GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PAH in Pseudomonas putida KT2440

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate PP_4490 PP_4490 phenylalanine-4-hydroxylase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4394
         (261 letters)



>FitnessBrowser__Putida:PP_4490
          Length = 262

 Score =  493 bits (1268), Expect = e-144
 Identities = 233/261 (89%), Positives = 249/261 (95%)

Query: 1   MKQTQYVAREPDAQGFIDYPAEEHAVWNTLITRQLKVIEGRACQEYLDGIEKLGLPHDRI 60
           MKQTQYVAREPDA GFIDYP +EHAVWNTLITRQLKVIEGRACQEYLDGI++L LPHDRI
Sbjct: 1   MKQTQYVAREPDAHGFIDYPQQEHAVWNTLITRQLKVIEGRACQEYLDGIDQLKLPHDRI 60

Query: 61  PQLGEINKVLAETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120
           PQLGEINKVL  TTGWQVARVPALIPFQTFFELLASK+FPVATFIRT EELDYLQEPDIF
Sbjct: 61  PQLGEINKVLGATTGWQVARVPALIPFQTFFELLASKRFPVATFIRTPEELDYLQEPDIF 120

Query: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLKASKEERVYLARLYWMTIEFGLLDTPQGQRIYG 180
           HEIFGHCPLLTNPWFAEFTHTYGKLGL A+KE+RVYLARLYWMTIEFGL++T QG++IYG
Sbjct: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLAATKEQRVYLARLYWMTIEFGLMETAQGRKIYG 180

Query: 181 GGILSSPKETVYSLSNEPEHQAFDPLECMRTPYRIDILQPLYFVLPNLKRLFDLAHEDIM 240
           GGILSSPKETVYSLS+EPEHQAFDP+E MRTPYRIDILQP+YFVLPN+KRLFDLAHEDIM
Sbjct: 181 GGILSSPKETVYSLSDEPEHQAFDPIEAMRTPYRIDILQPVYFVLPNMKRLFDLAHEDIM 240

Query: 241 GMVKQAMQMGLHTPKFPPKAA 261
           GMV +AMQ+GLH PKFPPK A
Sbjct: 241 GMVHKAMQLGLHAPKFPPKVA 261


Lambda     K      H
   0.322    0.140    0.435 

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: 385
Number of extensions: 9
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: 262
Length adjustment: 25
Effective length of query: 236
Effective length of database: 237
Effective search space:    55932
Effective search space used:    55932
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate PP_4490 PP_4490 (phenylalanine-4-hydroxylase)
to HMM TIGR01267 (phhA: phenylalanine-4-hydroxylase (EC 1.14.16.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.25187.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25187.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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