Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate PP_3120 PP_3120 methylglyoxal reductase
Query= BRENDA::F2YCN5 (340 letters) >FitnessBrowser__Putida:PP_3120 Length = 253 Score = 115 bits (288), Expect = 1e-30 Identities = 86/273 (31%), Positives = 129/273 (47%), Gaps = 44/273 (16%) Query: 45 ASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVGLDWTLTPDQS 104 A + + + I+LG+N+IDTA Y G AEEVVG+AI G+RD + + +KV Sbjct: 10 AEVAALQQGIELGLNLIDTAEMYAEGGAEEVVGQAIAGRRDRVFLVSKV----------- 58 Query: 105 MRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEALRKEGKIRSIG 164 N+S + E SL RLGTD IDLY +HW P+EET E LR++GKI+ G Sbjct: 59 YPHNASLRGMAAACERSLTRLGTDCIDLYLLHWRGQ-HPLEETVEGFERLREQGKIKRWG 117 Query: 165 VSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSG 224 VSN+ V + E + A +Q YN +R I+ D+LP+ K L + Y L + +G Sbjct: 118 VSNFDVDDLRELHN-PDCATNQVLYNPAQRGIEFDLLPWCGKRGLPTMAYCPLAQ---AG 173 Query: 225 RMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQGP 284 R+ Q P L ++A+ H + + + W+ Sbjct: 174 RL-----------------LQHP----------VLAEIAERH-GATPAQVCLAWVTRDDG 205 Query: 285 TLALWGACKPEQIDGIDEVFGWQISDEDLKQID 317 +A+ A PE + ++ EDL+ ID Sbjct: 206 VIAIPKAVAPEHVRLNAAAGALTLTGEDLRAID 238 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: 220 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 253 Length adjustment: 26 Effective length of query: 314 Effective length of database: 227 Effective search space: 71278 Effective search space used: 71278 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