GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argX in Pseudomonas simiae WCS417

Align Glutamate--LysW ligase ArgX; EC 6.3.2.- (characterized)
to candidate GFF233 PS417_01180 ribosomal protein S6 modification protein

Query= SwissProt::Q970U6
         (282 letters)



>FitnessBrowser__WCS417:GFF233
          Length = 301

 Score = 88.6 bits (218), Expect = 2e-22
 Identities = 75/244 (30%), Positives = 121/244 (49%), Gaps = 13/244 (5%)

Query: 42  KALGRYDVAIIRPVSMYRALYSSAVL---EAAGVHTINSSDVINVCGDKILTYSKLYREG 98
           K L  +D A+I  +      Y  AVL   E  GV  +N S  I    DK+ +   L R G
Sbjct: 53  KPLEGFD-AVIPRIGASVTFYGCAVLRQFEMMGVFPLNESVAIARSRDKLRSLQLLSRRG 111

Query: 99  IPIPDSIIALSAEAALKAYEQ-RGFPLIDKPPIGSWGRLVSLIRDVFEGKTIIEHRELMG 157
           I +P +  A S +      +   G PL+ K   G+ G  V L       +++IE    MG
Sbjct: 112 IGLPVTGFAHSPDDIPDLIDMVNGAPLVIKVLEGTQGIGVVLCETATAAESVIE--AFMG 169

Query: 158 NSALKAHI-VQEYIQYKG-RDIRCIAIGEELLGCYARNIPPNEWRANVALGGTPSNIEVD 215
              LK +I VQEYI+  G  DIRC  +G++++    R   P E+R+N+  GG+ S I++ 
Sbjct: 170 ---LKQNIMVQEYIKEAGGADIRCFVVGDKVIAAMKRQAKPGEFRSNLHRGGSASLIKIT 226

Query: 216 EKLKETVVKAVSIVHGEFVSIDILEHPNKGYVVNELNDVPEFKGFMVATNINVAQKLVEY 275
            + + T ++A  ++      +DIL   N G +V E+N  P  +G    T  +VA  ++++
Sbjct: 227 PEERMTALRAAKVMGLSVAGVDIL-RSNHGPLVMEVNSSPGLEGIETTTGKDVAGIIIQH 285

Query: 276 IKEN 279
           +++N
Sbjct: 286 LEKN 289


Lambda     K      H
   0.319    0.137    0.392 

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: 184
Number of extensions: 10
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: 282
Length of database: 301
Length adjustment: 26
Effective length of query: 256
Effective length of database: 275
Effective search space:    70400
Effective search space used:    70400
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 (21.7 bits)
S2: 48 (23.1 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