Align Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; Ory2DD; EC 1.3.1.20; EC 1.1.1.179 (characterized)
to candidate Echvi_3375 Echvi_3375 Predicted dehydrogenases and related proteins
Query= SwissProt::Q9TV70 (329 letters) >FitnessBrowser__Cola:Echvi_3375 Length = 382 Score = 81.6 bits (200), Expect = 3e-20 Identities = 82/295 (27%), Positives = 125/295 (42%), Gaps = 46/295 (15%) Query: 1 VVSAGLIAGDFVTVLQALPRSEHQVVAVAARDLRRAEEFARTHGIPKAYGSYEELAKDPD 60 +V G I + L+ +P E V+A+ + AEE A+ GIP+A+ ++EE+ K P+ Sbjct: 9 IVGTGFIGPAHLEALRRIPNIE--VIALCEVNQELAEEKAKLLGIPQAF-TFEEMLKQPE 65 Query: 61 VEVAYIGTQHPQHKAAVLLFLAAGKAVLCEKPLGVNAAEVREMVAEARSRGLFLMEAIWT 120 +EV +I T + H L AGK V+CEKPL E +VA A+ +GL Sbjct: 66 IEVVHICTPNFLHYNQSKAALEAGKHVVCEKPLATKIDEAEALVALAKEKGLVNAVHFNL 125 Query: 121 RCFPAVDALKSLLAQGALGDLRVARAEFGENLTQVLRSVDW-------------AQAGGG 167 R +P V +K++ G LGD+ + ++ + +W A G Sbjct: 126 RYYPMVRQMKTMRENGELGDIYSIMGSYLQDWLYLNTDYNWRLEPDKSGDSRAIADIGSH 185 Query: 168 LLDLGIY---------CVQFISMVFGGQKPEK-ISAVGRR------YE---TGVDDTVTV 208 LLDL Y F ++ KP K I + YE +D TV Sbjct: 186 LLDLTEYVTGLKITEVMADFSTVHKTRLKPLKPIETYSGKMLQESDYEEVPINTEDHATV 245 Query: 209 LLQYPGGVHGSFTCS---ISSKLSNTCSVSGTKGIAQLLEPCWC---PTELVVNK 257 LL++ G GS T S K ++G+K + WC P E+ + K Sbjct: 246 LLRFDNGNKGSVTVSQVNAGRKNRLNIEIAGSKSNFE-----WCSERPNEMWIGK 295 Lambda K H 0.319 0.135 0.399 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: 254 Number of extensions: 7 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: 329 Length of database: 382 Length adjustment: 29 Effective length of query: 300 Effective length of database: 353 Effective search space: 105900 Effective search space used: 105900 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 (21.8 bits) S2: 49 (23.5 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