Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate PP_3671 PP_3671 Oxidoreductase, aldo/keto reductase family
Query= BRENDA::P31867 (318 letters) >FitnessBrowser__Putida:PP_3671 Length = 274 Score = 137 bits (346), Expect = 2e-37 Identities = 99/309 (32%), Positives = 150/309 (48%), Gaps = 44/309 (14%) Query: 1 MPSIKLNSGYDMPAVGFGCWKVDVDTCSEQIYRAIKTGYRLFDGAEDYANEKLVGAGVKK 60 M + +G D+PA+G G W + C++ + +A+ GYR D A Y NE VG + Sbjct: 1 MQRLSTRTGLDLPAIGLGTWPMTGSECTQAVRQALDVGYRHIDTATAYENEAAVG----Q 56 Query: 61 AIDEGIVKREDLFLTSKLWNNYHHPDNVEKALNRTLSDLQVDYVDLFLIHFPVTFKFVPL 120 A+ + V RE + LT+K+W + P + ++L +L L + VDLF IH+P T Sbjct: 57 ALRDSDVPREQIHLTTKVWWDRLEPKAMRQSLEDSLRALGTEQVDLFHIHWPGT------ 110 Query: 121 EEKYPPGFYCGKGDNFDYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLLRGAT 180 D++ ++T AL GK R IGV+NFP LL ++ Sbjct: 111 ----------------DWDLARSIDTLVALR---DEGKARHIGVANFPLGLLRQVVETLG 151 Query: 181 IKPSVLQVEHHPYLQQPRLIEFAQSRGIAVTAYSSFGPQSFVELNQGRALNTSPLFENET 240 S +QVE+H L Q L++FA+ + +TAY+ L +G+A Sbjct: 152 APLSAIQVEYHVLLSQQPLLDFARGHDLLLTAYT--------PLARGQAA------AQPV 197 Query: 241 IKAIAAKHGKSPAQVLLRW-SSQRGIAIIPKSNTVPRLLENKDVNSFDLDEQDFADIAKL 299 I+AIA KHG P+QV L+W Q G+A IPK+++ L N + LD++D IA L Sbjct: 198 IQAIARKHGVLPSQVALKWLLDQDGVAAIPKASSRENQLANLAALTVPLDDEDRTAIAGL 257 Query: 300 DINLRFNDP 308 + R P Sbjct: 258 PKDQRVVSP 266 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: 217 Number of extensions: 10 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