GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Sphingomonas koreensis DSMZ 15582

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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