GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas fluorescens GW456-L13

Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate PfGW456L13_793 Acetylglutamate kinase (EC 2.7.2.8)

Query= BRENDA::Q0ASS9
         (441 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_793
          Length = 301

 Score =  110 bits (276), Expect = 5e-29
 Identities = 85/291 (29%), Positives = 138/291 (47%), Gaps = 28/291 (9%)

Query: 24  EIREYLHRFSGIDQERFAVIKVGGAVIQDD--LPGLASALAFLQTVGLTPVVVHGGGPQL 81
           E   Y+ R+ G    +  VIK GG  ++ +    G A  +  ++ VG+ PVVVHGGGPQ+
Sbjct: 17  EALPYIRRYVG----KTLVIKYGGNAMESEELKTGFARDIVLMKAVGINPVVVHGGGPQI 72

Query: 82  DAALEAADIPTERVDGLRVTRDEAIPIIRDTL-TQANLALVDAIRDAGGRAAAVPRGVFE 140
              L+   I +  VDG+RVT    + ++   L  Q N  +V+ I   GG A  +     +
Sbjct: 73  GDLLKRLSIESHFVDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGK--D 130

Query: 141 ADIVDADKL-----------------GRVGEPRHIHLDLVGSAARAGQAAILACLGETPD 183
           A+++ A KL                 G VGE   I+ DL+    +     ++A +G   +
Sbjct: 131 AELIRAKKLTVTRQTPEMTTPEIIDIGHVGEVVGINTDLLNLLVKGDFIPVIAPIGVGAN 190

Query: 184 GTLVNINADVAVRALVHALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGDLMQADWVN 243
           G   NINAD+    +  AL+  K++ LT   GL+D+ G +L+ +       DL+    + 
Sbjct: 191 GESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKSGTVLTGLT-TQQVDDLIADGTIY 249

Query: 244 GGMRLKLE-EIKRLLDDLPLSSSVSITRPSELARELFTHAGSGTLIRRGER 293
           GGM  K+   ++ +   +  S  +    P+ +  E+FT  G GTLI   +R
Sbjct: 250 GGMLPKIRCALEAVQGGVGSSLIIDGRVPNAILLEIFTDTGVGTLISNRKR 300


Lambda     K      H
   0.320    0.139    0.411 

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: 290
Number of extensions: 16
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: 441
Length of database: 301
Length adjustment: 29
Effective length of query: 412
Effective length of database: 272
Effective search space:   112064
Effective search space used:   112064
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