GapMind for catabolism of small carbon sources

 

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

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate PfGW456L13_2935 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2935
         (358 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935
          Length = 358

 Score =  728 bits (1878), Expect = 0.0
 Identities = 358/358 (100%), Positives = 358/358 (100%)

Query: 1   MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60
           MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN
Sbjct: 1   MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60

Query: 61  NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120
           NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI
Sbjct: 61  NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120

Query: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180
           GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE
Sbjct: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180

Query: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240
           KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ
Sbjct: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240

Query: 241 HVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS 300
           HVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS
Sbjct: 241 HVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS 300

Query: 301 ESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD 358
           ESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD
Sbjct: 301 ESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD 358


Lambda     K      H
   0.321    0.141    0.419 

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: 678
Number of extensions: 21
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: 358
Length of database: 358
Length adjustment: 29
Effective length of query: 329
Effective length of database: 329
Effective search space:   108241
Effective search space used:   108241
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: 49 (23.5 bits)

Align candidate PfGW456L13_2935 (4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))
to HMM TIGR01263 (hppD: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.28336.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28336.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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