Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate PfGW456L13_2966 Aldo-keto reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2966 Length = 309 Score = 154 bits (390), Expect = 2e-42 Identities = 97/288 (33%), Positives = 157/288 (54%), Gaps = 7/288 (2%) Query: 40 GTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVGLDWTL 99 GTD + T+HRA++LG+N++DTA YG EE++GKAI G+RD + +A+K G+ Sbjct: 8 GTDAREATATLHRALELGVNLLDTADMYGPHTNEELIGKAIAGKRDQVFLASKFGIVRDP 67 Query: 100 TPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEALRKEGK 159 + N I++ I+ +L+RLG D +DLY H DP V IEET + L GK Sbjct: 68 ANPTARGVNGRPQYIRQSIDGTLKRLGVDTLDLYYQHRIDPQVAIEETVGAMAELVSAGK 127 Query: 160 IRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKD-ILPYAKKNDLVVLGYGALC 218 +R +G+S S ++ K ++V QS Y+L+ R+ +++ L ++ + + Y L Sbjct: 128 VRYLGLSEASAATLERAHKVHPISVLQSEYSLWSRDQEENGCLAACQRLGVAFVPYSPLG 187 Query: 219 RGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLA--LAI 276 RG L+G + + F DD R+ P+FQ F L V++++ LA E K V A LA+ Sbjct: 188 RGFLTGALKSPDDFVADDYRRFSPRFQGENFAKNLLLVQQVQALAAE---KGVTAGQLAL 244 Query: 277 RWMLEQGPTL-ALWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAKN 323 W+L QG L + G + + ++ +S E+L ++A+ A N Sbjct: 245 AWVLAQGDYLIPIPGTKQRKYLEENVAALEVTLSAEELHALEAVFAAN 292 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: 248 Number of extensions: 9 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: 309 Length adjustment: 28 Effective length of query: 312 Effective length of database: 281 Effective search space: 87672 Effective search space used: 87672 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: 48 (23.1 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