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Table 2 Tests on prion sup35 fragments

From: FISH Amyloid – a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids

Positive fragments

Classification result

w s

7–17 GNNQQNYQQY

+

0.34

16–26 YSQNGNQQQG

-

0.08

28–38 RYQGYQAYNA

+

0.21

43–53 GGYYQNYQGY

+

0.53

46–56 YQNYQGYSGY

+

0.53

52–62 YSGYQQGGYQ

+

0.16

55–65 YQQGGYQQYN

+

0.13

94–104 PQGGRGNYKN

-

0.09

103–113 NFNYNNNLQG

+

0.22

106–116 YNNNLQGYQA

+

0.17

109–119 NLQGYQAGFQ

+

0.17

127–137 NDFQKQQKQA

-

0.11

Negative fragments

  

67-76 AGYQQQYNPQ

+

0.17

70-79 QQQYNPQGGY

-

0.08

73-82 YNPQGGYQQY

-

0.06

76-85 QGGYQQYNPQ

+

0.13

79-88 YQQYNPQGGY

+

0.13

82-91 YNPQGGYQQQ

-

0.03

139-148 KPKKTLKLVS

-

0.09

142-151 KTLKLVSSSG

-

0.09

145-154 KLVSSSGIKL

-

0.12

148-157 SSSGIKLANA

-

0,12

151-160 GIKLANATKK

-

0,07

154-163 LANATKKVGT

-

0,07

157-166 ATKKVGTKPA

-

0,03

160-169 KVGTKPAESD

-

0,03

163-172 TKPAESDKKE

-

0,03

166-175 AESDKKEEEK

-

0.03

169-178 DKKEEEKSAE

-

0.03

172-181 EEEKSAETKE

-

0.03

175-184 KSAETKEPTK

-

0.06

178-187 ETKEPTKEPT

-

0.06

181-190 EPTKEPTKVE

-

0.06

184-193 KEPTKVEEPV

-

0.09

187-196 TKVEEPVKKE

-

0.09

190-199 EEPVKKEEKP

-

0.03

193-202 VKKEEKPVQT

-

0.03

196-205 EEKPVQTEEK

-

0.03

199-208 PVQTEEKTEE

-

0.11

202-211 TEEKTEEKSE

-

0.11

205-214 KTEEKSELPK

-

0.08

208-217 EKSELPKVED

-

0.08

211-220 ELPKVEDLKI

-

0.11

Sensitivity

0.75

 

Specificity

0.91

 
  1. Classification efficiency tested on fragments of prion sup35. The method was trained on Waltz dataset with a sliding window 5-residue long, classification coefficient was set to w l  = 0.13. Emphasized are windows recognized by the classification method as potentially the most positive (amyloidogenic) of the whole tested fragment; the fragments obtained the actual distance value w s (window of a greatest distance).