Align Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase; Cmo2DD; D-xylose 1-dehydrogenase; D-xylose-NADP dehydrogenase; Dimeric dihydrodiol dehydrogenase; EC 1.3.1.20; EC 1.1.1.179 (characterized)
to candidate Synpcc7942_1665 Synpcc7942_1665 probable oxidoreductase
Query= SwissProt::Q9TQS6 (334 letters) >FitnessBrowser__SynE:Synpcc7942_1665 Length = 371 Score = 79.0 bits (193), Expect = 2e-19 Identities = 59/193 (30%), Positives = 90/193 (46%), Gaps = 7/193 (3%) Query: 3 LRWGIVSVGLISSDFTAVLQTLPRSEHQVVAVAARDLSRAKEFAQKHDIPKAYGSYEELA 62 LR ++ G S LQ SE V AV R RA A + IP AY ++L Sbjct: 10 LRVAVLGTGFGSKVHIPALQH--HSETTVQAVYHRQPDRAAAIAVQFGIPNAYSDLDQLL 67 Query: 63 KDPNVEVAYVGTQHPQHKAAVMLCLAAGKAVLCEKPMGVNAAEVREMVTEARSRGLFLME 122 DP +E + + H L+AGK+VL EKP +N E R + A S+GL + Sbjct: 68 ADPAIEAVTIASPPFLHYPMAWAALSAGKSVLLEKPTTLNVEEARALWKLASSQGLTVTL 127 Query: 123 AIWTRFFPASEALRSVLAQGTLGDLRVARAEF-GKNLTHVPRAVDW----AQAGGALLDL 177 RF PA + + +LA+G +G + + ++ + R +W +Q GGAL L Sbjct: 128 DFEYRFVPAWQYVAELLAEGVIGQPWLVKLDWLMSSRADASRPWNWYALRSQGGGALGAL 187 Query: 178 GIYCVQFISMVFG 190 G + +++ +FG Sbjct: 188 GSHSFDYLAWLFG 200 Lambda K H 0.320 0.134 0.401 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: 227 Number of extensions: 9 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: 334 Length of database: 371 Length adjustment: 29 Effective length of query: 305 Effective length of database: 342 Effective search space: 104310 Effective search space used: 104310 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