Align D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) (characterized)
to candidate GFF3849 PGA1_78p00130 putative oxidoreductase, GFO/IDH/MOCA family
Query= BRENDA::D4GP30 (325 letters) >FitnessBrowser__Phaeo:GFF3849 Length = 374 Score = 73.9 bits (180), Expect = 6e-18 Identities = 66/220 (30%), Positives = 99/220 (45%), Gaps = 25/220 (11%) Query: 28 AAIASRDEARASAVADELGIPT--AYGSYEALLA-----DDSLDAVYIPLPNGLHADWVR 80 A S D ARASA A ELGI +Y S+ + +D +DAV I PN LHA Sbjct: 40 AGALSSDPARASASAAELGIDPDRSYASFAEMAEAEAAREDGIDAVAIVTPNHLHAGPSI 99 Query: 81 AAADRGLHVLCEKPLTASADETAAVFDYCEDAGVTLMEAFMYRFHPLTERAAELVA-SEL 139 A + G+HV+C+KPL AS E A+ D + Y +PL +A +VA +L Sbjct: 100 AFLNAGIHVICDKPLAASVAEAEAIKDAARSSSARFFLTHNYTGYPLLRQARAMVARGDL 159 Query: 140 GAVVSVTSNFSFRLPDGADDI-----------RIDPDLAG-GSVMDVGCYAVSAARLFLG 187 G + V + ++ D ++ R DP +G G++ D+G +A + A G Sbjct: 160 GRIRLVQAEYA---QDWLTNVIEQEGHKQAAWRTDPAQSGAGAIGDIGTHAFNIACFVSG 216 Query: 188 TPDRVYATTTDTRDCG--VDTRMSGVLEYDSGATARVESS 225 + + + G VD +L Y GA + +S Sbjct: 217 LAPQALSAELHSFGPGRQVDDNAHILLRYAEGARGMLWAS 256 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: 278 Number of extensions: 13 Number of successful extensions: 1 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: 374 Length adjustment: 29 Effective length of query: 296 Effective length of database: 345 Effective search space: 102120 Effective search space used: 102120 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: 49 (23.5 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