Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate GFF42 HP15_42 short-chain dehydrogenase/reductase SDR
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Marino:GFF42 Length = 266 Score = 125 bits (314), Expect = 9e-34 Identities = 87/245 (35%), Positives = 127/245 (51%), Gaps = 3/245 (1%) Query: 16 LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVD 75 L+ K L+TG G GIG G+ F +QGA V +++ + + L A G KA F D Sbjct: 4 LENKVALITGAGGGIGEGVARYFVKQGAAVIIAELSEQLGEAVAADLRAQGGKALFCHTD 63 Query: 76 LTDVASLQAVIARLIKGAGGFDILVNNA-ANDDRHAIDEITEAYWDERLSVNLKHIFFCA 134 +++ +S++ +A + G D+LVNNA A ++E T+ + L+ + ++ Sbjct: 64 VSNKSSIENAVATAVDHFGSIDVLVNNAFAPTPNVKLEEKTDEMLTQTLNTTVWAAWWAM 123 Query: 135 QAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATC 194 +A P M RGGG+IVN SI +G Y T K+AI GLTRS A + GR IRA Sbjct: 124 KAAFPHMCERGGGSIVNFYSIDTEIGAWLHGDYNTAKSAILGLTRSAAAEWGRFNIRANA 183 Query: 195 VIPGNV-RTPRQLKWYSPEGEAEIVAAQCLDGRLAPE-DVAAMVLFLASDDARLVTGHSY 252 + P + T +L +P E A + L PE D+ +V FLAS+ +R VTG S Sbjct: 184 IAPTAMGATFHKLAAENPGFEERSAAMRPLGRCGEPEADIGPVVAFLASEMSRFVTGESI 243 Query: 253 FVDAG 257 VD G Sbjct: 244 HVDGG 248 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: 151 Number of extensions: 7 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: 266 Length adjustment: 25 Effective length of query: 234 Effective length of database: 241 Effective search space: 56394 Effective search space used: 56394 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 Apr 09 2024. 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