# Perl-RDB # PROFboth # # Copyright : Burkhard Rost, CUBIC NYC / LION Heidelberg # Email : rost@columbia.edu # WWW : http://cubic.bioc.columbia.edu # Version : 2000.02 # # -------------------------------------------------------------------------------- # About your protein : # # VALUE PROT_ID : unk # VALUE PROT_NRES : 133 # VALUE PROT_NALI : 1 # VALUE PROT_NFAR : 0 # # -------------------------------------------------------------------------------- # About the alignment: # # VALUE ALI_ORIG : target.fas # # -------------------------------------------------------------------------------- # About PROF specifics: # # VALUE PROF_FPAR : acc=/farm/users/kellere/spine/prof/net/PROFboth_best.par # VALUE PROF_NNET : acc=6 # # -------------------------------------------------------------------------------- # Notation used : # # ------------------------------------------------------------------------ # NOTATION HEADER : PROTEIN # NOTATION PROT_ID : identifier of protein [w] # NOTATION PROT_NRES : number of residues [d] # NOTATION PROT_NALI : number of proteins aligned in family [d] # NOTATION PROT_NFAR : number of distant relatives [d] # # ------------------------------------------------------------------------ # NOTATION HEADER : ALIGNMENT # NOTATION HEADER : ALIGNMENT: input file # # ------------------------------------------------------------------------ # NOTATION HEADER : INTERNAL # NOTATION PROF_FPAR : name of parameter file, used [w] # NOTATION PROF_NNET : number of networks used for prediction [d] # # # ------------------------------------------------------------------------ # NOTATION BODY : PROTEIN # NOTATION NO : counting residues [d] # NOTATION AA : amino acid one letter code [A-Z!a-z] # NOTATION CHN : protein chain [A-Z!a-z] # # ------------------------------------------------------------------------ # NOTATION BODY : PROF # # ------------------------------------------------------------------------ # NOTATION BODY : PROFsec # NOTATION PHEL : PROF predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PROF = PROF: Profile network prediction HeiDelberg # NOTATION RI_S : reliability index for PROFsec prediction (0=lo 9=high) Note: for the brief presentation strong predictions marked by '*' # NOTATION pH : 'probability' for assigning helix (1=high, 0=low) # NOTATION pE : 'probability' for assigning strand (1=high, 0=low) # NOTATION pL : 'probability' for assigning neither helix, nor strand (1=high, 0=low) # NOTATION OtH : actual neural network output from PROFsec for helix unit # NOTATION OtE : actual neural network output from PROFsec for strand unit # NOTATION OtL : actual neural network output from PROFsec for 'no-regular' unit # # ------------------------------------------------------------------------ # NOTATION BODY : PROFacc # NOTATION PACC : PROF predicted solvent accessibility (acc) in square Angstroem # NOTATION PREL : PROF 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%). # NOTATION RI_A : reliability index for PROFacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*' # NOTATION Pbe : PROF predicted relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%. # NOTATION Pbie : PROF predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%. # NOTATION Ot4 : actual neural network output from PROFsec for unit 0 coding for a relative solvent accessibility of 4*4 - 5*5 percent (16-25%). Note: OtN, with N=0-9 give the same information for the other output units! # # -------------------------------------------------------------------------------- # No AA PHEL RI_S PACC PREL RI_A pH pE pL Pbe Pbie OtH OtE OtL Ot0 Ot1 Ot2 Ot3 Ot4 Ot5 Ot6 Ot7 Ot8 Ot9 1 A L 9 95 90 9 0 0 9 e e 1 1 97 0 0 1 3 5 9 15 23 38 45 2 S L 7 117 90 4 0 0 8 e e 6 8 85 1 1 2 5 8 14 22 27 34 36 3 S L 5 93 72 4 0 1 7 e e 9 18 71 2 2 3 6 10 16 24 28 30 28 4 S L 0 72 56 4 1 4 4 e e 10 41 46 3 3 4 8 12 18 25 28 28 24 5 V E 3 28 20 1 0 6 3 e i 7 62 31 10 11 14 19 21 21 20 16 13 10 6 S E 4 54 42 2 0 6 2 e e 4 70 27 8 8 9 13 17 21 24 23 19 15 7 I E 5 33 20 2 0 7 2 e i 4 73 23 13 14 17 21 23 22 19 14 10 7 8 S E 3 54 42 3 0 6 2 e e 5 67 29 7 8 10 14 18 22 24 22 18 13 9 H E 3 77 42 1 1 6 2 e e 11 62 27 8 10 13 18 20 22 23 20 16 12 10 S E 1 54 42 2 0 5 3 e e 9 54 37 7 8 10 14 18 22 24 23 19 15 11 A L 0 44 42 2 1 4 4 e e 10 42 46 9 10 12 16 19 22 23 21 17 13 12 S L 2 54 42 1 0 3 5 e e 6 36 58 5 6 9 13 17 20 23 23 21 19 13 A L 4 44 42 0 0 2 7 e e 5 25 70 5 6 8 12 15 19 22 22 22 21 14 T L 6 102 72 3 0 1 8 e e 4 14 83 3 3 5 8 11 17 22 26 29 28 15 G L 8 60 72 2 0 0 9 e e 2 6 90 4 4 6 9 12 17 22 24 26 25 16 N L 3 87 56 3 0 3 6 e e 2 31 70 3 3 5 10 15 20 25 26 22 18 17 V E 4 42 30 2 0 7 2 e i 1 74 25 10 11 13 16 19 20 20 17 12 9 18 C E 7 27 20 2 0 8 1 e i 1 87 11 13 13 16 19 22 22 20 15 9 5 19 I E 8 33 20 2 0 9 0 e i 1 87 6 17 17 20 23 24 21 16 9 4 2 20 E E 8 38 20 3 0 9 0 e i 1 90 6 9 11 15 21 24 24 21 14 8 4 21 E E 8 58 30 3 0 9 0 e i 2 90 6 8 9 12 17 21 23 21 16 11 7 22 I E 7 33 20 1 0 8 1 e i 1 89 11 16 17 19 22 23 22 17 11 7 4 23 D E 4 68 42 3 0 6 2 e e 2 72 29 3 5 8 13 17 23 26 25 19 14 24 V L 1 42 30 1 0 3 5 e i 3 37 56 7 8 11 15 18 21 21 19 17 14 25 D L 7 117 72 3 0 1 8 e e 3 10 87 1 2 3 7 11 18 25 29 30 28 26 G L 5 35 42 1 0 2 7 e e 5 20 70 6 7 8 11 15 20 23 23 21 19 27 K E 1 114 56 3 0 5 4 e e 3 54 38 3 3 5 9 13 19 24 26 22 18 28 F E 7 39 20 1 0 8 0 e i 2 89 10 12 13 15 18 20 20 18 15 10 7 29 I E 8 33 20 2 0 9 0 e i 1 93 5 14 15 16 20 22 22 19 14 9 6 30 R E 8 74 30 3 0 9 0 e i 1 91 7 7 8 12 17 21 24 24 19 13 7 31 L E 6 32 20 2 0 8 1 e i 1 81 19 13 14 17 20 23 22 19 13 8 5 32 K E 2 86 42 1 0 5 3 e e 2 59 39 5 6 9 13 17 21 24 24 21 18 33 N L 3 65 42 1 0 3 6 e e 2 33 71 5 6 9 14 17 20 23 22 21 18 34 T L 5 59 42 0 0 1 7 e e 5 18 75 6 8 10 15 17 20 21 21 20 18 35 S L 4 72 56 2 1 2 6 e e 13 20 60 5 7 9 13 16 19 22 23 22 21 36 E L 2 108 56 3 3 0 5 e e 32 9 56 3 4 7 11 15 19 24 25 25 23 37 Q L 5 142 72 1 1 0 7 e e 19 8 72 4 6 8 13 15 18 20 21 23 23 38 D L 6 146 90 2 0 1 8 e e 8 11 79 3 4 6 9 12 16 20 23 27 28 39 Q L 7 178 90 1 0 0 8 e e 4 8 85 3 4 7 11 14 17 19 21 24 25 40 P L 7 122 90 2 0 0 8 e e 9 6 82 3 4 6 10 13 16 19 22 26 27 41 M L 7 135 72 0 0 0 8 e e 8 6 83 5 6 9 13 15 17 18 19 20 20 42 G L 7 47 56 3 1 0 8 e e 11 7 82 3 3 5 9 13 18 22 24 24 22 43 G L 0 47 56 2 4 0 4 e e 40 8 44 7 7 8 10 13 16 19 21 20 19 44 W H 3 45 20 1 5 2 2 e i 55 19 21 11 13 15 18 20 20 19 16 14 12 45 E H 2 81 42 2 5 2 1 e e 58 29 15 6 8 11 16 20 23 24 22 16 12 46 M H 1 37 20 1 4 3 1 e i 53 38 16 16 17 19 22 23 21 19 14 10 8 47 I H 1 33 20 1 4 3 1 e i 52 38 15 19 20 21 23 24 21 17 11 7 5 48 R H 1 74 30 2 4 3 1 e i 52 37 16 8 9 12 17 20 23 23 19 15 11 49 K H 1 114 56 3 4 3 1 e e 47 35 19 3 4 6 9 13 17 22 25 25 23 50 I H 0 33 20 1 3 2 3 e i 36 27 36 11 12 14 17 19 19 17 15 15 14 51 G L 6 60 72 2 1 1 7 e e 10 12 76 5 5 7 10 13 17 21 23 25 25 52 D L 7 117 72 4 0 0 8 e e 8 9 79 1 2 4 7 11 16 23 28 31 30 53 T L 4 79 56 2 0 2 7 e e 5 24 69 5 5 7 11 14 18 21 22 22 20 54 S L 1 72 56 2 0 4 5 e e 7 42 54 5 6 8 11 14 19 22 23 21 19 55 V E 1 42 30 1 0 5 3 e i 5 55 39 10 11 14 17 19 20 19 17 13 11 56 S E 3 39 30 2 0 6 3 e i 4 63 32 11 11 13 16 19 21 21 18 14 10 57 Y E 6 44 20 3 0 8 1 e i 3 80 17 13 14 18 22 24 22 18 13 8 5 58 K E 7 86 42 2 0 8 1 e e 3 83 12 6 7 10 15 19 22 23 20 15 12 59 Y E 6 44 20 2 0 8 1 e i 3 83 14 11 13 16 21 23 23 20 15 10 6 60 T E 5 42 30 2 0 7 2 e i 5 74 20 9 10 12 16 20 23 23 20 15 12 61 S E 5 39 30 2 1 7 1 e i 12 68 16 10 11 14 18 21 23 23 20 15 12 62 R E 3 104 42 2 1 6 1 e e 17 56 18 6 8 11 16 20 24 25 22 15 11 63 Y E 4 66 30 2 1 6 1 e i 17 60 17 12 14 17 21 23 24 21 16 10 7 64 V E 4 42 30 1 1 6 1 e i 16 62 13 16 15 15 18 20 21 20 16 12 9 65 L E 3 49 30 1 1 6 2 e i 13 58 20 15 16 17 19 20 21 19 16 12 9 66 K L 0 86 42 1 1 3 4 e e 16 37 41 5 6 8 12 17 22 25 25 22 19 67 A L 4 59 56 2 1 2 6 e e 12 19 64 6 7 8 12 15 18 21 23 23 22 68 G L 8 60 72 3 0 0 8 e e 6 6 87 3 4 5 9 12 17 22 25 27 27 69 Q L 4 83 42 2 0 2 6 e e 5 28 69 5 6 8 12 17 22 25 24 20 17 70 T E 6 59 42 2 0 7 1 e e 2 80 19 9 10 11 15 18 21 23 21 16 12 71 V E 8 28 20 1 0 9 0 e i 3 89 6 16 17 19 21 22 21 17 12 7 4 72 T E 8 42 30 2 0 8 0 e i 3 89 8 14 14 16 20 22 23 20 14 8 5 73 I E 7 33 20 1 0 8 0 e i 6 85 6 19 19 20 23 24 22 17 10 5 3 74 W E 6 45 20 2 0 8 1 e i 6 79 10 15 17 20 24 25 23 18 11 6 3 75 A E 4 31 30 1 1 7 1 e i 10 64 17 15 15 16 18 21 22 21 17 12 9 76 A L 0 31 30 1 1 3 4 e i 17 35 40 12 13 15 18 20 22 21 19 16 13 77 N L 4 87 56 2 1 1 6 e e 18 19 60 5 6 8 12 15 19 22 23 22 21 78 A L 5 44 42 0 1 1 7 e e 15 12 71 8 9 11 14 16 19 21 21 21 20 79 G L 6 47 56 2 0 1 7 e e 6 17 79 6 7 9 12 15 18 21 23 23 21 80 V L 1 42 30 1 0 3 5 e i 4 40 58 11 12 14 17 19 20 19 17 15 13 81 T L 0 79 56 1 0 5 4 e e 3 58 42 6 7 10 14 17 19 21 22 21 20 82 A L 1 76 72 1 0 4 5 e e 5 44 55 7 8 10 13 16 17 19 20 21 21 83 S L 6 117 90 2 0 1 8 e e 1 19 83 4 5 7 11 14 17 18 20 24 25 84 P L 7 122 90 1 0 0 8 e e 3 8 87 4 5 8 12 15 17 19 21 23 24 85 P L 7 97 72 2 1 0 8 e e 10 5 84 4 5 6 9 13 17 21 23 26 26 86 T L 4 59 42 0 2 0 6 e e 27 8 69 6 7 10 14 17 19 20 20 20 19 87 D L 2 91 56 4 3 0 5 e e 33 10 61 2 2 4 7 12 18 24 27 26 23 88 L L 0 32 20 1 3 2 4 e i 30 25 39 12 14 17 20 21 20 18 15 12 10 89 I E 3 33 20 1 2 5 2 e i 22 54 21 15 16 18 21 22 20 18 13 10 7 90 W E 3 45 20 2 1 5 2 e i 16 56 24 13 15 17 21 22 21 19 14 11 8 91 K E 0 61 30 2 1 4 4 e i 13 44 39 5 7 11 17 20 23 23 20 16 13 92 N L 4 65 42 1 1 1 6 e e 12 19 68 7 8 11 16 18 20 21 20 19 17 93 Q L 5 110 56 1 1 1 7 e e 13 15 69 6 7 10 14 17 19 21 22 22 21 94 N L 6 87 56 1 0 1 7 e e 8 14 75 5 6 9 13 16 19 21 22 22 21 95 S L 5 93 72 1 1 1 7 e e 11 15 71 5 6 7 11 14 17 20 22 23 22 96 W L 5 68 30 0 1 1 7 e i 11 14 72 6 8 11 15 17 18 17 17 18 18 97 G L 6 75 90 2 0 1 8 e e 4 13 82 4 5 6 9 12 15 19 21 25 26 98 T L 6 102 72 1 0 1 7 e e 6 14 79 4 5 8 12 15 18 19 20 22 22 99 G L 6 60 72 1 0 1 7 e e 9 11 77 4 5 8 11 14 17 20 21 23 22 100 E L 3 139 72 4 2 1 6 e e 24 12 61 1 2 4 7 11 16 22 27 31 31 101 D L 3 91 56 2 2 2 5 e e 19 21 54 3 4 7 11 15 20 23 24 22 19 102 V E 1 17 12 1 2 4 3 b i 20 42 27 17 18 21 23 23 21 17 12 7 5 103 K E 4 61 30 3 1 6 1 e i 15 64 13 7 9 12 17 20 22 22 17 10 6 104 V E 5 28 20 1 1 7 0 e i 14 73 7 17 17 18 22 23 21 16 10 5 3 105 I E 6 33 20 1 1 8 0 e i 10 78 7 19 19 21 24 25 22 15 8 4 2 106 L E 7 32 20 1 0 8 0 e i 7 82 9 16 16 18 20 22 21 17 11 6 4 107 K E 6 86 42 1 0 7 1 e e 6 78 16 5 6 8 12 16 20 23 23 21 18 108 N L 3 65 42 1 0 2 6 e e 6 25 63 5 6 9 13 17 21 22 21 20 18 109 S L 7 93 72 2 0 1 8 e e 2 10 87 3 4 6 10 13 18 21 24 26 26 110 Q L 8 142 72 2 0 0 9 e e 3 6 88 3 4 6 9 13 18 23 26 27 27 111 G L 6 47 56 3 0 0 8 e e 9 9 78 4 5 7 10 14 19 23 24 23 21 112 E L 1 108 56 3 0 3 5 e e 9 36 49 3 4 6 10 14 19 24 25 24 21 113 E E 4 81 42 2 0 6 2 e e 8 64 24 4 5 8 13 17 21 23 23 19 16 114 V E 4 28 20 2 0 6 2 e i 6 65 25 13 15 17 21 23 22 18 12 8 6 115 A E 3 31 30 2 0 6 2 e i 5 64 29 11 12 14 18 21 22 21 17 13 9 116 Q E 4 83 42 2 0 7 2 e e 6 71 22 7 8 11 16 20 22 23 21 17 14 117 R E 4 104 42 3 0 7 2 e e 8 68 21 6 7 10 14 18 22 24 22 18 14 118 S E 3 54 42 2 0 6 2 e e 6 65 26 8 9 10 14 17 21 23 22 19 16 119 T E 4 59 42 2 0 7 2 e e 6 71 23 7 8 11 15 19 22 23 22 18 15 120 V E 5 42 30 1 0 7 2 e i 3 76 20 11 11 13 17 19 22 22 20 16 13 121 F E 5 39 20 1 0 7 2 e i 2 77 21 11 13 15 20 23 23 21 17 13 10 122 K E 4 114 56 3 0 7 2 e e 3 73 26 4 5 7 10 14 20 24 26 23 20 123 T E 3 59 42 2 0 6 3 e e 1 67 36 8 9 12 16 20 22 23 21 18 15 124 T L 0 59 42 0 0 4 5 e e 1 52 53 6 7 10 14 17 20 21 21 20 18 125 I L 7 121 72 0 0 1 8 e e 0 17 87 6 7 10 14 17 19 19 19 20 19 126 P L 8 76 56 2 0 0 9 e e 3 5 90 3 4 7 11 15 19 22 23 23 22 127 E L 5 139 72 2 2 0 7 e e 21 3 75 2 3 6 10 14 18 23 25 26 24 128 E L 0 139 72 4 4 0 4 e e 45 7 47 1 1 3 6 11 17 24 29 31 30 129 E L 0 174 90 2 5 0 4 e e 54 7 42 1 2 5 8 12 16 20 24 28 29 130 E L 0 139 72 3 4 0 4 e e 42 9 47 1 2 5 9 13 17 22 24 28 28 131 E L 2 174 90 3 3 1 5 e e 29 16 51 1 2 4 8 12 16 21 24 31 33 132 E L 6 174 90 5 0 1 7 e e 8 12 78 0 0 2 5 9 13 18 23 33 37 133 E L 9 174 90 9 0 0 9 e e 1 4 94 0 0 1 2 4 8 15 22 39 46