GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Dechlorosoma suillum PS

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate Dsui_0443 Dsui_0443 shikimate 5-dehydrogenase

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__PS:Dsui_0443
          Length = 271

 Score =  308 bits (788), Expect = 1e-88
 Identities = 170/270 (62%), Positives = 192/270 (71%), Gaps = 4/270 (1%)

Query: 2   DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNVT 60
           D+Y VFGNPIGHSKSPLIH LFA    QD+ Y  LLAPLD F+   R F   G  G NVT
Sbjct: 3   DRYAVFGNPIGHSKSPLIHSLFAVACAQDMSYEALLAPLDGFAAALRAFADGGGRGANVT 62

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFKEEAFRL DSLTPRA RAGAVNTL  L  G + GDNTDGAGLV+DL VN  + LAGK
Sbjct: 63  VPFKEEAFRLADSLTPRAARAGAVNTLV-LEGGRILGDNTDGAGLVQDLQVNQSLPLAGK 121

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ-E 179
            IL+LGAGGA RG L P+LA  P  L IANRT  KA  LAR+F +LGPV   G+  L  +
Sbjct: 122 AILLLGAGGASRGALAPLLAAGPCRLHIANRTAAKAADLARDFADLGPVSGGGYGELAGQ 181

Query: 180 PVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGL 239
             DV+INATSASLAGELPP+   +   G  + YDMMYG+  TPF  +A   GA  ++DGL
Sbjct: 182 GFDVVINATSASLAGELPPLPPGIFNGG-ALAYDMMYGRGETPFLAFARLEGATHLVDGL 240

Query: 240 GMLAEQAAEAFFIWRGVRPDTAPVLAELRR 269
           GML EQAAEAF +WRGVRP TAPVL  LR+
Sbjct: 241 GMLVEQAAEAFQLWRGVRPATAPVLDRLRQ 270


Lambda     K      H
   0.319    0.137    0.405 

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: 310
Number of extensions: 11
Number of successful extensions: 5
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: 274
Length of database: 271
Length adjustment: 25
Effective length of query: 249
Effective length of database: 246
Effective search space:    61254
Effective search space used:    61254
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate Dsui_0443 Dsui_0443 (shikimate 5-dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.28241.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28241.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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