Align D-chiro-inositol 1-dehydrogenase (EC 1.1.1.369) (characterized)
to candidate WP_037154101.1 RHSP_RS23475 Gfo/Idh/MocA family oxidoreductase
Query= BRENDA::Q9WYP5 (334 letters) >NCBI__GCF_000359745.1:WP_037154101.1 Length = 339 Score = 197 bits (502), Expect = 2e-55 Identities = 117/334 (35%), Positives = 191/334 (57%), Gaps = 5/334 (1%) Query: 1 MRIGVIGLGRIGTIHAENL-KMIDDAILYAISDVREDRLREMKEKLGVEKAYKDPHELIE 59 + +G+IG GRIG+ H E + + + DA L AI+D ++ +KLG + +Y D +L+ Sbjct: 7 VNVGLIGAGRIGSFHGETIARRLVDAELVAIADPAPGAAAKLADKLGADTSYTDVADLLA 66 Query: 60 DPNVDAVLVCSSTNTHSELVIACAKAKKHVFCEKPLSLNLADVDRMIEETKKADVILFTG 119 P +DAV++ + HS +V+ A+A K +FCEKP++L L D DR I + A V L G Sbjct: 67 HPGLDAVIIATPARFHSNIVVQAAEAGKAIFCEKPMALTLEDADRAIAAARSAGVPLQVG 126 Query: 120 FNRRFDRNFKKLKEAVENGTIGKPHVLRITSRDPAPPPLDYIRVS-GGIFLDMTIHDFDM 178 FNRR+D+ F + + A++ G +G P ++R +RDP P D R+ IF + IHDFD Sbjct: 127 FNRRWDQAFAEGRAAIDAGKVGAPQLIRSLTRDPGPFGADPDRIPLWTIFYETLIHDFDT 186 Query: 179 ARYI-MGEEVEEVFADGSVLVDEEIGKAGDVDTAVVVLRFKSGALGVIDNSRRAVYGYDQ 237 ++ G + EVFA LV + + G +DTAVV +RF +G++ V + + A+YGYD Sbjct: 187 LLWLNPGAKPVEVFAMADALVRPDAREKGFLDTAVVNIRFDNGSIAVAEANFSALYGYDI 246 Query: 238 RIEVFGSKGRIFADNVRETTVVLTDEQGDRGSRYLYFFLERYRDSYLEELKTFIKNVKSG 297 R EVFGS G + +VR +++ D+ G + + + +Y +L +F+ V+ G Sbjct: 247 RGEVFGSGGMVTMGDVRRSSMTRFDKDGVSNDTWRR-DTDHFIHAYTAQLASFVNAVRDG 305 Query: 298 E-PPAVSGEDGKMALLLGYAAKKSLEEKRSVKLE 330 +G D + AL + A+ +S+ +K+ V L+ Sbjct: 306 ALKDGPTGLDARNALAIALASIQSVSKKQPVILK 339 Lambda K H 0.319 0.139 0.390 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: 252 Number of extensions: 12 Number of successful extensions: 3 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: 339 Length adjustment: 28 Effective length of query: 306 Effective length of database: 311 Effective search space: 95166 Effective search space used: 95166 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 (21.7 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