Example of verbose HTML output from NORSp

Links:

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Results from PredictProtein for predict_h24175

TOC for file /home/phd/server/work/predict_h24175

The following information has been received by the server (TOC)
predictor of NOn-Regular Secondary Structure (Jinfeng Liu & Burkhard Rost) (TOC)
PROF predictions (TOC)
PHD predictions (TOC)
COILS prediction (A Lupas) (TOC)

END of TOC

BEG of results for file /home/phd/server/work/predict_h24175

The following information has been received by the server

reference predict_h24175 (Mar 11, 2003 20:02:06)
reference pred_h24175 (Mar 11, 2003 19:59:26)
PPhdr from: liu@cubic.bioc.columbia.edu
PPhdr resp: MAIL
PPhdr orig: HTML
PPhdr want: HTML
PPhdr password(###)
run nors_only
ret html perline=60
ret store
ret nors verbose
expert nors ws=70 seccut=12 acclen=10
# default: single protein sequence
MARAEEVDGP APGEVLLSPV DGLHNHVIHV ALQEHGWATY AVHPVEAQPA
PHPGALLHQV EVPAPLDRVD PYPLIALYHH PRLECPPYSL PNTLLSLPPP
HITRRYIEYY GYVTPQPLLI LYHLPLAQLH PTVLEYLVGP RVRHNNTREP
EDPVYTLLGR LPSKALPKEV GVCNNLAEPG GPNLIHTNLL PIHVYDRKEG
GRLHNTMLCI DPADPPRQID IPNLKHRPGP TRNPSRLPTL IAPESKPPFE
GWMSVGQEA

predictor of NOn-Regular Secondary Structure (Jinfeng Liu & Burkhard Rost)

TOP - BOTTOM - NORSp

Sequence length	259
Secondary structure	Helix=9.7%, Strand=19.3%, Loop=71.0%

window size	70
Structure content cutoff	12%
Minimum consecutive exposed residues	10

NORS	N=NORS region
Secondary structure	H=helix, E=strand, ' '=loop
Coiled-coil region	c=coils
Transmembrane helix	m=transmembrane helix
Solvent accessibility	e=exposed, ' '=buried

NORS region predicted:

187-259

           .    :    .    :    .    :    .    :    .    5
SEQ    MARAEEVDGPAPGEVLLSPVDGLHNHVIHVALQEHGWATYAVHPVEAQPA
NORS                                                     
SEC        EE       EEEEE       EEEEEEHHH   EEEEE  EE    

COILS                                                    
HTM                                                      
ACC    eee ee eee e e    e ee ee       eeee       e e ee 
           .    :    .    :    .    :    .    :    .    10
SEQ    PHPGALLHQVEVPAPLDRVDPYPLIALYHHPRLECPPYSLPNTLLSLPPP
NORS                                                     
SEC          EEEEE            EEEEE                      

COILS                                                    
HTM                                                      
ACC    eeee    e e e e ee ee         ee e ee e eee  e eee

           .    :    .    :    .    :    .    :    .    15
SEQ    HITRRYIEYYGYVTPQPLLILYHLPLAQLHPTVLEYLVGPRVRHNNTREP
NORS                                                     
SEC       HHHHHHH EE  HHHHHHH   HHH    HHHHH             

COILS                                                    
HTM                                                      
ACC    e  ee  e  ee ee         e  e  ee  ee  e e eeeeeeee

           .    :    .    :    .    :    .    :    .    20
SEQ    EDPVYTLLGRLPSKALPKEVGVCNNLAEPGGPNLIHTNLLPIHVYDRKEG
NORS                                       NNNNNNNNNNNNNN

SEC       EEEEE            EE           EEE     EEEEE    

COILS                                                    
HTM                                                      
ACC    eee     ee eeee eee e  ee eeeeeee    e       eeeee

           .    :    .    :    .    :    .    :    .    25
SEQ    GRLHNTMLCIDPADPPRQIDIPNLKHRPGPTRNPSRLPTLIAPESKPPFE
NORS   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

SEC          EEE                                         
COILS                                                    
HTM                                                      
ACC    ee         eeeeeee e ee eeeeeeeeeeee ee   eeeeee e

           .    :    .    :    .    :    .    :    .    30
SEQ    GWMSVGQEA
NORS   NNNNNNNNN
SEC             
COILS           
HTM             
ACC    e  eeeeee

//

PROF predictions

TOP - BOTTOM - PROF

Bottom - Summary - Details - PredictProtein

PROF predictions for query

Contents:

SYNOPSIS of prediction for query

secondary structure class
secondary structure composition
surface/core ratio

HEADER information

about protein
about alignment
residue composition
about method used
please quote
copyright & contact
abbreviations used

BODY with predictions
Different levels of data:

PROF normal
PROF detail

SYNOPSIS of prediction for query

PROFsec 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:

sec str type H E L

% in protein 9.65 19.31 71.04

Predicted solvent accessibility composition (core/surface ratio) for your protein:
Classes used:
- e: residues exposed with more than 16% of their surface
- b: all other residues.
accessib type b e

% in protein 45.95 54.05

HEADER information

About your protein:

prot_id query

prot_nres 259

prot_nali 1

prot_nchn 1

prot_nfar 0

About the alignment used:

ali_orig /home/phd/server/work/predict_h24175.hsspPsiFil

Residue composition for your protein:

%A: 6.6 %C: 1.2 %D: 3.5 %E: 6.6 %F: 0.4

%G: 6.2 %H: 6.6 %I: 4.2 %K: 1.9 %L: 13.5

%M: 1.2 %N: 4.2 %P: 15.8 %Q: 2.7 %R: 5.8

%S: 2.7 %T: 4.2 %V: 7.3 %W: 0.8 %Y: 4.6

About the PROF methods used:

prof_fpar acc=/home/phd/server/pub/prof/net/PROFboth_best.par

prof_nnet acc=6

Please quote:
1. PROF: B Rost & C Sander (1993) J Mol Biol, 232:584-599
2. PROFhtm: B Rost, P Fariselli & R Casadio (1996) Prot Science, 7:1704-1718

Copyright & Contact:
- Burkhard Rost, CUBIC NYC / LION Heidelberg
- Email: rost@columbia.edu
- WWW: http://cubic.bioc.columbia.edu
- Fax: +1-212-305 3773

ABBREVIATIONS used:

AA :	amino acid sequence
OBS_sec:	observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PROF_sec:	PROF predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PROF = PROF: Profile network prediction HeiDelberg
Rel_sec:	reliability index for PROFsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_sec:	subset of the PROFsec 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_2_acc:	observerd relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
P_2_acc:	PROF predicted relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
O_3_acc:	observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
P_3_acc:	PROF predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
OBS_acc:	observed 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%).
PROF_acc:	PROF 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%).
Rel_acc:	reliability index for PROFacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_acc:	subset of the PROFacc 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


ali_orig:	input file
prof_fpar:	name of parameter file, used [w]
prof_nnet:	number of networks used for prediction [d]
prof_skip:	note: sequence stretches with less than 9 are not predicted, the symbol '*' is used!

BODY with predictions for query

PROF results (normal)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MARAEEVDGPAPGEVLLSPVDGLHNHVIHVALQEHGWATYAVHPVEAQPAPHPGALLHQV OBS_sec PROF_sec EE EEEEE EEEEEEHHH EEEEE EE EEEE Rel_sec 940020357776236751223345403443202158436745020213577866200122 SUB_sec L......LLLLL..EEE......L..........LL..EE.E......LLLLLL...... O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc eeebee eee e ebbbb eeb bbbbbbb e ebbbbbbbe eb e e eebbbb b Rel_acc 625023342124120153103202135927772232233152120302212112000122 SUB_acc e.e....e...e....b.........bb.bbb........b................... ....,....7....,....8....,....9....,....10.1.,....11.1.,....1 AA EVPAPLDRVDPYPLIALYHHPRLECPPYSLPNTLLSLPPPHITRRYIEYYGYVTPQPLLI OBS_sec PROF_sec E EEEEE HHHHHHH EE HHHHH Rel_sec 313655675762004431143221356556530025676200044455305106215655 SUB_sec ...LLLLLLLL..............LLLLLL....LLLL.......HH..L..L..HHHH O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc e e e ee e bbbbbbb e beb e e e bbe e e bb bbe b bbbb Rel_acc 412132331201035770010323323412201012210021223542110202102346 SUB_acc e.............bbb..........i.................bb...........bb ....,....13.1.,....14.1.,....15.1.,....16.1.,....17.1.,....1 AA LYHLPLAQLHPTVLEYLVGPRVRHNNTREPEDPVYTLLGRLPSKALPKEVGVCNNLAEPG OBS_sec PROF_sec HH HHH HHHHH EEEEE EE Rel_sec 523651103711221101873003567677673254412457533772020102345666 SUB_sec H..LL....L........LL....LLLLLLLL..E.....LLL..LL.........LLLL O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc bbbbebbe eebbe bb eb e eeeee bbbbb beeee eee bbe b eee Rel_acc 411220120122532310111022310111411313220323133304421001100034 SUB_acc b...........b.................e................ee..........e ....,....19.1.,....20.1.,....21.1.,....22.1.,....23.1.,....2 AA GPNLIHTNLLPIHVYDRKEGGRLHNTMLCIDPADPPRQIDIPNLKHRPGPTRNPSRLPTL OBS_sec PROF_sec EEE EEEEE EEE Rel_sec 663142143434666121476201112100566660013363223355666574546641 SUB_sec LL..........EEE....LL.........LLLLL.....L.....LLLLLLL.L.LL.. O_3_acc bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb P_3_acc bbbb bbbbbbb eee bbbbbbbb eee e e ebeebee e e eeb e Rel_acc 101220101135070033621212012334102222212312223032103010122001 SUB_acc ...........b.b....e..........b.............................. ....,....25.1.,.... AA IAPESKPPFEGWMSVGQEA OBS_sec PROF_sec Rel_sec 1675567622222434358 SUB_sec .LLLLLLL.........LL O_3_acc bbbbbbbbbbbbbbbbbbb P_3_acc eeee e ee e eeee Rel_acc 0015221113122211188 SUB_acc ...e.............ee

PROF results (detail)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MARAEEVDGPAPGEVLLSPVDGLHNHVIHVALQEHGWATYAVHPVEAQPAPHPGALLHQV 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 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc .. .. . . .. 100% PROF_acc .. ... . . . . .. 81% PROF_acc .. . ... . .. . . . . . .. 64% PROF_acc ... .. ... . . .. . . . . . . .. 49% PROF_acc ... .. ... . . . .. .. .... . . . . .. . 36% PROF_acc ... .. ... . . . .. .. .... . . .. .... . 25% PROF_acc ... .......... .... .. .... ... ....... . 16% PROF_acc ... .......... .... ... ..... .... ....... ... 9% PROF_acc ... .......... .... ... ..... .... ....... ... 4% ------------------------------------------------------------ ....,....7....,....8....,....9....,....10.1.,....11.1.,....1 AA EVPAPLDRVDPYPLIALYHHPRLECPPYSLPNTLLSLPPPHITRRYIEYYGYVTPQPLLI 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 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc .. . . . 100% PROF_acc . .. . . . . . 81% PROF_acc . . . .. . . . . . . 64% PROF_acc . . . .. . . . . . . . . . . 49% PROF_acc . . . .. .. .. . .. . . . . .... .. . . .. 36% PROF_acc . . . .. .. .. . .. . ... . .... .. . .. .. 25% PROF_acc ............ ... . ........ ...... .. ..... ... 16% PROF_acc ............ .............. ....... .. ..... ... 9% PROF_acc ............ .............. ....... .. ..... ... 4% ------------------------------------------------------------ ....,....13.1.,....14.1.,....15.1.,....16.1.,....17.1.,....1 AA LYHLPLAQLHPTVLEYLVGPRVRHNNTREPEDPVYTLLGRLPSKALPKEVGVCNNLAEPG 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 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc . . . ... . .. 100% PROF_acc . . .. .. ... .. .. 81% PROF_acc . . . . .. .. .... .. .. 64% PROF_acc . . .. . . . ..... .... ... . ... 49% PROF_acc . . .. . . . . ......... .. .... ... . . ... 36% PROF_acc . . .. .. . . ........... .. .... ... . .. .... 25% PROF_acc . ..... .. ... ........... .. .......... .. .... 16% PROF_acc . . ..... .. ... ........... ............. ....... 9% PROF_acc . .. ..... .. ... ........... . ............. ....... 4% ------------------------------------------------------------ ....,....19.1.,....20.1.,....21.1.,....22.1.,....23.1.,....2 AA GPNLIHTNLLPIHVYDRKEGGRLHNTMLCIDPADPPRQIDIPNLKHRPGPTRNPSRLPTL 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 ------------------------------------------------------------ OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------------------------------------------------ PROF_acc ... . . . . . . 100% PROF_acc ... .. . . .. . . . 81% PROF_acc ... ... . . .. .. . . . 64% PROF_acc ... ... . . . .. .. . . .. . 49% PROF_acc .. . ..... ... . . . .. .... ...... .. 36% PROF_acc ... . ....... ....... . .. ............ .. 25% PROF_acc ... . ....... .......... .. ............ ... 16% PROF_acc ... . ....... . .......... ................... 9% PROF_acc ... . ....... . .............................. 4% ------------------------------------------------------------ ....,....25.1.,.... AA IAPESKPPFEGWMSVGQEA 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 ------------------- OBS_acc 100% OBS_acc 81% OBS_acc 64% OBS_acc 49% OBS_acc 36% OBS_acc 25% OBS_acc 16% OBS_acc 9% OBS_acc 4% ------------------- PROF_acc .. . .. 100% PROF_acc .... . .... 81% PROF_acc .... . . .... 64% PROF_acc .... . .. . .... 49% PROF_acc .... . .. . .... 36% PROF_acc ...... .. ...... 25% PROF_acc ................... 16% PROF_acc ................... 9% PROF_acc ................... 4% -------------------

Top - Summary - Details - PredictProtein

PHD predictions

TOP - BOTTOM - PHD

PHD predictions for predict_h24175

Different levels of data:

PHD brief
PHD normal

PHDhtm summary
- NHTM=1
  PHDhtm detected 1 membrane helix for the best model.The second best model contained 0 helix.
- TOP=unk
  PHDhtm predicted the top

%A: 6.6	%C: 1.2	%D: 3.5	%E: 6.6	%F: 0.4
%G: 6.2	%H: 6.6	%I: 4.2	%K: 1.9	%L: 13.5
%M: 1.2	%N: 4.2	%P: 15.8	%Q: 2.7	%R: 5.8
%S: 2.7	%T: 4.2	%V: 7.3	%W: 0.8	%Y: 4.6

prof_fpar	acc=/home/phd/server/pub/prof/net/PROFboth_best.par
prof_nnet	acc=6

sec str type	H	E	L
% in protein	9.65	19.31	71.04

accessib type	b	e
% in protein	45.95	54.05