GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Pseudomonas fluorescens FW300-N1B4

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Pf1N1B4_5003 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

Query= reanno::pseudo3_N2E3:AO353_26925
         (358 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003
          Length = 358

 Score =  712 bits (1838), Expect = 0.0
 Identities = 349/358 (97%), Positives = 355/358 (99%)

Query: 1   MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGQINLILN 60
           MADLYENPMGLMGFEFIE ASPTPNTLEPIF+IMGFTKVATHRSKDVHLYRQGQINLILN
Sbjct: 1   MADLYENPMGLMGFEFIEFASPTPNTLEPIFQIMGFTKVATHRSKDVHLYRQGQINLILN 60

Query: 61  NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120
           NEP+SVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMEL+LPAIKGI
Sbjct: 61  NEPNSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELHLPAIKGI 120

Query: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180
           GGAPLYLIDRFGEGSSIYDIDFVFIEGVDR+PVGAGLKIIDHLTHNVYRGRMAYWANFYE
Sbjct: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180

Query: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240
           KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ
Sbjct: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240

Query: 241 HVAFLSDDLIKTWDHLKKIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQARGILLDGSS 300
           HVAFLSDDLIKTWDHLK IGMRFMT PPDTYYEMLEGRLPNHGEPVNELQARGILLDGSS
Sbjct: 241 HVAFLSDDLIKTWDHLKSIGMRFMTPPPDTYYEMLEGRLPNHGEPVNELQARGILLDGSS 300

Query: 301 EAGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTE 358
           E+GDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLST+
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: 685
Number of extensions: 23
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 Pf1N1B4_5003 (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.6929.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6929.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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