVGALEVTLSDADLQRIDGILP--- 309 Query: 325 PNPIGAEFMAPP 336 P E A P Sbjct: 310 PGAAAGERYAAP 321 Lambda K H 0.317 0.136 0.407 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: 279 Number of extensions: 12 Number of successful extensions: 3 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: 340 Length of database: 328 Length adjustment: 28 Effective length of query: 312 Effective length of database: 300 Effective search space: 93600 Effective search space used: 93600 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 (21.6 bits) S2: 49 (23.5 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