Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate AZOBR_RS19710 AZOBR_RS19710 2 5-didehydrogluconate reductase
Query= BRENDA::P31867 (318 letters) >FitnessBrowser__azobra:AZOBR_RS19710 Length = 274 Score = 139 bits (350), Expect = 8e-38 Identities = 92/290 (31%), Positives = 147/290 (50%), Gaps = 44/290 (15%) Query: 8 SGYDMPAVGFGCWKVDVDTCSEQIYRAIKTGYRLFDGAEDYANEKLVGAGVKKAIDEGIV 67 +G +PA+GFG +++ + A+K G+R D A+ Y NE VG +K + + Sbjct: 7 NGASIPALGFGTFRMSGPDVLRMVPEALKLGFRHIDTAQIYGNESEVGEAIKASN----L 62 Query: 68 KREDLFLTSKLWNNYHHPDNVEKALNRTLSDLQVDYVDLFLIHFPVTFKFVPLEEKYPPG 127 R ++FLT+K+W + + D+ ++++ +L+ L+ DYVDL L+H+P Sbjct: 63 PRGEVFLTTKVWVSNYKADDFRRSVDESLAKLRTDYVDLLLLHWP--------------- 107 Query: 128 FYCGKGDNFDYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLLRGATIKPSVLQ 187 E VP+ E ++L + AGK R IGVSNF LL + +R + Q Sbjct: 108 ----------NEAVPLAEQIESLNAVRAAGKTRHIGVSNFNRTLLDESVRLSKAPIVTNQ 157 Query: 188 VEHHPYLQQPRLIEFAQSRGIAVTAYSSFGPQSFVELNQGRALNTSPLFENETIKAIAAK 247 +E+HPYL Q ++E A+ G ++TAY A+ +F++ + IAA+ Sbjct: 158 IEYHPYLDQSVMLEAARRHGQSITAY--------------YAMADGKVFKDPVLTDIAAR 203 Query: 248 HGKSPAQVLLRW-SSQRGIAIIPKSNTVPRLLENKDVNSFDLDEQDFADI 296 GKS AQV+LRW Q G+ + K+ R EN + F+L E D A I Sbjct: 204 LGKSAAQVVLRWLVQQEGVIALSKTVGEKRAAENLAIFDFELSEADMAAI 253 Lambda K H 0.320 0.139 0.423 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: 211 Number of extensions: 9 Number of successful extensions: 5 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: 318 Length of database: 274 Length adjustment: 26 Effective length of query: 292 Effective length of database: 248 Effective search space: 72416 Effective search space used: 72416 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: 48 (23.1 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