GapMind for Amino acid biosynthesis

 

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

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate AO356_03975 AO356_03975 phenylalanine 4-monooxygenase

Query= reanno::pseudo5_N2C3_1:AO356_03975
         (261 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_03975
          Length = 261

 Score =  541 bits (1394), Expect = e-159
 Identities = 261/261 (100%), Positives = 261/261 (100%)

Query: 1   MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI 60
           MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI
Sbjct: 1   MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI 60

Query: 61  PQLDEINKVLGQTTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120
           PQLDEINKVLGQTTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF
Sbjct: 61  PQLDEINKVLGQTTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120

Query: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYG 180
           HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYG
Sbjct: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYG 180

Query: 181 GGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIM 240
           GGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIM
Sbjct: 181 GGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIM 240

Query: 241 GMVKRGRELGLHAPKFPPKAA 261
           GMVKRGRELGLHAPKFPPKAA
Sbjct: 241 GMVKRGRELGLHAPKFPPKAA 261


Lambda     K      H
   0.323    0.141    0.439 

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: 425
Number of extensions: 13
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: 261
Length of database: 261
Length adjustment: 25
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate AO356_03975 AO356_03975 (phenylalanine 4-monooxygenase)
to HMM TIGR01267 (phhA: phenylalanine-4-hydroxylase (EC 1.14.16.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.6668.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6668.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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