GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydratase in Pseudomonas fluorescens FW300-N2E2

Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Pf6N2E2_2520 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)

Query= BRENDA::Q9SSE7
         (381 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2520
          Length = 364

 Score =  155 bits (393), Expect = 1e-42
 Identities = 100/280 (35%), Positives = 153/280 (54%), Gaps = 16/280 (5%)

Query: 99  VRVAYQGVRGAYSESAAEKAYPNCE-AVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSI 157
           ++VAY G  G ++++AA K + +   + P    D  F  V    V+  V+P+ENS  G++
Sbjct: 94  LKVAYLGPEGTFTQAAAMKHFGHAVISKPMAAIDEVFREVAAGAVNFGVVPVENSTEGAV 153

Query: 158 HRNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTK--LG 215
           +   D  L H++ I GEV+L + H LL       + + R+ SH Q+LAQC   L      
Sbjct: 154 NHTLDSFLEHDMVICGEVELRIHHHLLVGENTKTDSISRIYSHAQSLAQCRKWLDAHYPN 213

Query: 216 LVREAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAR 275
           + R AV   A AAK++  E   ++AA+A + AA +YGL  +A+ I+D  DN TRFLM+  
Sbjct: 214 VERVAVSSNAEAAKRVKGE--WNSAAIAGDMAAGLYGLTRLAEKIEDRPDNSTRFLMIGS 271

Query: 276 EPIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLK 335
           + + P  +   KTSI+ S+   PG L + L  F    I+LT+IE+RP R      SG   
Sbjct: 272 QEVPPTGDD--KTSIIVSMSNKPGALHELLVPFHDNGIDLTRIETRPSR------SG--- 320

Query: 336 YFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYP 375
            + Y+F++DF     D + +  L  + + A  L+VLGSYP
Sbjct: 321 KWTYVFFIDFVGHHRDPLVKGVLEKISQEAVALKVLGSYP 360


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: 264
Number of extensions: 11
Number of successful extensions: 4
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: 364
Length adjustment: 30
Effective length of query: 351
Effective length of database: 334
Effective search space:   117234
Effective search space used:   117234
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 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:

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