Align glycerol dehydrogenase (EC 1.1.1.6) (characterized)
to candidate Synpcc7942_2285 Synpcc7942_2285 glycerol dehydrogenase
Query= BRENDA::B2ZPN8 (367 letters) >FitnessBrowser__SynE:Synpcc7942_2285 Length = 359 Score = 177 bits (450), Expect = 3e-49 Identities = 120/355 (33%), Positives = 180/355 (50%), Gaps = 25/355 (7%) Query: 12 IQGAGAIKRLGDYLKPLAERWLVVGDKFVLGFAEEMLRKSLADAGLAAEIAPFGGECSHN 71 ++G GA+ G + + +R LVVG ++ L ++ L +CS Sbjct: 2 LRGWGALSEAGSAIARVGQRPLVVGGDRARALVQDSLTAIASEQSLTLGWGSSLPDCSEA 61 Query: 72 EINRLRDIAGNAKCTAVLGIGGGKTLDTAKALAHFMNVPVAIAPTIASTDAPCSALSVIY 131 + RL+ A + +LG+GGGK LDTAK L H +++PV PT A+T A +AL+ +Y Sbjct: 62 VLARLQQAATEHQADCILGVGGGKALDTAKLLGHQLSLPVITVPTSAATCAAWTALANVY 121 Query: 132 TDEGEFDSYLMLPRNPNMVIVDTQIVAGAPARLLAAGIGDALATWFEARACSRSGATTMA 191 TD G + + L R P ++I+D +++A AP R LAAGIGDA+A W+EA S T+ Sbjct: 122 TDAGAWLYDVGLDRCPELLILDFELIAQAPPRTLAAGIGDAIAKWYEASVSSGHRQETL- 180 Query: 192 GGKCTQAALALAELCYNTLLEEGEKAMLAAEQHVVTPALER---VVEANTYLSGVGFESG 248 AA+ A + + L ++ A + P E+ VVEA L+GV G Sbjct: 181 ----VVAAVQQARVLRDLLFQKSAAA-------IAEPGGEQWYEVVEATVLLAGVIGGLG 229 Query: 249 G----LAAAHAIHNGMTAIPDAHHYYHGEKVAFGTLTQLVLEN------APVDEIETVAA 298 G AAHA+HNG+T +P H + HGEKVAFG L QL LE + + + Sbjct: 230 GAQCRTVAAHAVHNGLTHLPACHDWLHGEKVAFGILVQLRLEELQGTNPLAATARQQLLS 289 Query: 299 LCHSVGLPITLAQLDIKGDIPTKMRLVAEAACAEGETIHNMPGGVDSDQVYAALL 353 +GLP + + + ++ A ACA IH++P VD DQ+ AA++ Sbjct: 290 FYADLGLPRQWSDMGLASVSLADLQQAAILACAPESDIHHLPFAVDPDQLLAAMV 344 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: 366 Number of extensions: 16 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: 359 Length adjustment: 29 Effective length of query: 338 Effective length of database: 330 Effective search space: 111540 Effective search space used: 111540 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