GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Escherichia coli BW25113

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate 16923 b2842 2-deoxy-D-gluconate 3-dehydrogenase (NCBI)

Query= metacyc::MONOMER-16231
         (254 letters)



>FitnessBrowser__Keio:16923
          Length = 253

 Score =  154 bits (390), Expect = 1e-42
 Identities = 88/246 (35%), Positives = 136/246 (55%), Gaps = 5/246 (2%)

Query: 4   LEGKTVLVTGASTGIGRAAAIGAAQHGAD-VAINYAHSDGPAQSCVAEIEALGQRAIAVK 62
           LEGK  +VTG  TG+G+  A+G AQ G D V IN      P ++ + ++ ALG+R +++ 
Sbjct: 8   LEGKVAVVTGCDTGLGQGMALGLAQAGCDIVGINIVE---PTET-IEQVTALGRRFLSLT 63

Query: 63  GDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFM 122
            D+         + +AV  FG +D++V+NAG+      L+      +    +N+   +FM
Sbjct: 64  ADLRKIDGIPALLDRAVAEFGHIDILVNNAGLIRREDALEFSEKDWDDVMNLNIKSVFFM 123

Query: 123 VQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRC 182
            QAAA+  + QG+GG I+ ++S+ +  GG     YT +K+GV  + +  A    KH I  
Sbjct: 124 SQAAAKHFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGVTRLMANEWAKHNINV 183

Query: 183 NSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242
           N++ PG + T   +   AD+++   +  R P GR G P DL GPIVFLAS  + YV G  
Sbjct: 184 NAIAPGYMATNNTQQLRADEQRSAEILDRIPAGRWGLPSDLMGPIVFLASSASDYVNGYT 243

Query: 243 LLVDGG 248
           + VDGG
Sbjct: 244 IAVDGG 249


Lambda     K      H
   0.318    0.133    0.379 

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: 118
Number of extensions: 2
Number of successful extensions: 1
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: 254
Length of database: 253
Length adjustment: 24
Effective length of query: 230
Effective length of database: 229
Effective search space:    52670
Effective search space used:    52670
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: 47 (22.7 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