Align D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) (characterized)
to candidate 3609222 Dshi_2608 oxidoreductase domain protein (RefSeq)
Query= BRENDA::D4GP30 (325 letters) >FitnessBrowser__Dino:3609222 Length = 328 Score = 128 bits (321), Expect = 2e-34 Identities = 103/327 (31%), Positives = 143/327 (43%), Gaps = 14/327 (4%) Query: 1 MMFGILGTAGIGVKSVIPAVQASEHEA-AAIASRDEARAS---AVADELGIPTAYGSYEA 56 + +GILG A + + PA+ A+ AA+ASRD A+A+ A A L + T Y+A Sbjct: 5 LRWGILGAAKFAREQMGPAIHAARGATLAALASRDAAKAAPFRAFAPGLRVHT---DYDA 61 Query: 57 LLADDSLDAVYIPLPNGLHADWVRAAADRGLHVLCEKPLTASADETAAVFDYCEDAGVTL 116 LLAD +DAVYIPLP+ +H W A + G HVL EKPL +A E + G+ Sbjct: 62 LLADPEVDAVYIPLPHPMHVPWAMKALEAGKHVLAEKPLAMTAAEIDPLISRRNATGLHC 121 Query: 117 MEAFMYRFHPLTERAAELV-ASELGAVVSVTSNFSFRLPDGADDIRIDPDLAGGSVMDVG 175 EA+M HP +RA L+ +G +V V F++ +IR D GG + D+G Sbjct: 122 AEAYMIVHHPQWQRARALLREGAIGRLVHVAGIFTYDNRADPGNIRNAADQGGGGIPDIG 181 Query: 176 CYAVSAARLFLGTPDRVYATTTDTRDCGVDTRMSGVLEYDSGATARVESSFDTPETQYYR 235 Y R T + GVDT ++ V G TA +S Q Sbjct: 182 VYTYGCTRWMTEAEPEAITHADITWENGVDT-IARVSARFPGFTAHWVNSMRMAPFQDMV 240 Query: 236 VQTTDGRLEANPAFNVDPTAAAELTY-----ATDGRVVTETFDPTDSYRREVEAFARAVE 290 G L FN A + D V E F + Y +VEAF R V Sbjct: 241 FHGETGVLRLTAPFNAQVFGEARVELHRPGGGGDHTVTVERFPAANQYVAQVEAFGRTVR 300 Query: 291 TGETPRVDREESVSVMRTIDAIYESAE 317 G E++ IDA+Y +A+ Sbjct: 301 EGAEYPWSLEDARGTQAMIDAVYAAAK 327 Lambda K H 0.316 0.131 0.371 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: 11 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: 325 Length of database: 328 Length adjustment: 28 Effective length of query: 297 Effective length of database: 300 Effective search space: 89100 Effective search space used: 89100 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: 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