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Output format
DESCRIPTION
For each input sequence the following is shown (see the example below):
- Header line, quoting the name and length of the sequence.
- Sequence, in one-letter code, as it was interpreted by the server.
- Annotation overview, showing the predictions residue by residue,
as follows:
| . (dot) |
neutral place-holder |
| s |
predicted to be within a signal peptide |
| P |
predicted to be followed by a propeptide cleavage site |
- Prediction score table, quoting the position, context and score
for each arginine (R) and lysine (K) residue in the sequence.
If the score is >0.5 the residue is predicted to be followed by
a propeptide cleavage site; the higher the score the more confident
the prediction.
- Graph, in GIF, illustrating the predictions.
For each arginine (R) and lysine (K) the prediction score
is plotted against the position in the sequence. If a signal peptide
cleavage site has been predicted it is also shown in the graph.
The example below shows the output for glial cell line-derived neurotrophic
factor precursor (ATF-1), taken from the
Swiss-Prot
entry
GDNF_HUMAN.
The signal peptide prediction is consistent with the database annotation.
Two propeptide cleavage sites are predicted; one of them (pos. 77-78) is
annotated in the database. The other prediction (pos. 168-169) is false.
EXAMPLE OUTPUT
##### ProP v.1.0b ProPeptide Cleavage Site Prediction #####
##### Furin-type cleavage site prediction (Arginine/Lysine residues) #####
211 GDNF_HUMAN
MKLWDVVAVCLVLLHTASAFPLPAGKRPPEAPAEDRSLGRRRAPFALSSDSNMPEDYPDQFDDVMDFIQATIKRLKRSPD 80
KQMAVLPRRERNRQAAAANPENSRGKGRRGQRGKNRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCDAAETTYDKIL 160
KNLSRNRRLVSDKVGQACCRPIAFDDDLSFLDDNLVYHILRKHSAKRCGCI 240
sssssssssssssssssss.........................................................P... 80
................................................................................ 160
.......P........................................... 240
Signal peptide cleavage site predicted: between pos. 19 and 20: ASA-FP
Propeptide cleavage sites predicted: Arg(R)/Lys(K): 2
Name Pos Context Score Pred
____________________________v_________________
GDNF_HUMAN 2 -----MK|LW 0.069 .
GDNF_HUMAN 26 FPLPAGK|RP 0.054 .
GDNF_HUMAN 27 PLPAGKR|PP 0.120 .
GDNF_HUMAN 36 EAPAEDR|SL 0.134 .
GDNF_HUMAN 40 EDRSLGR|RR 0.074 .
GDNF_HUMAN 41 DRSLGRR|RA 0.163 .
GDNF_HUMAN 42 RSLGRRR|AP 0.124 .
GDNF_HUMAN 73 FIQATIK|RL 0.059 .
GDNF_HUMAN 74 IQATIKR|LK 0.140 .
GDNF_HUMAN 76 ATIKRLK|RS 0.062 .
GDNF_HUMAN 77 TIKRLKR|SP 0.802 *ProP*
GDNF_HUMAN 81 LKRSPDK|QM 0.062 .
GDNF_HUMAN 88 QMAVLPR|RE 0.090 .
GDNF_HUMAN 89 MAVLPRR|ER 0.108 .
GDNF_HUMAN 91 VLPRRER|NR 0.146 .
GDNF_HUMAN 93 PRRERNR|QA 0.152 .
GDNF_HUMAN 104 ANPENSR|GK 0.088 .
GDNF_HUMAN 106 PENSRGK|GR 0.071 .
GDNF_HUMAN 108 NSRGKGR|RG 0.099 .
GDNF_HUMAN 109 SRGKGRR|GQ 0.254 .
GDNF_HUMAN 112 KGRRGQR|GK 0.251 .
GDNF_HUMAN 114 RRGQRGK|NR 0.091 .
GDNF_HUMAN 116 GQRGKNR|GC 0.095 .
GDNF_HUMAN 137 GLGYETK|EE 0.058 .
GDNF_HUMAN 143 KEELIFR|YC 0.112 .
GDNF_HUMAN 158 AETTYDK|IL 0.054 .
GDNF_HUMAN 161 TYDKILK|NL 0.067 .
GDNF_HUMAN 165 ILKNLSR|NR 0.072 .
GDNF_HUMAN 167 KNLSRNR|RL 0.070 .
GDNF_HUMAN 168 NLSRNRR|LV 0.767 *ProP*
GDNF_HUMAN 173 RRLVSDK|VG 0.064 .
GDNF_HUMAN 180 VGQACCR|PI 0.080 .
GDNF_HUMAN 201 LVYHILR|KH 0.093 .
GDNF_HUMAN 202 VYHILRK|HS 0.074 .
GDNF_HUMAN 206 LRKHSAK|RC 0.095 .
GDNF_HUMAN 207 RKHSAKR|CG 0.222 .
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