GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Dyella japonica UNC79MFTsu3.2

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate N515DRAFT_0360 N515DRAFT_0360 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::Q09PG8
         (367 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0360
          Length = 364

 Score =  530 bits (1364), Expect = e-155
 Identities = 257/354 (72%), Positives = 293/354 (82%), Gaps = 2/354 (0%)

Query: 16  VATFENPMGIDGFEFVEFASPEPE--KLHELFRNLGFVQVARHKTRPIYNYRQNDCTFLI 73
           V TFENPMGIDGFEFVEFA+P     +LHELF ++GF  V +HK RPI  YRQ    FL+
Sbjct: 11  VTTFENPMGIDGFEFVEFAAPAGRGAELHELFGSMGFTAVLKHKRRPITVYRQGGVNFLV 70

Query: 74  NEDPDSFAADFARVHGPSACGFAIRVNKLAEWVRVQALKNGAKSIADKETSKAVAAPVIE 133
           NEDPDSFAA+FA  HGP A GFAIR  + A  V  + L NG +++ DKE SKAV APV++
Sbjct: 71  NEDPDSFAAEFAAQHGPCAAGFAIRFKQPAAEVYAKVLANGGEAVGDKEASKAVDAPVVK 130

Query: 134 GIGGCMLYIVDRYDDKGTIHDPDWEWLPGAQMMPKGFGLTFIDHLTHNVYFGNMSKWADY 193
           GIG CMLY+VDRY DKG+I+D D+  +PG +  P GFGLTFIDHLTHN+YFGNM KW+DY
Sbjct: 131 GIGDCMLYLVDRYGDKGSIYDGDYAPIPGVEQNPAGFGLTFIDHLTHNLYFGNMQKWSDY 190

Query: 194 YERLFQFREIRYFDIKGAKTGLLSKAMTAPDGMVRIPLNESPDPKSQINEYLDQYRGEGI 253
           YERLF FREIRYFDIKGAKTGL+SKAMTAPDG+VRIPLNES DPKSQINEYLD Y GEGI
Sbjct: 191 YERLFNFREIRYFDIKGAKTGLVSKAMTAPDGIVRIPLNESSDPKSQINEYLDAYHGEGI 250

Query: 254 QHIACFTDDIYATVEAMRAHGIEFLDTPNAYYAVIDERIPNHGEDVARMKESRILIDADP 313
           QHIACFTD+IY TVEAMRA G+ FLDTP+ Y+ VID RIPNHGEDV R+  ++ILIDADP
Sbjct: 251 QHIACFTDNIYETVEAMRAKGVSFLDTPDTYFDVIDLRIPNHGEDVPRLARNKILIDADP 310

Query: 314 ETKKKLLLQIFTKNCVGPIFFEIIQRKGNTGFGEGNFQALFESIEREQMARGVL 367
           ETK++ LLQIFT+N +GPIFFEIIQRKGN GFGEGNFQALFESIER+QM RGVL
Sbjct: 311 ETKQRKLLQIFTQNNIGPIFFEIIQRKGNEGFGEGNFQALFESIERDQMRRGVL 364


Lambda     K      H
   0.321    0.138    0.421 

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: 616
Number of extensions: 28
Number of successful extensions: 2
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: 367
Length of database: 364
Length adjustment: 30
Effective length of query: 337
Effective length of database: 334
Effective search space:   112558
Effective search space used:   112558
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: 49 (23.5 bits)

Align candidate N515DRAFT_0360 N515DRAFT_0360 (4-hydroxyphenylpyruvate dioxygenase)
to HMM TIGR01263 (hppD: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.18583.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18583.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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