GapMind for Amino acid biosynthesis

 

Aligments for a candidate for aro-dehydratase in Echinicola vietnamensis KMM 6221, DSM 17526

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Echvi_0123 Echvi_0123 Prephenate dehydratase

Query= BRENDA::Q9SSE7
         (381 letters)



>lcl|FitnessBrowser__Cola:Echvi_0123 Echvi_0123 Prephenate
           dehydratase
          Length = 279

 Score =  142 bits (357), Expect = 1e-38
 Identities = 89/277 (32%), Positives = 146/277 (52%), Gaps = 12/277 (4%)

Query: 100 RVAYQGVRGAYSESAAEKAY-PNCEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIH 158
           +VA QG++G+Y    A   +  +   + C  F    +++     D  VL +ENS+ G+I 
Sbjct: 9   KVAIQGIKGSYHYQVALNQFGQDIHVIECLTFSDLVKSITSNDADIGVLALENSIAGAIL 68

Query: 159 RNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTKLGLVR 218
            NYDL+ R+NL ++GE  L + H L+   G +I+D+  V SHP AL QC+    +   ++
Sbjct: 69  PNYDLMDRNNLQVIGEFYLPISHQLMVLKGQSIDDITEVRSHPMALLQCKAFFEQYPQIK 128

Query: 219 EAVD-DTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAREP 277
              D DTA  AK+I+ ++L    A+A + AA+ YGL+I+A DIQ   +N+TRF ++    
Sbjct: 129 LIEDLDTASVAKEISEQHLQGVGAIAGKSAAEFYGLDILASDIQTIKNNITRFCIVKNAA 188

Query: 278 IIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLKYF 337
                    K SI  +++   G L K L   +  +++LTKI+S P+   P         +
Sbjct: 189 DAKPVIGFDKASIKVTIKNEQGSLAKVLTTMSAYRLDLTKIQSLPVIDQP---------W 239

Query: 338 DYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSY 374
            Y F++D      ++  Q AL+ L+     ++VLG Y
Sbjct: 240 HYAFFIDLLFENLEDY-QQALKELKANGHQIKVLGEY 275


Lambda     K      H
   0.319    0.134    0.384 

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: 211
Number of extensions: 15
Number of successful extensions: 2
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: 381
Length of database: 279
Length adjustment: 28
Effective length of query: 353
Effective length of database: 251
Effective search space:    88603
Effective search space used:    88603
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: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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