Align glycerol dehydrogenase (EC 1.1.1.6) (characterized)
to candidate Ga0059261_2879 Ga0059261_2879 Glycerol dehydrogenase and related enzymes
Query= BRENDA::B2ZPN8 (367 letters) >FitnessBrowser__Korea:Ga0059261_2879 Length = 358 Score = 228 bits (582), Expect = 1e-64 Identities = 138/326 (42%), Positives = 184/326 (56%), Gaps = 4/326 (1%) Query: 1 MDRIIQSPGKYIQGAGAIKRLGDYLKPLAERWLVVGDKFVLGFAEEMLRKSLADAGLAAE 60 M RI P +Y+QG GAI LG + L +R L+V D VL F E L S A AG + Sbjct: 1 MIRIFGGPTRYVQGPGAIGELGTLTERLTKRPLLVVDADVLPFVEAQL--STAFAGRPSI 58 Query: 61 IAPFGGECSHNEINRLRDIAGNAKCTAVLGIGGGKTLDTAKALAHFMNVPVAIAPTIAST 120 F GE +H I+ L + AG+A C V+GIGGGK LD AK +A + +P P+IAS Sbjct: 59 TLAFRGEVTHAAIDLLVEQAGDADC--VIGIGGGKGLDAAKGVAFKLGLPFIAVPSIASN 116 Query: 121 DAPCSALSVIYTDEGEFDSYLMLPRNPNMVIVDTQIVAGAPARLLAAGIGDALATWFEAR 180 D+P IY DE + +P +P +V+ DTQ++A APAR L G+GDALA FEA Sbjct: 117 DSPTGRSMAIYNDEHVLVAIETIPDSPLLVVTDTQLIANAPARFLRTGMGDALAKKFEAE 176 Query: 181 ACSRSGATTMAGGKCTQAALALAELCYNTLLEEGEKAMLAAEQHVVTPALERVVEANTYL 240 GA+ G + + ALA+A+ CY TL E G AM AAE+H A E VVEAN + Sbjct: 177 RAVADGASNFFGTRQLRTALAIADACYQTLREHGVAAMAAAERHEPDEAFEAVVEANVLM 236 Query: 241 SGVGFESGGLAAAHAIHNGMTAIPDAHHYYHGEKVAFGTLTQLVLENAPVDEIETVAALC 300 +G+ +ESGGL+ AHA+ G+ A HG+ V + TL QL +E I V Sbjct: 237 AGLAWESGGLSYAHAVVRGLVKARGAASAPHGDHVGYATLVQLAIEGRDDGFILDVIGFN 296 Query: 301 HSVGLPITLAQLDIKGDIPTKMRLVA 326 SVGLP +LA+LD+ P ++ +A Sbjct: 297 RSVGLPASLAELDMGSPTPDEIAEIA 322 Lambda K H 0.319 0.134 0.395 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: 349 Number of extensions: 20 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: 367 Length of database: 358 Length adjustment: 29 Effective length of query: 338 Effective length of database: 329 Effective search space: 111202 Effective search space used: 111202 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