Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate HSERO_RS13585 HSERO_RS13585 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__HerbieS:HSERO_RS13585 Length = 329 Score = 119 bits (298), Expect = 1e-31 Identities = 90/282 (31%), Positives = 141/282 (50%), Gaps = 22/282 (7%) Query: 24 TRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIK-- 81 + + G WAIGG WG + +H A+D G++ IDTA YG G +E+++ + +K Sbjct: 14 SEIGFGAWAIGG-SWGDVSAQDAKAALHAALDAGVSFIDTADVYGDGRSEQLIAQVLKER 72 Query: 82 -GQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDP 140 G+R +ATK G L+P + N A ++ I+ SL+ LG D +DL Q+H P Sbjct: 73 GGERP--FVATKAGR--RLSPHVASGYNDRA-QLSAFIDRSLKNLGVDCLDLVQLHCPPT 127 Query: 141 LVPIE-ETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKD 199 V + E L+AL GKIR GVS V++ + +Y + Q +N+F + Sbjct: 128 EVYYQQEVFGHLDALVAAGKIRHYGVSVEKVEEALKAIEYPNVKSVQIIFNIFRQRPISL 187 Query: 200 ILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRK---------TDPKFQKPRFE 250 L A++ D+ V+ L GLL+G+M+A F DD R+ F +E Sbjct: 188 FLQEAQRRDIAVIARVPLASGLLTGKMSAQTTFAADDHRQFNRHGEAFDVGETFSGVPYE 247 Query: 251 HYLAAVEELKKLAKEHYNKSVLALAIRWML-EQGPTLALWGA 291 LAAVE+++ L + + A+RW+L E G + + GA Sbjct: 248 VALAAVEKIRALVPQ--GVPMAQFALRWILMESGISTVIPGA 287 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: 228 Number of extensions: 19 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: 340 Length of database: 329 Length adjustment: 28 Effective length of query: 312 Effective length of database: 301 Effective search space: 93912 Effective search space used: 93912 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 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