Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate CA265_RS00430 CA265_RS00430 2,5-diketo-D-gluconic acid reductase
Query= BRENDA::A0MTG4 (323 letters) >FitnessBrowser__Pedo557:CA265_RS00430 Length = 283 Score = 173 bits (439), Expect = 4e-48 Identities = 108/297 (36%), Positives = 160/297 (53%), Gaps = 44/297 (14%) Query: 10 KLNNGLEMPSIGFGCWKLGKSTAADQ-VYNAIKAGYRLFDGAEDYGNEQEVGEGVKRAID 68 KLNNG+EMP +GFG +++ ++ V +AI GYRL D A Y NE+ VG+ +K + Sbjct: 5 KLNNGIEMPLLGFGVFQVTDLAECERSVLDAIDTGYRLIDTAASYMNEEAVGQAIKNSH- 63 Query: 69 EGIVTREEIFLTSKLWNNYHDPKNVETALNKTLKDLKVDYVDLFLIHFPIAFKFVPIEEK 128 V RE +F+T+KLW + N + A +LK LK+DY+DL+LIH P Sbjct: 64 ---VPREALFVTTKLWIQSNGYTNTKKAFEASLKKLKLDYLDLYLIHQPY---------- 110 Query: 129 YPPGFYCGDGDNFVYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLFRGATIKP 188 GD VY + W+A+E+L K GK+R+IGVSNF L DL I P Sbjct: 111 ---------GD--VYGE------WRAMEELYKEGKVRAIGVSNFHPDRLADLIIHNEITP 153 Query: 189 AVLQVEHHPYLQQPKLIEYAQKVGITVTAYSSFGPQSFVEMNQGRALNTPTLFEHDVIKA 248 AV Q+E HP+ QQ + + + + ++ F A +F +++ A Sbjct: 154 AVNQIETHPFHQQLDTQRFLNENKVQIESWGPF------------AEGKHNIFNDELLLA 201 Query: 249 IAAKHNKVPAEVLLRWSAQRGIAVIPKSNLPERLVQNRSFNDFELTKEDFEEISKLD 305 IA+++NK A+V+LRW QRG+ IPKS ER+ +N + DF+L+ +D I +D Sbjct: 202 IASQYNKSVAQVILRWLIQRGVVAIPKSVRKERMAENLNVFDFKLSDDDMNSIKSMD 258 Lambda K H 0.319 0.139 0.422 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: 214 Number of extensions: 11 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: 323 Length of database: 283 Length adjustment: 27 Effective length of query: 296 Effective length of database: 256 Effective search space: 75776 Effective search space used: 75776 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: 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