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 CA265_RS12480 CA265_RS12480 oxidoreductase
Query= SwissProt::Q9TV69 (335 letters) >FitnessBrowser__Pedo557:CA265_RS12480 Length = 323 Score = 96.7 bits (239), Expect = 7e-25 Identities = 79/257 (30%), Positives = 127/257 (49%), Gaps = 18/257 (7%) Query: 3 LRWGIVSAGLISSDFTTVLR--LLPRSEH-QVVAVAARDLSRAKEFARKHDIPKAYGSYE 59 +RWGI+ G D T V + H ++VAV RD +A ++AR+H +PK Y Sbjct: 4 IRWGIIGCG----DVTEVKSGPAFNKVNHAKLVAVMRRDGEKAADYARRHQVPKWYDDAT 59 Query: 60 ELAKDPNVEVAYIGTQHPQHKATVLLCLAAGKAVLCEKPMGVNAAEVREMVAEARSRGLF 119 +L DP V YI T QH+A + L AGK V EKPM ++A + M A + Sbjct: 60 QLINDPEVNAIYIATPPLQHEAYTIEALKAGKPVYVEKPMTLDADAAQRMTDAANQLKVK 119 Query: 120 LMEAIWTRFFPAVEALRSVLAQETLGDLRVVQANFGKS--IANVPRSVD-W----AQAGG 172 L A + R P ++ +LA ++GD+R+V+ +S A + ++ D W A +GG Sbjct: 120 LSVAHYRRAQPMFLKVKELLAAHSIGDIRLVRLKMLQSPNPALIAKTADNWRINPAISGG 179 Query: 173 SLL-DLGIYCLQFISMVYGGQKPEKISAVGRRYETGVDDTVSVLLQYPGGV--QGSFTCS 229 L DL + L ++ +G K A ++ T VDD V+ + + G+ G++ S Sbjct: 180 GLFHDLAPHQLDLMTYYFGAVKNAIGIATRQQENTEVDDLVAGNILFENGIVFSGTWCFS 239 Query: 230 ITSQ-LSNTVSVSGTKG 245 + Q ++ + G+KG Sbjct: 240 VAPQDQADICVIYGSKG 256 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: 214 Number of extensions: 12 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: 335 Length of database: 323 Length adjustment: 28 Effective length of query: 307 Effective length of database: 295 Effective search space: 90565 Effective search space used: 90565 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