GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Pseudomonas fluorescens FW300-N1B4

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate Pf1N1B4_2121 Acetylglutamate kinase (EC 2.7.2.8)

Query= curated2:A0RWW1
         (266 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2121
          Length = 301

 Score =  128 bits (321), Expect = 2e-34
 Identities = 80/259 (30%), Positives = 142/259 (54%), Gaps = 16/259 (6%)

Query: 2   ITIKIGGSIVDS--LHPSAIPDIKKAAAGGV--VLVHGGGKEVTKVCEQLGKEPRFVTSP 57
           + IK GG+ ++S  L      DI    A G+  V+VHGGG ++  + ++L  E  F+   
Sbjct: 30  LVIKYGGNAMESEELKTGFARDIVLMKAVGINPVVVHGGGPQIGDLLKRLSIESHFIDG- 88

Query: 58  GNIKSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNAVGLSGIDGGLIRAERKSRLVI 117
                R TD +T ++  MV+ G++NK IV ++ +HG +A+GL+G D  LIRA++ +    
Sbjct: 89  ----MRVTDAQTMDVVEMVLGGQVNKDIVNLINRHGGSAIGLTGKDAELIRAKKLTVTRQ 144

Query: 118 VNERGRKQAIEGGYTGRITSVNSELLETLLGKGIVPVVSPIAMGNEYELLNVDGDRAAAN 177
             E  + + I+ G+ G +  +N++LL  L+    +PV++PI +G   E  N++ D  A  
Sbjct: 145 TPEMTQPEIIDIGHVGEVVGINTDLLNLLVKGDFIPVIAPIGVGANGESYNINADLVAGK 204

Query: 178 IAGATKSERILFVTDVDGLMMDEKLVSRLSAAEAEEIRPKIGP-----GMEKKVLAATEA 232
           +A A K+E+++ +T++ GLM  +K  + L+    +++   I       GM  K+  A EA
Sbjct: 205 VAEALKAEKLMLLTNIAGLM--DKSGTVLTGLTTQQVDDLIADGTIYGGMLPKIRCALEA 262

Query: 233 LKMGVREAIIARGSRENPV 251
           ++ GV  ++I  G   N +
Sbjct: 263 VQGGVGSSLIIDGRVPNAI 281


Lambda     K      H
   0.316    0.135    0.370 

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: 191
Number of extensions: 11
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: 266
Length of database: 301
Length adjustment: 26
Effective length of query: 240
Effective length of database: 275
Effective search space:    66000
Effective search space used:    66000
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 (21.6 bits)
S2: 47 (22.7 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