Align Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; Sus2DD; EC 1.3.1.20; EC 1.1.1.179 (characterized)
to candidate WP_009779681.1 MED217_RS06420 Gfo/Idh/MocA family oxidoreductase
Query= SwissProt::Q9TV69 (335 letters) >NCBI__GCF_000152985.1:WP_009779681.1 Length = 324 Score = 180 bits (456), Expect = 5e-50 Identities = 116/333 (34%), Positives = 177/333 (53%), Gaps = 19/333 (5%) Query: 3 LRWGIVSAGLISSDFTTVLRLLPRSEHQVVAVAARDLSRAKEFARKHDIPKAYGSYEELA 62 +RWGI+ G I+ F + + L+ SE V AVA+R +A F + K Y SYE+LA Sbjct: 4 IRWGILGLGKIAHSFASDVALVEGSE--VYAVASRSQEKADRFGATYSASKCYNSYEQLA 61 Query: 63 KDPNVEVAYIGTQHPQHKATVLLCLAAGKAVLCEKPMGVNAAEVREMVAEARSRGLFLME 122 KDPNV+ YI T H +H LLCL KAVLCEKP +N ++V EM+ A++ LME Sbjct: 62 KDPNVDAVYIATPHVRHHQDTLLCLKHKKAVLCEKPFAMNRSQVEEMITTAQANDTLLME 121 Query: 123 AIWTRFFPAVEALRSVLAQETLGDLRVVQANFGKSIANVP--RSVDWAQAGGSLLDLGIY 180 A+WTRF P + ++ LA G ++ + A+F P R + A GGSLLD+GIY Sbjct: 122 ALWTRFMPHFKFVKEELASGRYGAVKTLTADFCFEADFNPEGRLFNKALGGGSLLDIGIY 181 Query: 181 CLQFISMVYGGQKPEKISAVGRRYETGVDDTVSVLLQYPGGVQGSFTCSITSQLSNTVSV 240 + F ++ G KP+ A + +TGVD+ + + +Y G SI Q +T ++ Sbjct: 182 PI-FCALALLG-KPDSFEAKAKIGKTGVDEEIEMTFKYNSGTTAFLNSSIVKQTPSTATL 239 Query: 241 SGTKGMAQILDPCWCPTE---LVVKGEHKEFPLPSAPGEEFNYTNGMGMCYEAKHVRECL 297 G+ +L+ + T+ +++G E +F YT G G +E +H L Sbjct: 240 VCDNGIL-VLNSRFHQTDKITSILEGNKIE--------HDFAYT-GKGYYFEIEHFANLL 289 Query: 298 KKGLKESPMITLAESELLADILEEVRKAIGVTF 330 ++ KESP+++ S L +L+EVR I + + Sbjct: 290 RENQKESPLMSFEFSRQLISMLDEVRTRIDLHY 322 Lambda K H 0.319 0.134 0.397 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: 258 Number of extensions: 8 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: 335 Length of database: 324 Length adjustment: 28 Effective length of query: 307 Effective length of database: 296 Effective search space: 90872 Effective search space used: 90872 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 24 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