Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate GFF2310 Psest_2358 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__psRCH2:GFF2310 Length = 252 Score = 114 bits (286), Expect = 2e-30 Identities = 87/241 (36%), Positives = 121/241 (50%), Gaps = 18/241 (7%) Query: 18 GKRVLVTGGGSGIGAGIVEGFARQGADVTF-----FDIAGAESQLLVERLSADGHKACFE 72 G+ L+TG +GIG A +GA V D+A LVE+++A+G A Sbjct: 8 GQTALITGAATGIGRATALALAAEGARVWINHRDQHDLANQ----LVEQITANGGDAWAI 63 Query: 73 RVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFF 132 D++D A++ A+ I+ G D+LVNNA E +EA W L V+L ++ Sbjct: 64 EADVSDPAAVAAMF-ETIEAQGSLDLLVNNAGVILEKPFLETSEADWAMVLGVDLGGVYR 122 Query: 133 CAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRA 192 C + + M+ R GAIVN+ S LG V Y T KA + GLTRSLAR+ DGIR Sbjct: 123 CCRHALAQMQPRRSGAIVNVASDLGFLGREQYVAYCTAKAGVIGLTRSLAREFAADGIRV 182 Query: 193 TCVIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLA----PEDVAAMVLFLASDDARLVT 248 V PG + T SPE ++ A+ L +A PE+VAA ++FL S A T Sbjct: 183 NGVAPGPIAT----AMVSPEHMSDEWMAKELAIPMARLGTPEEVAAAIVFLLSPQASYFT 238 Query: 249 G 249 G Sbjct: 239 G 239 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: 162 Number of extensions: 11 Number of successful extensions: 5 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: 252 Length adjustment: 24 Effective length of query: 235 Effective length of database: 228 Effective search space: 53580 Effective search space used: 53580 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