GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroC in Dinoroseobacter shibae DFL-12

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate 3609893 Dshi_3275 Chorismate synthase (RefSeq)

Query= SwissProt::P12008
         (361 letters)



>FitnessBrowser__Dino:3609893
          Length = 367

 Score =  406 bits (1043), Expect = e-118
 Identities = 209/360 (58%), Positives = 256/360 (71%), Gaps = 7/360 (1%)

Query: 1   MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60
           M+ NT G LFRVTT+GESHG ALG  VDG PPG+P+TE  LQ  LD+R+PG +++TTQRR
Sbjct: 1   MSFNTFGHLFRVTTWGESHGPALGATVDGCPPGVPITEEALQVWLDKRKPGQNKFTTQRR 60

Query: 61  EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120
           EPD V+ILSGVFEG +TG+ I L+I N DQRS+DY  I + FRPGHAD TY QKYG+RDY
Sbjct: 61  EPDAVEILSGVFEGQSTGSPIQLMIRNADQRSKDYGDIAEKFRPGHADITYWQKYGIRDY 120

Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKF-GIEIRGCLTQMGDIPLDIK--DWSQVEQNP 177
           RGGGRSSARETA RVAAG +A+  L      + I G +TQMG   +D    DW Q++QNP
Sbjct: 121 RGGGRSSARETAARVAAGGVARAALGALVPDLRITGYMTQMGPHGIDRARFDWEQIDQNP 180

Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237
           F+ PD    +     +  L+K G S+GA + V A GVP GLG P++ +LD D+A A+MSI
Sbjct: 181 FWTPDAAAAEDWAAYLDGLRKAGSSVGAVIEVTARGVPVGLGAPIYAKLDTDLAAAMMSI 240

Query: 238 NAVKGVEIGDGFDVVALRGSQNRDEITKDG----FQSNHAGGILGGISSGQQIIAHMALK 293
           NAVK VEIG+G    +L G  N DEI   G    + SNHAGGILGGIS+GQ ++   A+K
Sbjct: 241 NAVKAVEIGEGMAAASLTGEANADEIFMGGDGPEYSSNHAGGILGGISTGQDVVVRFAVK 300

Query: 294 PTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNAD 353
           PTSSI    +TI + G   E+ITKGRHDPCVGIRAVP+AEAM+A VL+DHLL  R Q  D
Sbjct: 301 PTSSILTTRQTITKSGAPAEIITKGRHDPCVGIRAVPVAEAMMACVLLDHLLLHRGQVGD 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: 448
Number of extensions: 18
Number of successful extensions: 3
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: 367
Length adjustment: 29
Effective length of query: 332
Effective length of database: 338
Effective search space:   112216
Effective search space used:   112216
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 3609893 Dshi_3275 (Chorismate synthase (RefSeq))
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.796.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.796.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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