Align D-xylose 1-dehydrogenase (NADP(+)) 1; XDH 1; EC 1.1.1.179 (characterized)
to candidate CCNA_01283 CCNA_01283 NADP-dependent aldose oxidoreductase
Query= SwissProt::D4GP29 (390 letters) >FitnessBrowser__Caulo:CCNA_01283 Length = 398 Score = 169 bits (427), Expect = 2e-46 Identities = 113/340 (33%), Positives = 172/340 (50%), Gaps = 21/340 (6%) Query: 29 AMIGLGWWTRDEAIPAVEASEFCETTVVVSSSKEKAEG---ATALTESITHGLTYDEFHE 85 A++GLG++ +P E +VS + EK + + E TH +Y+ F Sbjct: 69 AILGLGYYATRIIMPRFAECEHSRLAALVSGTPEKLKTYGEQYGIPE--THRYSYETFDR 126 Query: 86 GVAADAYDAVYVVTPNGLHLPYVETAAELGKAVLCEKPLEASVERAEKLVAACDRADVPL 145 + D VYV+TPN LH P+ E AA GK V+CEKP+ +V E ++AAC +A L Sbjct: 127 IIDNPDVDIVYVITPNSLHRPFTERAARAGKHVMCEKPMANTVADCEAMIAACKKAGRKL 186 Query: 146 MVAYRMQTEPAVRRARELVEAGVIG---EPVFVHGHMSQRLLDEVVPDPDQWRLDPELSG 202 M+ YR + + A +LV G +G V HG + DP QWRL+ L+G Sbjct: 187 MIGYRSRFQAHNIEAIKLVRDGALGPVRTVVTDHGF--------TIGDPKQWRLNRALAG 238 Query: 203 GATVMDIGLYPLNTARFVLDADPVRVRATARVD--DEAFEAVGDEHVSFGVDFDDGTLAV 260 G ++MDIG+Y LN AR++ +PV V A D D F V ++ ++F + F G A Sbjct: 239 GGSLMDIGIYSLNAARYLTGEEPVAVNAVESTDRSDPRFGEV-EDIINFQLLFPSGATAN 297 Query: 261 CTASQSAYQLSHLRVTGTEGELEIEPA-FYNRQKRGFRLSWGDQSADYDFEQVNQMTEEF 319 C ++ S + RV+G +G +EI+PA Y Q +L + + NQ + + Sbjct: 298 CVSAYSV-NCNRYRVSGPKGWVEIDPATSYQGQAMRAQLGGPPAPREPAPQPKNQFSAQL 356 Query: 320 DYFASRLLSDSDPAPDGDHALVDMRAMDAIYAAAERGTDV 359 D+ + +L+ +P GD L D+R ++AIY AA G V Sbjct: 357 DHLSECILTGREPIVGGDDGLKDLRVIEAIYRAAREGRTV 396 Lambda K H 0.315 0.131 0.383 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: 344 Number of extensions: 12 Number of successful extensions: 4 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: 390 Length of database: 398 Length adjustment: 31 Effective length of query: 359 Effective length of database: 367 Effective search space: 131753 Effective search space used: 131753 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 (21.6 bits) S2: 50 (23.9 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