Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate AZOBR_RS16515 AZOBR_RS16515 S-(hydroxymethyl)glutathione dehydrogenase
Query= BRENDA::S6BFC0 (363 letters) >FitnessBrowser__azobra:AZOBR_RS16515 Length = 372 Score = 100 bits (248), Expect = 8e-26 Identities = 108/361 (29%), Positives = 155/361 (42%), Gaps = 47/361 (13%) Query: 24 EDRPVPVAGP--GQVIVNIKATGICGSDVHYWTHGRIGHFVCNGPMVLGHESAGIVTSLG 81 E V VA P G+V+V I ATG+C +D Y G V P +LGHE AGIV +G Sbjct: 17 EIEEVEVAAPRQGEVLVRIVATGVCHTDA-YTLSGMDSEGVF--PAILGHEGAGIVEEVG 73 Query: 82 EGVIDLKVGDRVALEPGVPCGRCEMCKIGKYNLCPDMAFAATPPY----DGTLCDYYRHS 137 GV ++VGD V CG+C+ C GK NLC A AT DGT + Sbjct: 74 PGVTSVQVGDHVIPLYTPECGKCKFCLSGKTNLC--QAIRATQGKGLMPDGTSRFTAKGQ 131 Query: 138 ADFCY------------------KLPDNVSLEEGALIE-PLSVGIHAARR-GEVRLGDRV 177 F Y K+ LE+ L+ ++ G+ A R +V G V Sbjct: 132 PVFHYMGTSTFSEYTVLPEIAVAKINKAAPLEKVCLLGCGVTTGMGAVRNTAKVEPGSTV 191 Query: 178 FVFGAGPVGLLTAAAARAAGASHITMADISESRLKFAKSYIADETVHMTSKPPRDVDTNE 237 +FG G +GL A A AS I DI+ + + AK A + V+ P+D D Sbjct: 192 AIFGLGGIGLSAIIGAVMAKASRIIGIDINPDKFEIAKQLGATDVVN-----PKDYD--- 243 Query: 238 FAKAEAEKLFQSGITPANVVFDCTG-VEVCVQMSVYLVKNNGKIILVGMGASVQSISVAD 296 + E L + + F+C G V+V K G+ +++G+ + + IS Sbjct: 244 --RPIQEVLVEMTDGGVDYSFECIGNVKVMRAALECCHKGWGESVIIGVAGAGEEISTRP 301 Query: 297 ---VSAR--EVDVRGVMRYCNTYPTAIEVLASEKVDLKSLITHRYKFEDSIKAFQHVKEG 351 V+ R G +R + P +E + +L + ITH ED KAF + EG Sbjct: 302 FQLVTGRVWRGSAFGGVRGRSELPDYVERYLKGEFELDTFITHTMGLEDINKAFDLMHEG 361 Query: 352 R 352 + Sbjct: 362 K 362 Lambda K H 0.319 0.136 0.405 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: 315 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 363 Length of database: 372 Length adjustment: 30 Effective length of query: 333 Effective length of database: 342 Effective search space: 113886 Effective search space used: 113886 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 (21.8 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