GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Magnetospirillum magneticum AMB-1

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate WP_011386705.1 AMB_RS22045 acetylglutamate kinase

Query= curated2:A0RWW1
         (266 letters)



>NCBI__GCF_000009985.1:WP_011386705.1
          Length = 300

 Score =  114 bits (285), Expect = 2e-30
 Identities = 70/215 (32%), Positives = 118/215 (54%), Gaps = 12/215 (5%)

Query: 2   ITIKIGGSIVDS-----LHPSAIPDIKKAAAGGVVLVHGGGKEVTKVCEQLGKEPRFVTS 56
           + IK GG  ++S     L    +  +K+     VV VHGGG ++  + ++L      + +
Sbjct: 38  LVIKFGGHAMESDDLARLFARDVVLLKQVGINPVV-VHGGGPQIDAMLKRLD-----IQT 91

Query: 57  PGNIKSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNAVGLSGIDGGLIRAERKSRLV 116
           P     R+TD+ T E+  M+++G+INK IV  + + G  AVGLSG DG LIRA +  R  
Sbjct: 92  PRVDGLRFTDEATVEVVEMILAGKINKQIVSAINEAGGFAVGLSGKDGHLIRARKLRRTK 151

Query: 117 IVNERGRKQAIEGGYTGRITSVNSELLETLLGKGIVPVVSPIAMGNEYELLNVDGDRAAA 176
              +   ++ ++ G+ G    +N  +L+       +PV++P+ MG   E  N++ D AA 
Sbjct: 152 KDPDSNIEKVLDLGFVGEPAEINPHILDQFKKSDTIPVIAPVGMGGAGETYNINADTAAG 211

Query: 177 NIAGATKSERILFVTDVDGLM-MDEKLVSRLSAAE 210
            IAGAT ++R+L +TDV G++     L+  ++AA+
Sbjct: 212 AIAGATNAKRLLMLTDVAGVLDKSGNLIPEMTAAQ 246


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: 177
Number of extensions: 5
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: 300
Length adjustment: 26
Effective length of query: 240
Effective length of database: 274
Effective search space:    65760
Effective search space used:    65760
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.

Links

Downloads

Related tools

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