GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Synechococcus elongatus PCC 7942

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate Synpcc7942_0061 Synpcc7942_0061 CDP-glucose 4,6-dehydratase

Query= BRENDA::P9WN67
         (314 letters)



>FitnessBrowser__SynE:Synpcc7942_0061
          Length = 368

 Score = 59.7 bits (143), Expect = 1e-13
 Identities = 88/342 (25%), Positives = 137/342 (40%), Gaps = 39/342 (11%)

Query: 2   RALVTGAAGFIGSTLVDRLLADGHSVVGL-----DNFATGRATNLEHLADNSAHVFVEAD 56
           + L+TG  GF GS L   LL  G  V G         +   A +L +        F    
Sbjct: 10  QVLITGHTGFKGSWLTLWLLMQGADVWGYALPPESERSLFTALDLANQRQAGWGYFQYRL 69

Query: 57  IVTADLHAI---LEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIGTVRLAEAARQTGV 113
               D  A+   +EQ +PEVVFHLAAQ  VRRS ADP      NV+G+++L EA +    
Sbjct: 70  GEMNDAEALRQWVEQAQPEVVFHLAAQPLVRRSYADPLGTWQTNVLGSLQLLEALKSLQH 129

Query: 114 RKIVHTSSGGSIYGTPP-EYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIA 172
              +   +   +Y      Y   ET       PY+A K A E+ + ++R  +  D +H  
Sbjct: 130 PCAMVMVTTDKVYENREWVYGYRETDCLGGHDPYSASKAAMELAVASWRSSFCGDAAHQT 189

Query: 173 P---------ANVYGPRQDPHGEAGVVAIFAQAL--LSGKPTRVFGDGTNTRDYVFVDDV 221
           P          NV G      G+  V  I   A+  LS        +  +TR +  V + 
Sbjct: 190 PYLAIATARAGNVIG-----GGDWAVDRIVPDAVRSLSAGAAIAVRNSHSTRPWQHVLEP 244

Query: 222 VDAFVRVSADV------------GGGLRFNIGTGKET--SDRQLHSAVAAAVGGPDDPEF 267
           +  ++ ++  +                 FN G   E+  S ++L + V     G    + 
Sbjct: 245 LGGYLLLAQRLLEHQQSAEKTVNPFARAFNFGPAIESNRSVKELITTVLQHWPGQWVDQS 304

Query: 268 HPPRLGDLKRSCLDIGLAERVLGWRPQIELADGVRRTVEYFR 309
            P    +     L    A ++LGW+P+ +    V RT+ ++R
Sbjct: 305 DPTAPHEAGLLHLVSDQARQLLGWQPRWDFETTVSRTIHWYR 346


Lambda     K      H
   0.320    0.137    0.410 

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: 247
Number of extensions: 15
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 314
Length of database: 368
Length adjustment: 28
Effective length of query: 286
Effective length of database: 340
Effective search space:    97240
Effective search space used:    97240
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 (21.8 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