GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Dechlorosoma suillum PS

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate Dsui_3204 Dsui_3204 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__PS:Dsui_3204
          Length = 368

 Score =  474 bits (1221), Expect = e-138
 Identities = 234/360 (65%), Positives = 285/360 (79%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNT G LF VT+FGESHG A+GC+VDG PPG+ LTEAD+Q +LDRR+PGTSR+ TQRR
Sbjct: 1   MSGNTFGTLFTVTSFGESHGPAIGCVVDGCPPGLELTEADIQAELDRRKPGTSRHVTQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD V+ILSGVFEG TTGT IGLLI N DQRS+DY  I   FRPGHADY Y QKYG RDY
Sbjct: 61  EPDTVEILSGVFEGKTTGTPIGLLIRNQDQRSKDYGNIASTFRPGHADYGYTQKYGFRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETA+RVAAGAIA+K+L +++GI IRG ++Q+G I +   D + ++ N FF 
Sbjct: 121 RGGGRSSARETAVRVAAGAIARKWLQQRYGISIRGWMSQLGPIEIPFVDAAAIDGNAFFA 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P+   +  L+  M AL+K  DS+GAK+TV A+GVP G GEPV+DRLDA+IA+A+M INAV
Sbjct: 181 PNAAIVPELEAYMDALRKSLDSVGAKITVTATGVPPGWGEPVYDRLDAEIAYAMMGINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  +A +GS++ DE+T  GF SNHAGG+LGGIS+GQ I+ +MA+KPTSSI  
Sbjct: 241 KGVEIGAGFASIAQKGSEHGDEMTPAGFLSNHAGGVLGGISTGQDIVVNMAIKPTSSIAQ 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360
           P R+++  G  VE+ T+GRHDPCVGIRA PIAEAMLA+VLMDH LR RAQ  DV    PR
Sbjct: 301 PRRSVDVQGNAVEVATEGRHDPCVGIRATPIAEAMLALVLMDHALRHRAQCGDVVCATPR 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: 449
Number of extensions: 9
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: 361
Length of database: 368
Length adjustment: 29
Effective length of query: 332
Effective length of database: 339
Effective search space:   112548
Effective search space used:   112548
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 Dsui_3204 Dsui_3204 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.31346.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31346.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.