GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Pseudomonas fluorescens FW300-N2E3

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate AO353_10670 AO353_10670 shikimate dehydrogenase

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10670
          Length = 273

 Score =  437 bits (1123), Expect = e-127
 Identities = 215/272 (79%), Positives = 244/272 (89%)

Query: 1   MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60
           MD+YVVFGNPIGHSKSPLIHRLFAEQT Q L+Y+TLLAPLD+FS CA  FF++G G NVT
Sbjct: 1   MDRYVVFGNPIGHSKSPLIHRLFAEQTAQKLDYSTLLAPLDDFSGCATEFFREGRGANVT 60

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFKEEA+RL +SLT RA+RAGAVNTLSKLADG+L GDNTDGAGLVRDLTVNAG  L GK
Sbjct: 61  VPFKEEAYRLANSLTERAQRAGAVNTLSKLADGSLLGDNTDGAGLVRDLTVNAGFSLRGK 120

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180
           RIL+LGAGGAVRG LEP+LA +P S++IANRT+EKAE LA  F +LGPV ASGF WL+EP
Sbjct: 121 RILLLGAGGAVRGALEPLLAEQPASVIIANRTLEKAELLAELFADLGPVSASGFDWLREP 180

Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240
           VD+IINATSASL+G++PPIA SL+E G+TVCYDMMYGKEPT FC+WA++ GAA  +DGLG
Sbjct: 181 VDLIINATSASLSGDVPPIASSLIEPGKTVCYDMMYGKEPTSFCRWASEHGAAVSMDGLG 240

Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272
           MLAEQAAEAFF+WRGVRPDTAPVLAELRRQLA
Sbjct: 241 MLAEQAAEAFFLWRGVRPDTAPVLAELRRQLA 272


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: 328
Number of extensions: 11
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: 274
Length of database: 273
Length adjustment: 25
Effective length of query: 249
Effective length of database: 248
Effective search space:    61752
Effective search space used:    61752
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 AO353_10670 AO353_10670 (shikimate dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.19149.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19149.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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