PROF prediction (8rnt)

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# PROF predictions for 9rnt

Contents:

- SYNOPSIS of prediction for 9rnt

1. secondary structure class
2. secondary structure composition

- HEADER information

1. about protein
2. about alignment
3. residue composition
4. about method used
5. please quote
6. copyright & contact
7. abbreviations used

- BODY with predictions
  Different levels of data:

1. PROF normal
2. PROF detail

### SYNOPSIS of prediction 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

### HEADER information

- 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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