PredictProtein - [Output Example]

PHD predictions for fragment of prio_human

Different levels of data:

PHD brief
PHD normal
PHD detail

PHDsec summary overall your protein can be classified as:
mixed given the following classes:
- 'all-alpha': %H > 45% AND %E < 5%
- 'all-beta': %H < 5% AND %E > 45%
- 'alpha-beta': %H > 30% AND %E > 20%
- 'mixed': all others

Predicted secondary structure composition for your protein:

%H: 0.0 %E: 11.7 %L: 88.3

Residue composition for your protein:

%A: 5.0 %C: 1.7 %D: 2.8 %E: 1.7 %F: 1.7

%G: 23.3 %H: 5.0 %I: 1.1 %K: 3.9 %L: 3.9

%M: 4.4 %N: 5.6 %P: 8.3 %Q: 5.6 %R: 4.4

%S: 5.0 %T: 2.2 %V: 3.9 %W: 5.0 %Y: 5.6

AA :	amino acid sequence
PHD_sec:	PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PHD = PHD: Profile network prediction HeiDelberg
Rel_sec:	reliability index for PHDsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_sec:	subset of the PHDsec prediction, for all residues with an expected average accuracy > 82% (tables in header) NOTE: for this subset the following symbols are used: L: is loop (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 5

pH_sec:	'probability' for assigning helix (1=high, 0=low)
pE_sec:	'probability' for assigning strand (1=high, 0=low)
pL_sec:	'probability' for assigning neither helix, nor strand (1=high, 0=low)
P_3_acc:	PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
Rel_acc:	reliability index for PHDacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_acc:	subset of the PHDacc prediction, for all residues with an expected average correlation > 0.69 (tables in header) NOTE: for this subset the following symbols are used: I: is intermediate (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 4

PHD_acc:	PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between nn % and (n+1)(n+1) % (e.g. for n=5: 16-25%).

PHD results (brief)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP PHD_sec EEEEEEEEEEEEE Rel_sec ** ******** **************************************** ** P_3_acc bbebbbbbbbbbbbbbeeebeeeeeeeeebeeebbee ebeb ebbeeeeeeebbbeb b Rel_acc * * ***** ....,....7....,....8....,....9....,....10...,....11...,....12 AA HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA PHD_sec Rel_sec **** ****** *** **** ****************** * P_3_acc ebbbeb eebbbeb bebbbeb eeb bebebbbeeeeeeeeeeeeeeeeebebbbebbb Rel_acc ....,....13...,....14...,....15...,....16...,....17...,....18 AA VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV PHD_sec EEEEE EE E Rel_sec **** *** ****** ****** ** **** ****** * * P_3_acc ebbbebbeeebeeeeeee eebeeeeeeeeeeebeebeeeeeb ebeeeeeee bbbbbb Rel_acc ** **

PHD results (normal)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP PHD_sec EEEEEEEEEEEEE Rel_sec 971014899999974215788888888887677886558887667777677676655455 SUB_sec LL....EEEEEEEE...LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL.LL P_3_acc bbebbbbbbbbbbbbbeeebeeeeeeeeebeeebbee ebeb ebbeeeeeeebbbeb b Rel_acc 211534367454321100010001001100100000101111000001000001010200 SUB_acc ...b.b.bbbbb................................................ ....,....7....,....8....,....9....,....10...,....11...,....12 AA HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA PHD_sec Rel_sec 566533336786553246753223578631334341368988886556576766522454 SUB_sec LLLL....LLLLLL...LLL....LLLL.........LLLLLLLLLLLLLLLLLL...L. P_3_acc ebbbeb eebbbeb bebbbeb eeb bebebbbeeeeeeeeeeeeeeeeebebbbebbb Rel_acc 120102000101030001001100010002010100001011110000001002010110 SUB_acc ............................................................ ....,....13...,....14...,....15...,....16...,....17...,....18 AA VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV PHD_sec EEEEE EE E Rel_sec 655544433565479887544688987311356333688533430444798986351149 SUB_sec LLLL.....LLL.LLLLLL..LLLLLL....LL...LLLL........LLLLLL.E...L P_3_acc ebbbebbeeebeeeeeee eebeeeeeeeeeeebeebeeeeeb ebeeeeeee bbbbbb Rel_acc 111101100010000110000111001100110001000000110001010100461164 SUB_acc ......................................................bb..bb

PHD results (detail)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP pH_sec 1.0 pH_sec 0.9 pH_sec 0.8 pH_sec 0.7 pH_sec 0.6 pH_sec 0.5 pH_sec . 0.4 pH_sec . .. . ...... 0.3 pH_sec .... . .. .... .... ................... 0.2 ------------------------------------------------------------ pE_sec ..... 1.0 pE_sec ........ 0.9 pE_sec ........ 0.8 pE_sec .......... 0.7 pE_sec ........... 0.6 pE_sec .............. 0.5 pE_sec ............... 0.4 pE_sec ................ 0.3 pE_sec .................. 0.2 ------------------------------------------------------------ pL_sec . 1.0 pL_sec . ........... .. ... . . 0.9 pL_sec .. ...................................... 0.8 pL_sec .. ........................................... 0.7 pL_sec .. ............................................ 0.6 pL_sec .... ............................................ 0.5 pL_sec ..... .............................................. 0.4 pL_sec ...... .............................................. 0.3 pL_sec ....... ............................................... 0.2 ------------------------------------------------------------ P_3_acc bbebbbbbbbbbbbbbeeebeeeeeeeeebeeebbee ebeb ebbeeeeeeebbbeb b PHD_acc 100% PHD_acc 81% PHD_acc . . ... .... . . . ... 64% PHD_acc . ... ......... ... .. . . . ....... . 49% PHD_acc . ... ......... ... .... . .. ....... . . 36% PHD_acc . ... ......... ... .... . .. ....... . . 25% PHD_acc . ... ......... ... .... . .. ....... . . 16% PHD_acc . ... ......... ... .... . .. ....... . . 9% PHD_acc . ... ......... ... .... . .. ....... . . 4% ------------------------------------------------------------ ....,....7....,....8....,....9....,....10...,....11...,....12 AA HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA pH_sec 1.0 pH_sec 0.9 pH_sec 0.8 pH_sec 0.7 pH_sec 0.6 pH_sec . . . . 0.5 pH_sec .... ... .... ......... ... 0.4 pH_sec ......... ...... ...... .......... ..... ...... 0.3 pH_sec ...................................... . ................. 0.2 ------------------------------------------------------------ pE_sec 1.0 pE_sec 0.9 pE_sec 0.8 pE_sec 0.7 pE_sec 0.6 pE_sec 0.5 pE_sec 0.4 pE_sec 0.3 pE_sec . 0.2 ------------------------------------------------------------ pL_sec 1.0 pL_sec .. .. ...... 0.9 pL_sec ... ..... ... .... ................. 0.8 pL_sec .... ......... ..... ..... .... .................. ... 0.7 pL_sec ............................................................ 0.6 pL_sec ............................................................ 0.5 pL_sec ............................................................ 0.4 pL_sec ............................................................ 0.3 pL_sec ............................................................ 0.2 ------------------------------------------------------------ P_3_acc ebbbeb eebbbeb bebbbeb eeb bebebbbeeeeeeeeeeeeeeeeebebbbebbb PHD_acc 100% PHD_acc 81% PHD_acc .. ....... ... . 64% PHD_acc . . .. . . . .. . . ................. . . 49% PHD_acc . . ... . . . . ... . . . ................. . . 36% PHD_acc . . ... . . . . ... . . . ................. . . 25% PHD_acc . . ... . . . . ... . . . ................. . . 16% PHD_acc . . ... . . . . ... . . . ................. . . 9% PHD_acc . . ... . . . . ... . . . ................. . . 4% ------------------------------------------------------------ ....,....13...,....14...,....15...,....16...,....17...,....18 AA VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV pH_sec 1.0 pH_sec 0.9 pH_sec 0.8 pH_sec 0.7 pH_sec 0.6 pH_sec 0.5 pH_sec ... 0.4 pH_sec ........ .. . 0.3 pH_sec .............. ... . . ... 0.2 ------------------------------------------------------------ pE_sec 1.0 pE_sec 0.9 pE_sec . 0.8 pE_sec ... .. 0.7 pE_sec .... .. . 0.6 pE_sec . ..... .... 0.5 pE_sec .... .. ....... .... 0.4 pE_sec .. ..... .... ......... ..... 0.3 pE_sec .. .. ..... ....................... ...... 0.2 ------------------------------------------------------------ pL_sec . 1.0 pL_sec .... ..... .. ..... . 0.9 pL_sec . . . ..... ...... . .... ...... . 0.8 pL_sec ....... .................. .. ..... ......... .. 0.7 pL_sec ............................ .......... ......... .. 0.6 pL_sec ........................................ .......... .... 0.5 pL_sec ....................................................... .... 0.4 pL_sec ............................................................ 0.3 pL_sec ............................................................ 0.2 ------------------------------------------------------------ P_3_acc ebbbebbeeebeeeeeee eebeeeeeeeeeeebeebeeeeeb ebeeeeeee bbbbbb PHD_acc 100% PHD_acc 81% PHD_acc . . .... . . .. .. .. .. ... ... 64% PHD_acc . . ... ....... .. ........... .. ..... . ....... 49% PHD_acc . . ... .......... ........... .. ..... . ....... 36% PHD_acc . . ... .......... ........... .. ..... .. ........ 25% PHD_acc . . ... .......... ........... .. ..... .. ........ 16% PHD_acc . . ... .......... ........... .. ..... .. ........ 9% PHD_acc . . ... .......... ........... .. ..... .. ........ 4% ------------------------------------------------------------