Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate GFF3147 PGA1_c31980 short chain dehydrogenase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Phaeo:GFF3147 Length = 253 Score = 116 bits (290), Expect = 5e-31 Identities = 84/251 (33%), Positives = 131/251 (52%), Gaps = 12/251 (4%) Query: 16 LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDI----AGAESQLLVERLSADGHKACF 71 L GK +VTGG SG GAGIV F +GA V DI A A + + E D +A Sbjct: 3 LAGKCAIVTGGASGFGAGIVTKFLTEGARVMIADINADAAAAAASDVCETYGPD--RAIA 60 Query: 72 ERVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHA-IDEITEAYWDERLSVNLKHI 130 + VD++D AS+ + + G DILVNNA +++++E +D ++VN+K + Sbjct: 61 QTVDVSDRASVDQMAQAALNHFGQIDILVNNAGVSHLPTPLEDVSEEDFDRVVAVNMKSV 120 Query: 131 FFCAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGI 190 + A+A+VP M++R GAI+N+ S + +L Y K + TR++A +L G+ Sbjct: 121 YLTARALVPHMKSRQSGAILNVASTAGVSPRPNLNWYNASKGWMITATRTMAVELAPAGV 180 Query: 191 RATCVIPGNVRTPRQLKWY----SPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARL 246 R + P TP LK + +PE A+ ++ + PED+ +L SD+A + Sbjct: 181 RVNAINPVAGETP-LLKTFMGEDTPEVRAKFLSTIPIGRFSTPEDMGNAACYLCSDEASM 239 Query: 247 VTGHSYFVDAG 257 VTG + VD G Sbjct: 240 VTGVALEVDGG 250 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: 144 Number of extensions: 9 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: 259 Length of database: 253 Length adjustment: 24 Effective length of query: 235 Effective length of database: 229 Effective search space: 53815 Effective search space used: 53815 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