Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate PP_0552 PP_0552 2,3-butanediol dehydrogenase
Query= SwissProt::Q9WYP3 (395 letters) >FitnessBrowser__Putida:PP_0552 Length = 362 Score = 144 bits (362), Expect = 5e-39 Identities = 115/360 (31%), Positives = 174/360 (48%), Gaps = 38/360 (10%) Query: 28 TWLGSKVWR-YPEVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGL 86 T + + VW ++RVE+VP P P + IKV CGICGSD+H G + P Sbjct: 7 THMRAAVWHGRHDIRVEQVPLPADPAPGWVQIKVDWCGICGSDLHEYVA---GPVFIPVE 63 Query: 87 TGFPVT-------LGHEFSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAE 139 P+T LGHEF G + + G + + +G+PV A+ CG C C Sbjct: 64 APHPLTGIQGQCILGHEFCGHIAKLGEGV------EGYAVGDPVAADACQHCGTCYYCTH 117 Query: 140 GFPNHCENLNELGFNVDGAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAY 199 G N CE L G +GAFAE V V A + L + + + AG+L+EP +V Sbjct: 118 GLYNICERLAFTGLMNNGAFAELVNVPANLLYRLPQ---GFPAE----AGALIEPLAVGM 170 Query: 200 NAVIVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADH 259 +AV + G G VV++G G IGL + K AGA++VI E S R+ AKE GA+ Sbjct: 171 HAV--KKAGSLLGQTVVVVGAGTIGLCTIMCAKAAGAAQVIALEMSSARKAKAKEAGANV 228 Query: 260 VIDPTKENFVEAVLDYTNGLGAKLFLEATGVPQLVWPQIEEVIWRARGINATVAIVARAD 319 V+DP++ + + + T GLGA + E G I+ + R G V I Sbjct: 229 VLDPSQCDALAEIRALTAGLGADVSFECIGNKHTAKLAIDTI--RKAGKCVLVGIFEE-- 284 Query: 320 AKIPLTGEVFQV--RRAQIVGSQGHSGHGTFPRVISLMASG-MDMTKIISKTVSMEEIPE 376 P F++ Q++G+ ++G F VI+ +A G +D+ +++ + +E+I E Sbjct: 285 ---PSEFNFFELVSTEKQVLGALAYNGE--FADVIAFIADGRLDIRPLVTGRIGLEQIVE 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: 384 Number of extensions: 22 Number of successful extensions: 4 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: 362 Length adjustment: 30 Effective length of query: 365 Effective length of database: 332 Effective search space: 121180 Effective search space used: 121180 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