Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate BWI76_RS24305 BWI76_RS24305 2,5-didehydrogluconate reductase A
Query= BRENDA::C1K8Y9 (324 letters) >FitnessBrowser__Koxy:BWI76_RS24305 Length = 275 Score = 184 bits (468), Expect = 2e-51 Identities = 116/313 (37%), Positives = 162/313 (51%), Gaps = 45/313 (14%) Query: 3 TTPTIPTIKLNSGYEMPLVGFGCWKVNNETAADQIYNAIKTGYRLFDGAEDYGNEKEVGE 62 T PT+ IKL+ G MP +G G WK NE I+ A++ GYR FD A Y NE Sbjct: 2 THPTV--IKLHDGNLMPQLGLGVWKAGNEEVVSAIHKALEVGYRSFDTAAVYQNET---- 55 Query: 63 GINRAIKEGLVKREELFITSKLWNNFHDPKNVETALNKTLSDLNLDYVDLFLIHFPIAFK 122 G+ A+ V R+ELF+T+KLWN+ D K + AL ++L L LDYVDL+LIH+P Sbjct: 56 GVGNALSSAGVPRDELFVTTKLWND--DQKQPKEALQESLKKLKLDYVDLYLIHWP---- 109 Query: 123 FVPIEEKYPPGFYCGDGDNFHYEDVPLLDTWKALEKLVEAGKIKSIGISNFTGALIYDLI 182 VP + +D WK+L +L + G KSIG+ NF + +I Sbjct: 110 -VPATNHF-------------------VDAWKSLIELQQQGLAKSIGVCNFQVHHLQKII 149 Query: 183 RGATIKPAVLQIEHHPYLQQPKLIEYVQKAGIAITGYSSFGPQSFLELESKRALNTPTLF 242 + P + QIE HP +QQ +L + I +S A +F Sbjct: 150 DETGVAPVINQIELHPLMQQRQLHAWNATHKIQTESWSPL------------AQGGEGVF 197 Query: 243 EHETIKSIADKHGKSPAQVLLRWATQRNIAVIPKSNNPERLAQNLSVVDFDLTKDDLDNI 302 + + I+ +ADK+GK+PAQ+++RW + VIPKS P R+A+N +V DF L KD+L I Sbjct: 198 DQKIIRQLADKYGKTPAQIVIRWHLDSGLVVIPKSVTPSRIAENFNVWDFRLDKDELSEI 257 Query: 303 AKLDIGLRFN-DP 314 KLD R DP Sbjct: 258 TKLDQNKRLGPDP 270 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: 273 Number of extensions: 13 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: 275 Length adjustment: 27 Effective length of query: 297 Effective length of database: 248 Effective search space: 73656 Effective search space used: 73656 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