Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Pf1N1B4_2461 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= BRENDA::Q86ZV0 (358 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2461 Length = 399 Score = 98.6 bits (244), Expect = 3e-25 Identities = 81/275 (29%), Positives = 118/275 (42%), Gaps = 30/275 (10%) Query: 10 NLSFVLEGIHKVKFEDRPIPQLRDA------HDVLVDVRFTGICGSDVHYWEHGSIGQFV 63 N V G KV+ + P+++D H V++ V T ICGSD H G+ Sbjct: 4 NRGVVYLGAGKVEVQKIDYPKMQDPRGRKIEHGVILRVVSTNICGSDQHMVR----GRTT 59 Query: 64 VKDPMVLGHESSGVISKVGSAVTTLKVGDHVAMEPGIPCRRCEPCKEGKYNLCEKM---- 119 + +VLGHE +G + + GS V L++GD V++ + C RC CKE +C + Sbjct: 60 AQTGLVLGHEITGEVIEKGSGVENLQIGDLVSVPFNVACGRCRSCKEQHTGVCLSVNPAR 119 Query: 120 -----AFAATPPYDGTLAKYYVLP-EDF-CYKLPENINLQE-----AAVMEPLSVAVHIV 167 + + G A+Y +P DF KLP+ E + + L H Sbjct: 120 PGGAYGYVDMGDWTGGQAEYAFVPYADFNLLKLPDRDRAMEKIRDLTCLSDILPTGYHGA 179 Query: 168 KQANVAPGQSVVVFGAGPVGLLCCAVARAFGSPKVIAVDIQKGRLEFAKKYAATAIFEPS 227 A V PG +V + GAGPVGL A AR G+ VI D+ RL AK + Sbjct: 180 VTAGVGPGSTVYIAGAGPVGLAAAASARLLGAAVVIIGDVNPIRLAHAKAQGFEIADLST 239 Query: 228 KVSALENAERIVNENDLGRGADIVIDASGAEPSVH 262 E ++ E ++ D +DA G E H Sbjct: 240 DTPLHEQIAALLGEPEV----DCAVDAVGFEARGH 270 Lambda K H 0.319 0.137 0.406 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: 364 Number of extensions: 17 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: 358 Length of database: 399 Length adjustment: 30 Effective length of query: 328 Effective length of database: 369 Effective search space: 121032 Effective search space used: 121032 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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