Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate BPHYT_RS22485 BPHYT_RS22485 NADP-dependent aryl-alcohol dehydrogenase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS22485 Length = 326 Score = 131 bits (329), Expect = 3e-35 Identities = 103/324 (31%), Positives = 160/324 (49%), Gaps = 29/324 (8%) Query: 13 KISIKGIDKSATRVALGTWAIG----GWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYG 68 K+ G+D S R+ LG + G G DD+A+ I +A+D GIN DTA Y Sbjct: 5 KLGRTGLDVS--RLCLGCMSYGVPSRGTHPWSLDDEAARPFIKQALDHGINFFDTANVYS 62 Query: 69 RGHAEEVVGKAIK--GQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLG 126 G +EE+VG+A+K +RD +++ATKV P+ + S I EI+ SLRRLG Sbjct: 63 DGTSEEIVGRALKDFAKRDEIVLATKVNSRMHPGPNGA---GLSRKAIMSEIDHSLRRLG 119 Query: 127 TDYIDLYQVHWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAE----- 181 TDY+DLYQ+H D PIEET L + K GK R IG S+ Q + AE Sbjct: 120 TDYVDLYQIHRWDYGTPIEETMEALHDVVKAGKARYIGASSMYAWQFAKALHVAEKNGWT 179 Query: 182 -LAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKT 240 Q+ NL RE ++++LP + + V+ + L RG L+ R + + R Sbjct: 180 RFVTMQNYVNLLYREEEREMLPLCESEGIGVIPWSPLARGRLT------RDWNTESARSE 233 Query: 241 DPKFQKPRFEHYLAA----VEELKKLAKEHYNKSVLALAIRWMLEQGP-TLALWGACKPE 295 +F + + A VE + ++AKE +A+ W+L++ P T + GA K Sbjct: 234 TDEFGQTLYAQTEDADRRVVERVSQIAKER-GVPRAQVALAWVLQKKPITAPIVGATKLH 292 Query: 296 QIDGIDEVFGWQISDEDLKQIDAI 319 +D +S ++++Q++ + Sbjct: 293 HLDDAVAALSLSLSADEIRQLEEL 316 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: 267 Number of extensions: 16 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: 326 Length adjustment: 28 Effective length of query: 312 Effective length of database: 298 Effective search space: 92976 Effective search space used: 92976 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