GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Burkholderia phytofirmans PsJN

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate BPHYT_RS13705 BPHYT_RS13705 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__BFirm:BPHYT_RS13705
          Length = 366

 Score =  482 bits (1240), Expect = e-141
 Identities = 234/360 (65%), Positives = 284/360 (78%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GNT+G LF VTTFGESHG A+GC++DG PPG+ L EAD+Q +LDRR+PGTSR+ TQR+
Sbjct: 1   MSGNTLGTLFTVTTFGESHGPAIGCVIDGCPPGMALNEADIQFELDRRKPGTSRHVTQRQ 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D+V+ILSGVFEG TTG  I LLI NTDQRS+DY  I D FRPGHADYTY QKYG+RDY
Sbjct: 61  EEDKVEILSGVFEGQTTGAPIALLIRNTDQRSKDYGNIADTFRPGHADYTYWQKYGIRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSAR TA  VAAGA+AKK+L EKFG EI G +  +G+I +   DW+ V +NPFF 
Sbjct: 121 RGGGRSSARLTAPTVAAGAVAKKWLREKFGTEIHGYMAALGEIDVPFVDWAHVRENPFFA 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           P+   +  L+  M AL+K+GDSIGA++ VVASGVP GLGEP+FDRLDADIAHA+M INAV
Sbjct: 181 PNAQIVPQLETYMDALRKDGDSIGARINVVASGVPVGLGEPLFDRLDADIAHAMMGINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GF  +A RGS + DE+T +GF  NHAGG+LGGIS+GQ +   +A+KPTSSI  
Sbjct: 241 KGVEIGAGFASIAQRGSVHGDELTPEGFVGNHAGGVLGGISTGQDVTVSIAIKPTSSIRT 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360
           P R+I++ G+ V + T GRHDPCVGIRA PIAE+MLA+VL+DH LR RAQ  DV    P+
Sbjct: 301 PRRSIDKAGQPVVVETFGRHDPCVGIRATPIAESMLALVLIDHALRHRAQCGDVAVSTPK 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: 442
Number of extensions: 11
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: 366
Length adjustment: 29
Effective length of query: 332
Effective length of database: 337
Effective search space:   111884
Effective search space used:   111884
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 BPHYT_RS13705 BPHYT_RS13705 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.15097.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15097.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.