PHD predictions for 1prcL

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: 50.9 %E: 11.7 %L: 37.4

PHDhtm summary

NHTM=5
PHDhtm detected 5 membrane helices for the best model.The second best model contained 4 helices.
TOP=in
PHDhtm predicted the topology in, i.e. the first loop region is in (Note: this prediction may be problematic when the sequence you sent starts or ends with a region predicted in a membrane helix!)
Reliability of best model=4 (0 is low, 9 is high)
Zscore for best model=1.213
Difference of positive charges (K+R) inside - outside=-9.771 (the higher the value, the more reliable)
Reliability of topology prediction =9 (0 is low, 9 is high)

Details of the strength of each predicted membrane helix:
(sorted by strength, strongest first)

N HTM	Total score	Best HTM	c-N
1	0.5490	0.8922	29 - 53
2	0.6063	0.8910	231 - 250
3	0.6704	0.8810	117 - 139
4	0.7262	0.8808	173 - 192
5	0.7755	0.8737	85 - 102

Overview over transmembrane segments:

Positions	Segments	Explain
1- 28	i1	inside region 1
29- 53	M1	membrane helix 1
54- 84	o1	outside region 1
85- 102	M2	membrane helix 2
103- 116	i2	inside region 2
117- 139	M3	membrane helix 3
140- 172	o2	outside region 2
173- 192	M4	membrane helix 4
193- 230	i3	inside region 3
231- 250	M5	membrane helix 5
251- 273	o3	outside region 3

Residue composition for your protein:

%A: 7.3 %C: 1.1 %D: 3.3 %E: 2.6 %F: 9.5

%G: 12.8 %H: 2.9 %I: 6.6 %K: 1.8 %L: 11.7

%M: 1.5 %N: 3.3 %P: 5.5 %Q: 1.8 %R: 3.3

%S: 6.6 %T: 2.6 %V: 6.6 %W: 5.5 %Y: 3.7

AA : amino acid sequence

OBS_sec: observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)

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)

O_3_acc: observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.

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

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

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

PHD_htm: PHD predicted membrane helix: M=helical transmembrane region, blank=non-membrane
PHD = PHD: Profile network prediction HeiDelberg

Rel_htm: reliability index for PHDhtm prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'

SUB_htm: subset of the PHDhtm prediction, for all residues with an expected average accuracy > 98% (tables in header)
NOTE: for this subset the following symbols are used:
N: is non-membrane region (for which above ' ' is used)
.: means that no prediction is made for this residue, as the reliability is: Rel < 5

PiMohtm: PHD prediction of membrane topology: T=helical transmembrane region, i=inside of membrane, o=outside of membrane

pT_htm: 'probability' for assigning transmembrane helix

pN_htm: 'probability' for assigning globular region

PHD results (brief)

PHD results (normal)

PHD results (detail)

....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10...,....11...,....12...,....13...,....14...,....15...,....16...,....17...,....18...,....19...,....20...,....21...,....22...,....23...,....24...,....25...,....26...,....27...,....28 AA ALLSFERKYRVRGGTLIGGDLFDFWVGPYFVGFFGVSAIFFIFLGVSLIGYAASQGPTWDPFAISINPPDLKYGLGAAPLLEGGFWQAITVCALGAFISWMLREVEISRKLGIGWHVPLAFCVPIFMFCVLQVFRPLLLGSWGHAFPYGILSHLDWVNNFGYQYLNWHYNPGHMSSVSFLFVNAMALGLHGGLILSVANPGDGDKVKTAEHENQYFRDVVGYSIGALSIHRLGLFLASNIFLTGAFGTIASGPFWTRGWPEWWGWWLDIPFWS P_3_acc bbbebeeebeeebbbbbbbebbebebbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeebe bbbbbe eeeebbbbbbbbeebbbbbbbbbbbbbbbbbbbb bbebbeebbbb bbbbbbbbbbbbbbbbbbbbbbbbbbbbebbbbbbbbbbebbbbbbbebbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbeeeeeeebebeeebbebb bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbebbeee eebb bbbebeb e OBS_acc . . . .. 100% OBS_acc OBS_acc . . . . . . . . . . . . . . . .. 81% OBS_acc OBS_acc .. . . .. . . . . . . . . . .. . . . .. . . . . . . . . .. 64% OBS_acc OBS_acc . . . .. .. . . . .. ... .. ... .... .... .. ... .... . . .. . . . . . . .. . . . . . .. . ..... . . . . . . ... 49% OBS_acc OBS_acc . . .. ... . .. . . . ...... ...... ......... . ...... .... . . . .. . . . . .. . . . .. . . . . . . . .. .. . . ..... . . . .. . . . .. .... 36% OBS_acc OBS_acc .. . . .. ... . .... . . ...... ...... ......... .. ...... .... . . .. .. . . ... . .... . . .. .. . . ... .. . .. ..... ...... . . . ..... . . . . . . .. ... . . . . . .. .... . 25% OBS_acc OBS_acc .. . . . ....... . .... . .. .. ............. ............. ............. .. . ...... ... . ... ...... .... . .. .... . . .... .. . .. .. ............ ... . . ..... . . . ... .. . .. ... .. ... . .. . ... ...... .... . 16% OBS_acc OBS_acc .. . . . . ....... . .... . ..... ............................ ............. .. ................ .. . ...... ........... . .. ........ . .... .. .. .... . .. ............ ... .. . ....... .. ... . ....... .. .. ............. ... ..... ...... ...... 9% OBS_acc OBS_acc ..... .. . ............. ...... ................................... .................................... . ...... ............. ... ........ . .... .. ... .... .... ............ ....... .... ................. .. ........... .................... ....... ...... ...... 4% OBS_acc --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PHD_acc . . 100% PHD_acc PHD_acc . . 81% PHD_acc PHD_acc . . . . ... . .... .. . . ...... .. .. . 64% PHD_acc PHD_acc . ... ... . . . ..... . . .... .. . .. . . . ....... . ... . . ... .. . . . 49% PHD_acc PHD_acc . ... ... . . . ..... .. . .... .. . . .. . . . . ....... . ... . . . ... .. . . . 36% PHD_acc PHD_acc . ... ... . . . ..... .. ...... .. . . .. . . . . ....... . ... . .. . ... .. . . . . 25% PHD_acc PHD_acc . ... ... . . . ..... .. ...... .. . . .. . . . . ....... . ... . .. . ...... . . . .. 16% PHD_acc PHD_acc . ... ... . . . ..... .. ...... .. . . .. . . . . ....... . ... . .. . ...... . . . .. 9% PHD_acc PHD_acc . ... ... . . . ..... .. ...... .. . . .. . . . . ....... . ... . .. . ...... . . . .. 4% PHD_acc --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- pT_htm ............. ..... .................. ............ ............ . . .. . ........... .. . 1.0 pT_htm pT_htm ................. ......................... ............. ... ............. .... ...... . ................ ...... 0.9 pT_htm pT_htm ................... ......................... ................. .. .................. ..... .......... .................. ........ 0.8 pT_htm pT_htm .................... .......................... ................... ... . ................... ...... .......... .................. ........ 0.7 pT_htm pT_htm ....................... .. .......................... ....................... ..... .. . ............................ ............ ................... .. ......... 0.6 pT_htm pT_htm . ....................... ... ........................... ....................... . .............. ............................ ............ ................... ... ......... 0.5 pT_htm pT_htm ... .......................... .... ............................ ......................... .... ............... ............................ .............. ........................... ......... 0.4 pT_htm pT_htm ....... .. . ........................... .. . .................................. .................................. ................. . ............................. ........................................... ... .......... 0.3 pT_htm pT_htm ......... ............. ............................ .... ... ............................................................................................. .............................. ............................................... .... ............ 0.2 pT_htm --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- pN_htm . ... .. .... ...... ... . ..... .. . ... 1.0 pN_htm pN_htm .. ....... ..... ..... ...... ........ ....... . . .. .. ........ .... .. .... 0.9 pN_htm pN_htm ... ....................... ....................... . ... .. .... ...... .......... . ......... ..... 0.8 pN_htm pN_htm .............................. . ........................ .. ... ...... ..... ....... .......... ..... ... .......... ..... 0.7 pN_htm pN_htm ................................. ......................... .. .... ............ ... .. ........ .......... ..... ... ........... ..... 0.6 pN_htm pN_htm .................................. .............................. ..... ................ ..... ............ .. ........... ...... ................. ..... 0.5 pN_htm pN_htm ................................... ............................... ...... .................. .................. ... ............ ...... ................. ..... 0.4 pN_htm pN_htm .................................... ................................ ....... ........................................... . ... ............. .. ........ ................... ...... 0.3 pN_htm pN_htm ..................................... .................................... . ........ ................................................ ... . ............... . ............... ...................... . ....... 0.2 pN_htm ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

%A: 7.3	%C: 1.1	%D: 3.3	%E: 2.6	%F: 9.5
%G: 12.8	%H: 2.9	%I: 6.6	%K: 1.8	%L: 11.7
%M: 1.5	%N: 3.3	%P: 5.5	%Q: 1.8	%R: 3.3
%S: 6.6	%T: 2.6	%V: 6.6	%W: 5.5	%Y: 3.7

AA :	amino acid sequence
OBS_sec:	observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)
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)
O_3_acc:	observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
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

OBS_acc:	observerd 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_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_htm:	PHD predicted membrane helix: M=helical transmembrane region, blank=non-membrane PHD = PHD: Profile network prediction HeiDelberg
Rel_htm:	reliability index for PHDhtm prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_htm:	subset of the PHDhtm prediction, for all residues with an expected average accuracy > 98% (tables in header) NOTE: for this subset the following symbols are used: N: is non-membrane region (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 5

PiMohtm:	PHD prediction of membrane topology: T=helical transmembrane region, i=inside of membrane, o=outside of membrane
pT_htm:	'probability' for assigning transmembrane helix
pN_htm:	'probability' for assigning globular region