Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate AO353_19655 AO353_19655 2,5-diketo-D-gluconic acid reductase
Query= BRENDA::C1K8Y9 (324 letters) >FitnessBrowser__pseudo3_N2E3:AO353_19655 Length = 267 Score = 140 bits (354), Expect = 3e-38 Identities = 102/306 (33%), Positives = 141/306 (46%), Gaps = 46/306 (15%) Query: 18 MPLVGFGCWKVNNETAADQIYNAIKTGYRLFDGAEDYGNEKEVGEGINRAIKEGLVKREE 77 +P G G +++ + D + ++ GYR D A+ Y NE +VG+ AI + REE Sbjct: 3 VPAFGLGTFRLQGQVVIDSVSTGLELGYRAIDTAQIYDNEADVGQ----AIAASGIAREE 58 Query: 78 LFITSKLWNNFHDPKNVETALNKTLSDLNLDYVDLFLIHFPIAFKFVPIEEKYPPGFYCG 137 LFITSK+W + +L +L L DY+DL LIH+P VP+ E + G Sbjct: 59 LFITSKIWIANFAKDQLIASLKDSLRKLQTDYLDLTLIHWPSPENQVPVHE------FMG 112 Query: 138 DGDNFHYEDVPLLDTWKALEKLVEAGKIKSIGISNFTGALIYDLIRGATIKP-AVLQIEH 196 AL + G + IG+SNFT L+ I A QIE Sbjct: 113 -----------------ALLEAKALGLTRQIGVSNFTVDLMQQAIDAVGADNIATNQIEL 155 Query: 197 HPYLQQPKLIEYVQKAGIAITGYSSFGPQSFLELESKRALNTPTLFEHETIKSIADKHGK 256 HPYLQ ++E+ Q GI IT Y + L L P I+ IA++H Sbjct: 156 HPYLQNRTVVEFAQSQGIQITSY--------MTLAYGEVLKDPV------IQQIAERHQA 201 Query: 257 SPAQVLLRWATQRNIAVIPKSNNPERLAQNLSVVDFDLTKDDLDNIAKLDIGLRFNDPW- 315 +PAQV L WA Q+ AVIP S L NL+ + L++ D+ IA L+ G R P Sbjct: 202 TPAQVTLAWAMQQGYAVIPSSTQRANLDSNLAARELTLSEADMTLIAGLERGQRLTSPKG 261 Query: 316 ---DWD 318 DWD Sbjct: 262 IAPDWD 267 Lambda K H 0.318 0.139 0.420 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: 206 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: 324 Length of database: 267 Length adjustment: 26 Effective length of query: 298 Effective length of database: 241 Effective search space: 71818 Effective search space used: 71818 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: 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