PROF predictions for 9rnt

• 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	9.62	37.50	52.88

• About your protein:

  prot_id	9rnt
  prot_nres	104
  prot_nali	14
  prot_nchn	1
  prot_nfar	3

• About the alignment used:

  ali_orig	8rnt.msf
  ali_used	PROF1443438rnt.hssp

• Residue composition for your protein:

  %A: 6.7	%C: 3.9	%D: 5.8	%E: 5.8	%F: 3.9
  %G: 11.5	%H: 2.9	%I: 1.9	%K: 1.9	%L: 2.9
  %M: 0.0	%N: 8.7	%P: 3.9	%Q: 1.9	%R: 1.0
  %S: 14.4	%T: 5.8	%V: 7.7	%W: 1.0	%Y: 8.7

• About the PROF methods used:

  prof_fpar	sec=/nfs/home1/yachdav/work/SNAP/prof/net/PROFsec_best.par
  prof_nnet	sec=2

• 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)
  ali_orig:	input file
  ali_used:	input file used
  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 9rnt

PROF results (normal)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10...
AA         ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT
OBS_sec                                                                                                            
PROF_sec     EEE   EEE HHHHHHHHHH   EE                     EEEE   EEEEEEE   EEEE       EEEEE    EEEEEEEE      EEE  
Rel_sec    90111053000123577777302201014543455654543234332013205851444331145033056565534788156512335764023345044308
SUB_sec    L.....L.......HHHHHH.........L...LLLL.L.............LLL.........L....LLLLLL..EEE.LLL....EEE......L.....L





PROF results (detail)

           ....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,....9....,....10...
AA         ACDYTCGSNCYSSSDVSTAQAAGYKLHEDGETVGSNSYPHKYNNYEGFDFSVSSPYYEWPILSSGDVYSGGSPGADRVVFNENNQLAGVITHTGASGNNFVECT
 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 
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