GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Escherichia coli BW25113

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 17613 b3553 putative dehydrogenase (VIMSS)

Query= BRENDA::O66939
         (334 letters)



>FitnessBrowser__Keio:17613
          Length = 324

 Score =  136 bits (342), Expect = 8e-37
 Identities = 85/255 (33%), Positives = 133/255 (52%), Gaps = 19/255 (7%)

Query: 52  DKLTEELLSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEHTFAMILT 111
           + +   LL KMP+L+   T SVG+D+ D+D    + IL+ H P    E+VA+   A++L+
Sbjct: 54  ENVNAALLEKMPKLRATSTISVGYDNFDVDALTARKILLMHTPTVLTETVADTLMALVLS 113

Query: 112 LVKRLKRIEDRVK--KLNFSQDSEILARELNRLTLGVIGTGRIGSRVAMYG-LAFGMKVL 168
             +R+  + +RVK  +   S   +    +++  TLG++G GRIG  +A      F M +L
Sbjct: 114 TARRVVEVAERVKAGEWTASIGPDWYGTDVHHKTLGIVGMGRIGMALAQRAHFGFNMPIL 173

Query: 169 CYDVVKREDLKEK-GCVYTSLDELLKESDVISLHVPYTKETHHMINEERISLMKDGVYLI 227
                  ++ +E+    Y  LD LL+ESD + L +P T ETHH+   E+ + MK     I
Sbjct: 174 YNARRHHKEAEERFNARYCDLDTLLQESDFVCLILPLTDETHHLFGAEQFAKMKSSAIFI 233

Query: 228 NTARGKVVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKNLKILELACKD 287
           N  RG VVD +AL  A Q+G+    GLDVFE E + +            +  +L +A   
Sbjct: 234 NAGRGPVVDENALIAALQKGEIHAAGLDVFEQEPLSV------------DSPLLSMA--- 278

Query: 288 NVIITPHIAYYTDKS 302
           NV+  PHI   T ++
Sbjct: 279 NVVAVPHIGSATHET 293


Lambda     K      H
   0.319    0.138    0.383 

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: 204
Number of extensions: 9
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: 334
Length of database: 324
Length adjustment: 28
Effective length of query: 306
Effective length of database: 296
Effective search space:    90576
Effective search space used:    90576
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