GapMind for Amino acid biosynthesis

 

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

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate N515DRAFT_0107 N515DRAFT_0107 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0107
          Length = 362

 Score =  477 bits (1227), Expect = e-139
 Identities = 233/360 (64%), Positives = 286/360 (79%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ N+ G++F VTTFGESHG A+GC++DG PPG+ + E++ ++DLDRR  G SR+T+QRR
Sbjct: 1   MSSNSFGKIFTVTTFGESHGPAIGCVIDGCPPGLAIDESEFRNDLDRRATGKSRHTSQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D V+ILSGV+EG TTGT I LLI NTDQRS+DY  I + FRPGHADY+Y QKYG+RD 
Sbjct: 61  EADDVEILSGVYEGRTTGTPIALLIRNTDQRSKDYGDIVNTFRPGHADYSYWQKYGIRDP 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARET MRVAA  IAKK+LAE+ G+ +RG L Q+G+I     DW+ VEQNPFF 
Sbjct: 121 RGGGRSSARETTMRVAAAVIAKKWLAERHGVRVRGYLAQLGEIAPQGFDWAAVEQNPFFW 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P   ++ AL++ M AL+K GDS+GA+V VVA GVP G GEP++ +LD D+A ALMSINAV
Sbjct: 181 PHAAQVPALEKAMDALRKSGDSVGARVNVVADGVPPGWGEPIYGKLDGDLAAALMSINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIGDGF  VA RGS++RDE++  GF SNHAGGILGGIS+GQ + A +ALKPTSSI +
Sbjct: 241 KGVEIGDGFAAVAQRGSEHRDEMSPAGFASNHAGGILGGISTGQAVTASIALKPTSSILI 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360
           PG ++N  GE VE++TKGRHDPCVGIRA PIAEAM+A+VLMDH LR RAQ  DV    PR
Sbjct: 301 PGHSVNLAGEPVEVVTKGRHDPCVGIRATPIAEAMMALVLMDHALRHRAQCGDVGEVSPR 360


Lambda     K      H
   0.319    0.138    0.404 

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: 439
Number of extensions: 11
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: 361
Length of database: 362
Length adjustment: 29
Effective length of query: 332
Effective length of database: 333
Effective search space:   110556
Effective search space used:   110556
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate N515DRAFT_0107 N515DRAFT_0107 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.1884.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1884.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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