GapMind for Amino acid biosynthesis

 

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

Align Phosphoribosyl-AMP cyclohydrolase; PRA-CH; EC 3.5.4.19 (characterized)
to candidate PfGW456L13_302 Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19)

Query= SwissProt::O26347
         (138 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_302
          Length = 133

 Score =  124 bits (312), Expect = 4e-34
 Identities = 62/121 (51%), Positives = 80/121 (66%), Gaps = 3/121 (2%)

Query: 19  NGEDLIIAVAQDHETGEVLMVAYMNREALRRTLETGTAHYWSTSRGKLWLKGESSGHVQR 78
           + + L+ A+AQDH+TG VLM+A+MNREAL  T     A YWS SRGKLW KGE SGHVQ 
Sbjct: 11  DADGLVPAIAQDHKTGRVLMMAWMNREALELTAAENRAIYWSRSRGKLWRKGEESGHVQT 70

Query: 79  VKDVLVDCDGDAVVLKVEQEGG-ACHTGYRSCFYRSIDGDELKVREDAVKVFDPEEIYGD 137
           + ++ +DCD D ++L VEQ G  ACHTG +SCFYR  +  +    +  +K  DP  IY  
Sbjct: 71  LHEMRLDCDADVIILMVEQIGDIACHTGRQSCFYRVYENGDWTTVDPVLK--DPHAIYSA 128

Query: 138 G 138
           G
Sbjct: 129 G 129


Lambda     K      H
   0.318    0.137    0.410 

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: 101
Number of extensions: 5
Number of successful extensions: 2
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: 138
Length of database: 133
Length adjustment: 15
Effective length of query: 123
Effective length of database: 118
Effective search space:    14514
Effective search space used:    14514
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 (21.7 bits)
S2: 42 (20.8 bits)

Align candidate PfGW456L13_302 (Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19))
to HMM PF01502 (PRA-CH)

Software error:

../bin/blast/fastacmd -i /tmp/list.14126.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14126.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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