Align D-chiro-inositol 1-dehydrogenase (EC 1.1.1.369) (characterized)
to candidate Pf1N1B4_4388 Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
Query= BRENDA::Q9WYP5 (334 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4388 Length = 340 Score = 219 bits (557), Expect = 1e-61 Identities = 129/334 (38%), Positives = 194/334 (58%), Gaps = 8/334 (2%) Query: 1 MRIGVIGLGRIGTIHAENL-KMIDDAILYAISDVREDRLREMKEKLGVEKAYKDPHELIE 59 +R+G+IG GR+G+ H + I A L AI+D + + +LGV++ Y DP +L++ Sbjct: 7 IRLGLIGAGRMGSFHGLTAARHIPGACLAAIADPTPGQAARLAAELGVQRVYTDPQQLLD 66 Query: 60 DPNVDAVLVCSSTNTHSELVIACAKAKKHVFCEKPLSLNLADVDRMIEETKKADVILFTG 119 DP +DAVL+ + +H+ELVI+ A+A K VFCEKP+++ L + DR I A V L G Sbjct: 67 DPEIDAVLIAAPARSHAELVISAARAGKGVFCEKPMAITLDEADRAIAAAADARVPLQVG 126 Query: 120 FNRRFDRNFKKLKEAVENGTIGKPHVLRITSRDPAPPPLDYIRVSGG--IFLDMTIHDFD 177 FNRRF ++F+ + V G IG P +LR +RDPA L+ S IFL+ IHDFD Sbjct: 127 FNRRFAKSFRAAHQDVVAGRIGTPQLLRSLTRDPA---LNNPAASPQWVIFLETLIHDFD 183 Query: 178 MARYI-MGEEVEEVFADGSVLVDEEIGKAGDVDTAVVVLRFKSGALGVIDNSRRAVYGYD 236 RY+ G E EVF L+ + G +DTAVV +RF +GA+ + + +AVYGYD Sbjct: 184 TLRYLNPGAEAVEVFVMADALIAPDYKAKGFLDTAVVTIRFDNGAIATAEANFQAVYGYD 243 Query: 237 QRIEVFGSKGRIFADNVRETTVVLTDEQGDRGSRYLYFFLERYRDSYLEELKTFIKNVKS 296 R EVFGS G + +V E+ +V G + + RD+Y+ EL F+ +++ Sbjct: 244 VRGEVFGSAGMLTMGSVNESDLVRYLANGIQADTQ-RLDTDLLRDAYVAELNHFVDCLRT 302 Query: 297 GEPPAVSGEDGKMALLLGYAAKKSLEEKRSVKLE 330 GE P SGED + AL + A +S ++ + V+++ Sbjct: 303 GEKPLASGEDARAALAIARACIESFQQGKPVRVQ 336 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: 11 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: 334 Length of database: 340 Length adjustment: 28 Effective length of query: 306 Effective length of database: 312 Effective search space: 95472 Effective search space used: 95472 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 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