Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate Pf1N1B4_4693 Oxidoreductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4693 Length = 331 Score = 156 bits (394), Expect = 8e-43 Identities = 99/302 (32%), Positives = 163/302 (53%), Gaps = 7/302 (2%) Query: 26 VALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRD 85 + LG + + G D + T+HRA++LGIN++DTA YG EE++GKAI G+RD Sbjct: 16 IGLGCMGMTDFYTTGVDTREATATLHRALELGINLLDTADMYGPHTNEELIGKAIAGKRD 75 Query: 86 NLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIE 145 + +A+K G+ + + N I K I+ +L+RLG + +DLY H DP V IE Sbjct: 76 QVFLASKFGIVRDPSSPGARGVNGRPEYIHKSIDGTLKRLGVETLDLYYQHRIDPQVAIE 135 Query: 146 ETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKD-ILPYA 204 ET + L K GK+R +G+S SV ++ K ++ QS Y+L+ R+ +++ L Sbjct: 136 ETVGAMAELVKAGKVRYLGLSEASVTTLERANKIHPISALQSEYSLWSRDQEENGCLAAC 195 Query: 205 KKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAK 264 ++ + + Y L RG L+G + + F DD R+ P+FQ F L V++++ LA Sbjct: 196 QRLGVAFVPYSPLGRGFLTGALRSPDDFAADDYRRFSPRFQGENFAKNLLLVQQVQTLAT 255 Query: 265 EHYNKSVLA--LAIRWMLEQGPTL-ALWGACKPEQIDGIDEVFGWQISDEDLKQIDAILA 321 + K V A LA+ W+L QG L + G + + ++ ++S E+L+ ++AI Sbjct: 256 D---KGVTAGQLALAWVLAQGDYLIPIPGTKQRKYLEENVAALDVKLSREELQALEAIFP 312 Query: 322 KN 323 N Sbjct: 313 AN 314 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: 259 Number of extensions: 8 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: 331 Length adjustment: 28 Effective length of query: 312 Effective length of database: 303 Effective search space: 94536 Effective search space used: 94536 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