Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_053546284.1 CDES_RS13820 S-(hydroxymethyl)mycothiol dehydrogenase
Query= BRENDA::Q86ZV0 (358 letters) >NCBI__GCF_001277995.1:WP_053546284.1 Length = 368 Score = 134 bits (338), Expect = 3e-36 Identities = 107/346 (30%), Positives = 166/346 (47%), Gaps = 36/346 (10%) Query: 35 HDVLVDVRFTGICGSDVHYWEHGSIGQFVVKDPMVLGHESSGVISKVGSAVTTLKVGDHV 94 HDV+V ++ TG+C +D+ Y + +F P +LGHES+GV+ VG AVT ++VGD V Sbjct: 30 HDVIVKIQSTGVCHTDLAYRDGDISDEF----PFLLGHESAGVVETVGDAVTHVEVGDFV 85 Query: 95 AMEPGIPCRRCEPCKEGKYNLC-------EKMAFA----ATPPYD-GTLAKYYVLPEDFC 142 + C C C++G C +KM TP G+ A+ ++ E C Sbjct: 86 VLNWRAVCGECRACRKGDLEYCFNTHNASKKMTLTDGTELTPALGIGSFAEKTLVHEGQC 145 Query: 143 YKL-----PENINLQEAAVMEPLSVAVHIVKQANVAPGQSVVVFGAGPVGLLCCAVARAF 197 K+ P L +M L AV+ V G+SV VFG G VG+ A A+ Sbjct: 146 TKVNPDADPAAAGLLGCGIMAGLGSAVNT---GEVKRGESVAVFGLGGVGMAAVAGAKIA 202 Query: 198 GSPKVIAVDIQKGRLEFAKKYAATAIFEPSKVSAL-ENAE--RIVNENDLGRGADIVIDA 254 G+ +IAVDI +LE+AK++ AT + + S++S EN+E + V E G G D+ IDA Sbjct: 203 GATTIIAVDIDAKKLEWAKEFGATHVIDSSQLSGEGENSEVAQKVREITDGFGTDVAIDA 262 Query: 255 SGAEPSVHTGIHVLRPGGTYVQGGMGRNEITFPIMAACTKELNVRGSFR---YG----SG 307 G P+ + G V +G +T I GS R YG Sbjct: 263 VGIMPTWQQAFYSRDHAGRMVM--VGVPNLTSRIEVPAIDFYGRGGSLRPAWYGDCLPER 320 Query: 308 DYKLAVNLVASGKVSVKELITGVVSFEDAEQAFHEVKAGKGIKTLI 353 D+ V+L G+ + + ++ + D E+AF +KAG +++++ Sbjct: 321 DFPTYVDLYLQGRFPLDKFVSERIGLGDVEEAFTTMKAGDVLRSVV 366 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: 350 Number of extensions: 20 Number of successful extensions: 6 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: 368 Length adjustment: 29 Effective length of query: 329 Effective length of database: 339 Effective search space: 111531 Effective search space used: 111531 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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