Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate Pf6N2E2_668 2,3-butanediol dehydrogenase, R-alcohol forming, (R)- and (S)-acetoin-specific (EC 1.1.1.4)
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_668 Length = 364 Score = 154 bits (389), Expect = 4e-42 Identities = 119/346 (34%), Positives = 169/346 (48%), Gaps = 37/346 (10%) Query: 39 EVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVT------ 92 ++RVE+VP P + I+V+ CGICGSD+H G + P P+T Sbjct: 21 DIRVEDVPLPVSPPAGWVQIRVQWCGICGSDLHEYVA---GPVFIPVDAPHPLTGIKGQC 77 Query: 93 -LGHEFSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLNEL 151 LGHEF G +VE G + F +GEPV A+ CG C C G N CENL Sbjct: 78 ILGHEFCGEIVELGAGV------EGFSVGEPVAADACQHCGTCYYCTHGLYNICENLAFT 131 Query: 152 GFNVDGAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAVIVRGGGIRP 211 G +GAFAE V V A + L D AG+L+EP +V +AV + G Sbjct: 132 GLMNNGAFAELVNVPANLLYKL-------PADFPAEAGALIEPLAVGMHAV--KKAGSLL 182 Query: 212 GDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVIDPTKENFVEA 271 G NVV++G G IGL + K AGA++VI E S R+ A E+GA HVIDP + + + Sbjct: 183 GQNVVVVGAGTIGLCTIMCAKAAGAAQVIALEMSGARKAKALEVGASHVIDPNECDALAE 242 Query: 272 VLDYTNGLGAKLFLEATGVPQLVWPQIEEVIWRARGINATVAIVARADAKIPLTGEVFQV 331 V T GLGA + E G I+ + R G V I P F++ Sbjct: 243 VRRLTGGLGADVSFECIGNKHTAKLAIDLI--RKAGKCVLVGIFEE-----PSQFNFFEL 295 Query: 332 --RRAQIVGSQGHSGHGTFPRVISLMASG-MDMTKIISKTVSMEEI 374 Q++G+ ++G F VI+ +A G +D++ +++ + +EEI Sbjct: 296 VSTEKQVLGALAYNGE--FADVIAFIADGRLDISPLVTGRIQLEEI 339 Lambda K H 0.319 0.138 0.418 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: 399 Number of extensions: 20 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: 395 Length of database: 364 Length adjustment: 30 Effective length of query: 365 Effective length of database: 334 Effective search space: 121910 Effective search space used: 121910 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: 50 (23.9 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