GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Pseudomonas fluorescens FW300-N2E2

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Pf6N2E2_4497 N-acetylglutamate synthase (EC 2.3.1.1)

Query= BRENDA::Q9HTN2
         (301 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4497
          Length = 432

 Score =  111 bits (277), Expect = 3e-29
 Identities = 86/293 (29%), Positives = 145/293 (49%), Gaps = 24/293 (8%)

Query: 15  LSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVVVHGGGPQIGD 74
           L  A PYI      T ++   G+ +E          D+VL+ ++G+  V+VHG  PQI  
Sbjct: 8   LRHASPYINAHRDCTFIVMLPGDGVEHPNF-GNIVHDLVLLHSLGVRLVLVHGSRPQIET 66

Query: 75  LLKRLSIESHFIDGMRVTDAATMDVVEMVLG-------GQVNKDIVNLINRHGGSAIGLT 127
            L    +  H+  GMR+TDAAT++ V   +G        +++ D+ +  +   GS + + 
Sbjct: 67  RLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMAS--SPMQGSRLRVA 124

Query: 128 GKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAPIGV 187
                L+ A+ + V          E +D  H GEV  V+   +N L+    I +++P+G 
Sbjct: 125 S--GNLVTARPIGVL---------EGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPLGY 173

Query: 188 GSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIAD-G 246
              GE +N+  + VA + A  L A+KL+L  +  GL+ + G+++  L  +QV   I   G
Sbjct: 174 SPTGEIFNLACEDVATRAAIDLAADKLLLFGSEQGLIGEDGRLVRELRPQQVPAHIQRLG 233

Query: 247 TIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLISNRK 299
           + Y   L  +  A +A +GGV  +HI+      A+L E+FT  G GTL++  +
Sbjct: 234 SDYQAEL--LDAAAQACRGGVARSHIVSYVENGALLAELFTRDGSGTLVAQEQ 284


Lambda     K      H
   0.318    0.138    0.381 

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: 267
Number of extensions: 13
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: 301
Length of database: 432
Length adjustment: 29
Effective length of query: 272
Effective length of database: 403
Effective search space:   109616
Effective search space used:   109616
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: 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