Align glycerol dehydrogenase (EC 1.1.1.6) (characterized)
to candidate Synpcc7942_1653 Synpcc7942_1653 glycerol dehydrogenase
Query= BRENDA::A0MLR7 (380 letters) >FitnessBrowser__SynE:Synpcc7942_1653 Length = 398 Score = 265 bits (676), Expect = 2e-75 Identities = 157/360 (43%), Positives = 211/360 (58%), Gaps = 5/360 (1%) Query: 16 RIIQSPGKYIQGADVINRLGEYLKPL-AERWLVVGDKFVLGFAQSTVEKSFKDAGLVVEI 74 R+ SP +YIQG V+ +G YL L A+R ++ + + + AG+ + Sbjct: 24 RVFISPQRYIQGRGVLRSVGRYLSLLQAKRAGLLMSQRSSRNEGDLLLAGLRSAGVDAVV 83 Query: 75 APFGGECSQNEIDRLRGIAETAQCGAILGIGGGKTLDTAKALAHFMGVPVAIAPTIASTD 134 + F GEC+ +EI + ++ GGGK +DT KA+A +G+PV + PT+AS D Sbjct: 84 STFQGECTTDEITAHTTAFSKERIDCVIAAGGGKCIDTGKAIAFRLGIPVVVVPTLASND 143 Query: 135 APCSALSVIYTDEGEFDRYLLLPNNPNMVIVDTKIVAGAPARLLAAGIGDALATWFEARA 194 APCSALSV+Y+ EG PN+P +V+VDT I+A AP R L AG+GDA+ATW+EA Sbjct: 144 APCSALSVLYSPEGISQGVEFYPNSPAIVVVDTDIIAAAPERYLVAGMGDAMATWYEASV 203 Query: 195 CSRS-GATTMAGGKCTQAALALAELCYNTLLEEGEKAMLAAEQHVVTPALERVIEANTYL 253 C R+ A T G + T AA A+ E+C +TL +EG A A V ALE V+EANT L Sbjct: 204 CLRNPAAVTTVGARPTLAACAIGEVCAHTLFQEGCAAAAAVASKTVNDALESVVEANTLL 263 Query: 254 SGVGFESGGLAAAHAVHNGLTAIPDAH-HYYHGEKVAFGTLTQLVLENAPVEEIETVAAL 312 SG+GFESGGLA AHAV TAIP +Y HGE VA GTL QL++E+ P +E VA Sbjct: 264 SGLGFESGGLAGAHAVAQSYTAIPHVRANYLHGEMVAMGTLAQLMMESRP-KEATRVAEF 322 Query: 313 SHAVGLPITLAQLDIKEDVPAKMRIVAEAACAEGETIHNMPGGATPDQVYAALLVADQYG 372 AVGLPI L QL + + IV+EA+ + NMP TP+ V +A+L A G Sbjct: 323 FAAVGLPIHLGQLSLSSSDTQALEIVSEASLG-FPFVGNMPMKITPEFVKSAILDAHHLG 381 Lambda K H 0.318 0.134 0.393 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: 398 Number of extensions: 22 Number of successful extensions: 6 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: 380 Length of database: 398 Length adjustment: 30 Effective length of query: 350 Effective length of database: 368 Effective search space: 128800 Effective search space used: 128800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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