GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Pseudomonas fluorescens FW300-N2C3

Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate AO356_13085 AO356_13085 N-acetylglutamate synthase

Query= curated2:A6VI50
         (294 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_13085
          Length = 432

 Score =  110 bits (274), Expect = 7e-29
 Identities = 88/286 (30%), Positives = 139/286 (48%), Gaps = 11/286 (3%)

Query: 10  LIEALPYICKFHDQKVLIKYGGHAMVNEQAKNWIAKDLVLLKYVGINPIVVHGGGPEINR 69
           L  A PYI    D   ++   G  + +    N I  DLVLL  +G+  ++VHG  P+I  
Sbjct: 8   LRHASPYINAHRDCTFIVMLPGDGVEHPNFGN-IVHDLVLLHSLGVRLVLVHGSRPQIET 66

Query: 70  AMEKMGKTPEFIHGLRVTDEETLEIVKMVLIGKINGDIVSKLELYGGKAVGLSGKSGQLI 129
            +   G TP + HG+R+TD  TLE V +  +G++   I ++L +     +  S   G  +
Sbjct: 67  RLAARGLTPHYHHGMRITDAATLECV-IDAVGQLRIAIEARLSM----DMASSPMQGSRL 121

Query: 130 KAKKKIQYLMKDSQKIE-VDLGMVGEVEHVDTKLIDILVEKRYIPVISPIGVDHQGNDLN 188
           +         +    +E VD    GEV  VD K I+ L+++R I ++SP+G    G   N
Sbjct: 122 RVASGNLVTARPIGVLEGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPLGYSPTGEIFN 181

Query: 189 LNADIAAGDIAGAMNAEKLIMVTDVDGIMDDIKDPSTLHRKLTISQIEGMIERGLITGGM 248
           L  +  A   A  + A+KL++     G+   I +   L R+L   Q+ G ++R L +   
Sbjct: 182 LACEDVATRAAIDLAADKLLLFGAEQGL---IGEDGRLVRELRPQQVPGHMQR-LGSDYQ 237

Query: 249 IPKIEACINALDKGVQSVHIVNGKTPHAVLLEIFTEDGVGTMVVRE 294
              ++A   A   GV   HIV+     A+L E+FT DG GT+V +E
Sbjct: 238 AELLDAAAQACRGGVARSHIVSYAEDGALLAELFTRDGSGTLVAQE 283


Lambda     K      H
   0.318    0.139    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: 276
Number of extensions: 9
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: 294
Length of database: 432
Length adjustment: 29
Effective length of query: 265
Effective length of database: 403
Effective search space:   106795
Effective search space used:   106795
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: 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