Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 7023067 Shewana3_0305 alcohol dehydrogenase (RefSeq)
Query= BRENDA::P22144 (363 letters) >FitnessBrowser__ANA3:7023067 Length = 358 Score = 97.4 bits (241), Expect = 5e-25 Identities = 88/305 (28%), Positives = 130/305 (42%), Gaps = 43/305 (14%) Query: 14 DISFETYDAPEISEPTDVLVQVKKTGICGSDIHFYAH-GRIGNF-----VLTK------P 61 +++ + D P+ + VLV+ GICGSDIH H + +F V+ + P Sbjct: 18 EVTLQQVDLPK-PQVGQVLVRSLACGICGSDIHITRHYSEVFSFYRKLGVMPEGVDDHVP 76 Query: 62 MVLGHESAGTVVQVGKGVT-SLKVGDNVAIEPGIPSRFSDEYKSGHYNLCPHMAFAATPN 120 ++LGHE VV+ G +L VG V P + S+ TP Sbjct: 77 VMLGHEFCAEVVEFGPQTQQTLAVGTRVTSVPILMSQNG-------------AGVGVTPG 123 Query: 121 SKEGEPNPPGTLCKYFKSPEDFLVKLPDHVSLELGALVEPLSVGVHASKLGSVAFGDYVA 180 G +YF E L+ +P+H+ E AL EPL+VG+HA G V D Sbjct: 124 VN-------GAYSEYFILDEALLMPVPEHLPPEAVALTEPLAVGLHAVNRGDVGVEDTAL 176 Query: 181 VFGAGPVGLLAAAVAKTFGAKGVIVVDIFDNKLKMAKDIGAATHTFNSKTGGSEELIKAF 240 V G GP+GL A + G + +I D+ KL++A++ G ATHT N G +E+ A+ Sbjct: 177 VVGCGPIGLAAISALHLRGVRNIIAADLQGEKLQLAREFG-ATHTVN--PGEQDEV--AY 231 Query: 241 GGNVPN----VVLECTGAEPCIKLGVDAIAPGGRFVQVGNAAGPVSFPITVFAMKELTLF 296 V V+ EC G I+ V V G + +KEL + Sbjct: 232 AAEVAEGHRVVIFECVGIHKLIEGFVKRAPAKATIVVTGIHTAEANINYAYATVKELDMR 291 Query: 297 GSFRY 301 S+ Y Sbjct: 292 FSYYY 296 Lambda K H 0.318 0.138 0.411 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: 297 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 363 Length of database: 358 Length adjustment: 29 Effective length of query: 334 Effective length of database: 329 Effective search space: 109886 Effective search space used: 109886 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 (21.7 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