Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate BWI76_RS24895 BWI76_RS24895 galactitol-1-phosphate 5-dehydrogenase
Query= BRENDA::Q86ZV0 (358 letters) >FitnessBrowser__Koxy:BWI76_RS24895 Length = 347 Score = 159 bits (403), Expect = 8e-44 Identities = 109/353 (30%), Positives = 175/353 (49%), Gaps = 36/353 (10%) Query: 12 SFVLEGIHKVKFEDRPIPQLRDAHDVLVDVRFTGICGSDV--------HYWEHGSIGQFV 63 S V+ V+ E+RPIP L+ +DVLV V +G+CGSD+ HY+ Sbjct: 3 SVVIHAEGTVRVEERPIPTLQTENDVLVKVVSSGLCGSDIPRIFAKGAHYY--------- 53 Query: 64 VKDPMVLGHESSGVISKVGSAVTTLKVGDHVAMEPGIPCRRCEPCKEGKYNLCEKMAFAA 123 P+ LGHE SG + GSAVT L+ GD VA P +PC C C+ ++LC++ F Sbjct: 54 ---PITLGHEFSGYVESYGSAVTDLQPGDAVACVPLLPCFNCPQCQREYFSLCKQYQFVG 110 Query: 124 TPPYDGTLAKYYVLPEDFCYKLPENINLQEAAVMEPLSVAVHIVKQANVAPGQSVVVFGA 183 + G A+Y V+ ++LP+ + + + A +EP++V +H A G++V++ GA Sbjct: 111 SRSEGGN-AEYVVVKRANLFRLPDRMPIDDGAFIEPMTVGLHAFHLAQGCEGKNVIIIGA 169 Query: 184 GPVGLLCCAVARAFGSPKVIAVDIQKGRLEFAKKYAATAIFEPSKVSALENAERIVNEND 243 G +GLL AR G+ + A+DI RL AK AT +F ++S+ E + + E Sbjct: 170 GTIGLLALQCARELGAKSITAIDINPQRLALAKTLGATYVFNSKEMSSKE-IQTALEEIQ 228 Query: 244 LGRGADIVIDASGAEPSVHTGIHVLRPGGTYVQGGMGRNEITF---PIMAACTKELNVRG 300 + +V++ +G +V GI V P G +++T KEL + G Sbjct: 229 FDQ---LVLETAGTPQTVALGIEVAGPRAQLALVGTLHHDLTLLSATFGQILRKELTIVG 285 Query: 301 SFRYGSG-----DYKLAVNLVASGKVSVKELITGVVSFEDAEQAFHEVKAGKG 348 S+ SG +++ AV L+ ++ + LI + +AE EV+A G Sbjct: 286 SWMNYSGPWPGEEWQTAVRLLTEKRIQLVPLIAHI---GNAESFAREVQALNG 335 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: 274 Number of extensions: 14 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: 347 Length adjustment: 29 Effective length of query: 329 Effective length of database: 318 Effective search space: 104622 Effective search space used: 104622 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 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