GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Marinobacter adhaerens HP15

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate GFF1881 HP15_1838 chorismate synthase

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Marino:GFF1881
          Length = 364

 Score =  523 bits (1347), Expect = e-153
 Identities = 252/359 (70%), Positives = 301/359 (83%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+GN+ G+LF VT+FGESHG ALGCI+DG PPG+ L+EAD+Q DLDRR+PGTSR+TTQRR
Sbjct: 1   MSGNSFGKLFTVTSFGESHGPALGCIIDGCPPGLELSEADMQRDLDRRKPGTSRHTTQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           E D+V+ILSGVFEG TTGT IGLLIENTDQRS+DYS I + FRP HADYTY  KYG+RDY
Sbjct: 61  EADEVRILSGVFEGKTTGTPIGLLIENTDQRSKDYSKISEQFRPAHADYTYMHKYGVRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180
           RGGGRSSARETAMRVAAGA+A+K+L ++ GI IRG L+Q+G I  +  DW QV QNPFFC
Sbjct: 121 RGGGRSSARETAMRVAAGAVARKFLEQRLGIRIRGYLSQLGPIKAEKLDWDQVHQNPFFC 180

Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240
           PD DK+  ++  M AL+KEGDSIGA++ VVA GVP GLGEP+FDRLDAD+AHALMSINAV
Sbjct: 181 PDADKVPEMEAYMDALRKEGDSIGARINVVADGVPPGLGEPIFDRLDADLAHALMSINAV 240

Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300
           KGVEIG GFD +  +G+++RDE+T +GF SN+AGG+LGGISSGQ I+A +ALKPTSS+ +
Sbjct: 241 KGVEIGAGFDCIDQKGTEHRDEMTPEGFLSNNAGGVLGGISSGQPIVASIALKPTSSLRL 300

Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359
            GR+I+  G+  E+IT GRHDPCVGIRA PIAEAM+AIVLMDH LR R QNADV    P
Sbjct: 301 SGRSIDVNGDPCEVITTGRHDPCVGIRATPIAEAMMAIVLMDHYLRHRGQNADVSVSTP 359


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: 474
Number of extensions: 12
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: 364
Length adjustment: 29
Effective length of query: 332
Effective length of database: 335
Effective search space:   111220
Effective search space used:   111220
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 GFF1881 HP15_1838 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.32614.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32614.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.