Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate GFF722 PGA1_c07370 putative short chain dehydrogenase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Phaeo:GFF722 Length = 256 Score = 217 bits (552), Expect = 2e-61 Identities = 117/252 (46%), Positives = 159/252 (63%), Gaps = 4/252 (1%) Query: 8 SAAAVYPSLKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSAD-G 66 S A++P LKG V +TGGGSGIGA + EGF RQGA V F + +++ VER+ A+ G Sbjct: 2 SDTAIFPDLKGASVFITGGGSGIGAALSEGFLRQGAKVAF--VGRSDATDFVERMEAETG 59 Query: 67 HKACFERVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVN 126 ++ F + D+TD+ +L+A I + + G LVNNAAND RHA ++ E +WD ++N Sbjct: 60 NRPLFIQCDITDIPALKAAIKQAAEAHGPITTLVNNAANDQRHATLDVDEEFWDWAQAIN 119 Query: 127 LKHIFFCAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLG 186 LK FF QAV+P M+A GGG+IVN SIS+ +G + Y T A I G+TRSLAR+ G Sbjct: 120 LKAYFFACQAVLPGMQAAGGGSIVNFTSISYMMGNNGYPAYTTANAGINGMTRSLAREFG 179 Query: 187 RDGIRATCVIPGNVRTPRQL-KWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDAR 245 D IR + PG V T +QL +W +PE A + QCL LAP+D+ LFLAS +R Sbjct: 180 PDRIRVNALAPGWVLTDKQLDQWATPEALAAHLERQCLKDHLAPQDIVGSTLFLASATSR 239 Query: 246 LVTGHSYFVDAG 257 +VTG + VD G Sbjct: 240 MVTGQTLVVDGG 251 Lambda K H 0.321 0.137 0.409 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: 170 Number of extensions: 9 Number of successful extensions: 3 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: 259 Length of database: 256 Length adjustment: 24 Effective length of query: 235 Effective length of database: 232 Effective search space: 54520 Effective search space used: 54520 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 (21.9 bits) S2: 47 (22.7 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