Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate HSERO_RS16785 HSERO_RS16785 aldo/keto reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__HerbieS:HSERO_RS16785 Length = 335 Score = 162 bits (410), Expect = 1e-44 Identities = 96/282 (34%), Positives = 157/282 (55%), Gaps = 2/282 (0%) Query: 42 DDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVGLDWTLTP 101 DD S+ TI RA++LGIN++DTA YG EE++G+AIKG+RD IATK G+ + Sbjct: 37 DDAESLATIDRALELGINLLDTADMYGPYTNEELLGRAIKGRRDKFFIATKFGIRRDPSD 96 Query: 102 DQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEALRKEGKIR 161 + + S + I++ +E SL+RLG + IDLY H DP PIE T +L L + GKIR Sbjct: 97 PGARGVDGSPAYIRQAVEGSLKRLGVETIDLYYQHRIDPATPIEVTMGVLADLVQAGKIR 156 Query: 162 SIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGL 221 IG+S S ++ + + QS Y+L+ R+ + ++L + + + Y L RG Sbjct: 157 YIGLSEASAATLERAHRVHPVTALQSEYSLWTRDPEAEVLAACRTLGIGFVAYSPLGRGF 216 Query: 222 LSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLE 281 L+G + DD R+++P+FQ F L E++K++A +H + LA+ W++ Sbjct: 217 LTGAIQRFEDLAEDDFRRSNPRFQGENFARNLQLAEKVKEMAGQH-GCTPSQLALAWVMA 275 Query: 282 QGPTLA-LWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAK 322 Q P + + G + ++ G +++ EDL+ +DAI + Sbjct: 276 QDPHIVPIPGTKRRRYLEDNAGSVGVKLAPEDLQALDAIFPR 317 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: 291 Number of extensions: 17 Number of successful extensions: 2 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: 335 Length adjustment: 28 Effective length of query: 312 Effective length of database: 307 Effective search space: 95784 Effective search space used: 95784 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