GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Shewanella sp. ANA-3

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate 7025322 Shewana3_2482 4-hydroxyphenylpyruvate dioxygenase (RefSeq)

Query= reanno::MR1:201123
         (346 letters)



>FitnessBrowser__ANA3:7025322
          Length = 346

 Score =  684 bits (1764), Expect = 0.0
 Identities = 335/346 (96%), Positives = 341/346 (98%)

Query: 1   MASELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNK 60
           MASELNPLGLLGIEFTEFAS D+DFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLN 
Sbjct: 1   MASELNPLGLLGIEFTEFASPDSDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNN 60

Query: 61  QREGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDS 120
           +REGFSA+FAKSHGPAI SMGWRVEDASFAHRVAVERGAKA  DSAKDLPYPAIYGIGDS
Sbjct: 61  EREGFSAEFAKSHGPAISSMGWRVEDASFAHRVAVERGAKAVADSAKDLPYPAIYGIGDS 120

Query: 121 LIYFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFG 180
           LIYFIDTFGA+NNIYATDFEDLSEPVITQEKGF+EVDHLTNNVYKGTMEHWANFYKNIFG
Sbjct: 121 LIYFIDTFGADNNIYATDFEDLSEPVITQEKGFVEVDHLTNNVYKGTMEHWANFYKNIFG 180

Query: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240
           FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF
Sbjct: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240

Query: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLL 300
           RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENR+RIKHHQILVDGDESGYLL
Sbjct: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRERIKHHQILVDGDESGYLL 300

Query: 301 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346
           QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL
Sbjct: 301 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346


Lambda     K      H
   0.321    0.140    0.414 

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: 657
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: 346
Length of database: 346
Length adjustment: 29
Effective length of query: 317
Effective length of database: 317
Effective search space:   100489
Effective search space used:   100489
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 7025322 Shewana3_2482 (4-hydroxyphenylpyruvate dioxygenase (RefSeq))
to HMM TIGR01263 (hppD: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.18330.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18330.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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