Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 350543 BT1015 putative oxidoreductase (NCBI ptt file)
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Btheta:350543 Length = 295 Score = 97.8 bits (242), Expect = 2e-25 Identities = 74/247 (29%), Positives = 118/247 (47%), Gaps = 15/247 (6%) Query: 15 SLKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERV 74 SLK KR+ VTGG GIG IVE F + G V F DI Q +A A F V Sbjct: 51 SLK-KRIFVTGGAEGIGRAIVEAFCKDGHQVAFCDINAVSGQQ-----TARDTGAIFHPV 104 Query: 75 DLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCA 134 D++D +L++ + +++ DI++NN +I E + +D+ LSVNL+ +F + Sbjct: 105 DVSDKEALESCMQQILDEWKDIDIVINNVGISKFSSITETSVEDFDKILSVNLRPVFITS 164 Query: 135 QAVVPAMRARGG----GAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGI 190 + + +A+ G I+N+ S + + Y K I LT +LA L I Sbjct: 165 RLLAIHRKAQSDSNPYGRIINICSTRYLMSEPGSEGYAASKGGIYSLTHALALSLSEWNI 224 Query: 191 RATCVIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARLVTGH 250 + PG ++T + PE ++ + + G+ PED+A M LFL D+ + G Sbjct: 225 TVNSIAPGWIQT-QNYDQLRPEDHSQHPSRRV--GK--PEDIARMCLFLCRDENDFINGE 279 Query: 251 SYFVDAG 257 + +D G Sbjct: 280 NITIDGG 286 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: 159 Number of extensions: 12 Number of successful extensions: 2 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: 295 Length adjustment: 25 Effective length of query: 234 Effective length of database: 270 Effective search space: 63180 Effective search space used: 63180 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