# 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 : PaR198 # VALUE PROT_NCHN : 1 # VALUE PROT_NRES : 132 # VALUE PROT_NALI : 138 # VALUE PROT_NFAR : 138 # VALUE PROT_NFAR50-5: 58 # VALUE PROT_NFAR40-5: 58 # VALUE PROT_NFAR30-5: 58 # VALUE PROT_NFAR5-5: 0 # # -------------------------------------------------------------------------------- # About the alignment: # # VALUE ALI_ORIG : PaR198.fasta.hsspFil # # -------------------------------------------------------------------------------- # About PROF specifics: # # VALUE PROF_FPAR : acc=/farm/users/tong/work/devel/prof/test/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_NCHN : number of chains (if PDB protein) [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 OHEL : observed secondary structure: H=helix, E=extended (sheet), blank=other (loop) # 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 OACC : observed solvent accessibility (acc) in square Angstroem (taken from DSSP: W Kabsch and C Sander, Biopolymers, 22, 2577-2637, 1983) # NOTATION PACC : PROF predicted solvent accessibility (acc) in square Angstroem # NOTATION OREL : observed 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 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 Obe : observerd relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%. # NOTATION Pbe : PROF predicted relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%. # NOTATION Obie : observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%. # 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 OHEL PHEL RI_S OACC PACC OREL PREL RI_A pH pE pL Obe Pbe Obie Pbie OtH OtE OtL Ot0 Ot1 Ot2 Ot3 Ot4 Ot5 Ot6 Ot7 Ot8 Ot9 1 M L L 9 0 169 0 90 2 0 0 9 b e b e 1 0 97 10 10 9 12 13 14 15 16 21 23 2 T L L 6 0 102 0 72 0 1 0 8 b e b e 10 7 78 6 7 9 13 17 21 23 23 24 22 3 R L L 4 0 178 0 72 2 1 1 6 b e b e 18 13 64 2 3 5 9 13 19 24 26 27 25 4 A L L 1 0 31 0 30 1 3 1 4 b e b i 31 19 48 14 14 14 17 19 21 21 20 17 14 5 I L L 3 0 20 0 12 0 2 2 5 b b b i 23 20 54 22 22 22 23 22 19 15 12 11 10 6 N L L 6 0 65 0 42 0 1 1 7 b e b e 10 12 77 8 9 12 16 19 21 23 22 22 20 7 D L L 7 0 117 0 72 0 1 0 8 b e b e 10 4 85 6 8 10 14 17 19 20 20 21 20 8 P L L 6 0 122 0 90 1 1 0 8 b e b e 11 4 80 7 7 9 13 15 18 20 22 24 25 9 G L L 5 0 60 0 72 1 1 0 7 b e b e 18 4 73 7 8 10 14 17 19 21 22 23 22 10 N L L 6 0 113 0 72 2 1 0 8 b e b e 12 3 81 5 6 8 12 16 19 22 23 26 26 11 E L L 7 0 174 0 90 2 0 0 8 b e b e 7 4 84 3 4 6 10 13 16 21 24 29 30 12 D L L 8 0 68 0 42 1 0 0 9 b e b e 5 3 88 7 8 11 15 18 21 22 21 19 16 13 P L L 3 0 40 0 30 1 3 0 6 b e b i 31 2 63 12 13 14 18 20 22 22 21 18 16 14 G L H 1 0 60 0 72 3 5 0 4 b e b e 54 2 39 5 5 7 9 12 15 20 24 25 24 15 S L H 2 0 54 0 42 2 6 0 3 b e b e 60 4 32 9 10 12 15 18 21 24 23 18 14 16 L L H 3 0 0 0 0 0 6 0 2 b b b b 64 3 26 23 22 21 22 20 18 14 12 9 8 17 L L H 3 0 49 0 30 2 6 0 3 b e b i 63 2 32 12 13 14 17 20 22 22 19 14 11 18 E L H 4 0 108 0 56 3 7 0 2 b e b e 68 2 25 5 5 7 10 14 20 24 26 24 22 19 T L H 6 0 79 0 56 3 8 0 1 b e b e 76 2 15 6 6 8 10 14 18 22 24 23 21 20 D L H 7 0 68 0 42 2 8 0 1 b e b e 82 3 11 12 13 15 18 22 24 25 21 15 11 21 A L H 7 0 0 0 0 3 8 0 0 b b b b 86 1 9 29 26 20 18 16 13 11 9 7 5 22 D L H 8 0 68 0 42 2 9 0 0 b e b e 89 1 6 6 7 9 13 17 21 25 25 21 17 23 A L H 8 0 44 0 42 2 9 0 0 b e b e 88 1 7 10 10 11 13 16 20 24 24 20 16 24 L L H 7 0 0 0 0 2 8 0 0 b b b b 85 1 9 26 23 20 19 19 17 16 13 11 9 25 L L H 5 0 0 0 0 1 8 0 1 b b b b 75 2 16 24 23 20 20 20 18 17 14 11 8 26 G L H 3 0 47 0 56 2 6 0 3 b e b e 62 2 28 12 12 11 13 15 19 23 24 22 19 27 G L H 2 0 0 0 0 0 5 0 3 b b b b 54 3 34 22 21 19 19 19 19 18 17 15 13 28 A L H 3 0 0 0 0 1 6 0 3 b b b b 60 4 30 25 23 20 19 19 17 16 14 13 11 29 A L H 1 0 76 0 72 0 5 0 4 b e b e 51 4 39 12 12 12 14 16 18 19 20 21 21 30 A L L 1 0 44 0 42 0 4 0 5 b e b e 40 3 51 12 13 14 17 19 20 21 20 20 19 31 Q L L 2 0 142 0 72 2 3 0 6 b e b e 33 4 59 7 7 9 11 15 19 22 24 26 26 32 A L L 3 0 31 0 30 2 3 0 6 b e b i 30 2 67 10 11 13 17 21 23 23 20 16 13 33 P L H 3 0 57 0 42 1 6 0 3 b e b e 64 1 30 11 11 12 14 17 19 21 21 19 17 34 E L H 6 0 108 0 56 2 8 0 1 b e b e 81 1 13 8 9 11 14 17 20 23 24 22 20 35 E L H 7 0 108 0 56 4 8 0 1 b e b e 86 0 10 4 5 6 9 13 17 24 27 26 23 36 R L H 8 0 74 0 30 2 9 0 0 b e b i 88 1 8 13 14 15 19 21 22 21 17 12 8 37 C L H 7 0 0 0 0 4 9 0 0 b b b b 87 1 8 35 31 23 19 15 11 7 4 2 1 38 R L H 8 0 104 0 42 2 9 0 0 b e b e 89 1 6 8 9 11 16 20 24 25 20 13 7 39 L L H 8 0 68 0 42 3 9 0 0 b e b e 92 0 4 7 8 11 15 19 23 25 23 16 11 40 A L H 8 0 0 0 0 4 9 0 0 b b b b 93 0 4 32 27 19 17 15 13 10 8 5 4 41 A L H 9 0 0 0 0 4 9 0 0 b b b b 95 0 3 33 29 20 17 14 11 8 5 3 2 42 Q L H 9 0 83 0 42 3 9 0 0 b e b e 95 0 3 7 7 9 13 17 22 26 24 18 13 43 A L H 9 0 31 0 30 2 9 0 0 b e b i 94 0 4 14 15 17 21 23 24 22 16 10 6 44 C L H 8 0 0 0 0 8 9 0 0 b b b b 93 0 4 41 33 19 13 10 7 5 3 1 1 45 I L H 9 0 0 0 0 0 9 0 0 b b b b 94 0 4 24 24 22 22 20 16 12 8 5 3 46 R L H 9 0 138 0 56 4 9 0 0 b e b e 94 0 4 4 5 6 9 14 21 28 29 22 16 47 A L H 8 0 0 0 0 1 9 0 0 b b b b 93 0 4 24 22 20 20 20 18 15 11 8 5 48 C L H 8 0 0 0 0 7 9 0 0 b b b b 92 0 4 39 32 20 15 11 8 5 3 1 1 49 E L H 8 0 81 0 42 2 9 0 0 b e b e 91 0 5 10 10 12 16 20 23 24 21 16 12 50 R L H 8 0 138 0 56 3 9 0 0 b e b e 91 0 5 4 5 7 11 16 22 26 27 22 17 51 Y L H 8 0 0 0 0 2 9 0 0 b b b b 90 0 6 28 25 21 19 17 14 10 7 5 3 52 L L H 8 0 0 0 0 1 9 0 0 b b b b 90 0 6 26 25 22 22 20 16 12 8 6 4 53 A L H 7 0 59 0 56 5 9 0 0 b e b e 86 0 9 5 5 6 8 11 16 24 29 27 24 54 L L H 7 0 49 0 30 3 8 0 0 b e b i 85 1 9 9 10 14 19 23 26 25 21 15 11 55 C L H 5 0 0 0 0 4 7 0 2 b b b b 73 1 19 33 29 23 19 16 12 8 6 4 3 56 T L H 4 0 59 0 42 1 7 0 2 b e b e 71 0 24 13 14 15 18 21 23 24 21 16 12 57 E L H 4 0 139 0 72 3 7 0 2 b e b e 68 1 26 3 4 5 8 11 15 21 26 28 28 58 S L H 2 0 39 0 30 1 6 0 3 b e b i 61 1 32 12 13 15 18 21 22 21 19 16 14 59 S L H 2 0 26 0 20 0 6 0 3 b e b i 57 1 37 16 15 15 17 19 19 19 17 15 14 60 R L H 3 0 138 0 56 2 6 0 3 b e b e 63 2 29 6 7 9 13 17 20 23 24 22 20 61 E L H 4 0 108 0 56 2 7 0 2 b e b e 67 1 27 7 7 9 12 16 19 23 25 23 21 62 Q L H 3 0 83 0 42 1 6 0 2 b e b e 67 1 28 13 13 13 16 18 19 20 19 17 15 63 R L H 1 0 104 0 42 1 5 0 4 b e b e 55 2 39 10 11 13 15 18 20 21 21 19 17 64 Q L H 1 0 142 0 72 2 5 0 4 b e b e 53 2 41 5 6 8 10 13 17 21 24 25 25 65 H L L 0 0 77 0 42 1 4 0 5 b e b e 46 2 50 11 12 14 17 19 20 21 19 18 16 66 A L L 0 0 31 0 30 0 4 0 4 b e b i 48 2 48 17 17 16 17 18 19 19 18 17 15 67 G L L 0 0 25 0 30 1 4 0 5 b e b i 43 3 52 10 11 13 17 21 23 23 20 17 15 68 D L H 1 0 48 0 30 2 5 0 4 b e b i 56 2 40 12 12 14 17 21 24 24 20 15 11 69 C L H 6 0 0 0 0 5 8 0 1 b b b b 80 2 16 35 30 22 18 15 12 8 6 4 3 70 A L H 8 0 0 0 0 2 9 0 0 b b b b 90 1 7 26 24 19 19 17 15 13 10 7 5 71 D L H 8 0 68 0 42 2 9 0 0 b e b e 93 1 4 12 13 13 17 20 23 24 20 13 7 72 L L H 9 0 0 0 0 4 9 0 0 b b b b 94 0 3 33 28 21 18 16 13 9 6 3 2 73 C L H 8 0 0 0 0 6 9 0 0 b b b b 93 0 4 38 32 20 15 11 8 5 3 1 0 74 R L H 9 0 74 0 30 3 9 0 0 b e b i 94 0 3 12 13 14 18 22 25 23 18 11 7 75 L L H 9 0 0 0 0 1 9 0 0 b b b b 95 0 2 24 23 20 20 19 17 14 10 7 5 76 A L H 9 0 0 0 0 6 9 0 0 b b b b 95 0 2 37 30 17 14 11 8 6 4 2 1 77 A L H 9 0 0 0 0 2 9 0 0 b b b b 95 0 2 26 24 18 17 16 15 13 10 6 4 78 L L H 9 0 49 0 30 3 9 0 0 b e b i 94 1 3 11 12 15 20 24 26 24 19 12 7 79 L L H 8 0 0 0 0 1 9 0 0 b b b b 93 1 4 26 24 21 20 19 16 13 9 6 4 80 L L H 8 0 0 0 0 3 9 0 0 b b b b 88 1 7 31 27 21 18 16 13 11 8 6 5 81 E L H 5 0 81 0 42 1 7 0 2 b e b e 73 1 22 11 12 13 15 18 20 21 21 18 16 82 R L H 1 0 104 0 42 1 5 0 4 b e b e 51 1 41 7 8 11 16 20 23 24 22 20 18 83 R L L 4 0 138 0 56 2 2 0 7 b e b e 26 1 70 7 8 9 12 15 19 22 24 24 24 84 S L L 7 0 15 0 12 1 1 0 8 b b b i 11 2 85 17 19 22 23 23 20 17 14 12 11 85 P L L 5 0 97 0 72 2 2 0 7 b e b e 22 3 72 6 6 7 10 14 19 24 27 28 27 86 W L L 2 0 27 0 12 1 3 0 6 b b b i 35 3 59 17 19 21 23 22 20 17 13 10 8 87 A L H 4 0 0 0 0 0 7 0 2 b b b b 68 1 27 21 21 19 20 20 19 16 13 9 7 88 P L H 8 0 76 0 56 2 9 0 0 b e b e 88 0 6 7 7 9 12 16 20 24 25 21 18 89 A L H 8 0 31 0 30 2 9 0 0 b e b i 92 1 3 11 12 15 19 22 23 22 18 12 8 90 A L H 9 0 0 0 0 5 9 0 0 b b b b 93 1 3 34 28 19 16 14 11 7 5 2 1 91 C L H 9 0 0 0 0 1 9 0 0 b b b b 93 1 3 27 25 22 22 19 15 10 6 3 2 92 E L H 9 0 81 0 42 3 9 0 0 b e b e 94 1 3 7 7 9 12 16 21 25 24 17 11 93 L L H 9 0 0 0 0 0 9 0 0 b b b b 94 0 4 24 23 21 21 20 17 13 8 5 3 94 A L H 9 0 0 0 0 7 9 0 0 b b b b 96 0 2 39 32 19 15 12 9 6 4 2 1 95 A L H 9 0 0 0 0 1 9 0 0 b b b b 94 0 3 25 23 19 19 18 16 13 10 6 4 96 R L H 9 0 104 0 42 3 9 0 0 b e b e 95 0 3 6 7 9 13 18 23 26 23 16 11 97 Y L H 8 0 0 0 0 3 9 0 0 b b b b 93 0 4 29 26 21 19 17 15 11 7 4 2 98 A L H 9 0 0 0 0 6 9 0 0 b b b b 94 0 3 36 30 20 16 13 10 7 4 2 1 99 L L H 9 0 68 0 42 2 9 0 0 b e b e 94 0 3 7 8 9 12 17 21 25 25 20 16 100 A L H 9 0 31 0 30 3 9 0 0 b e b i 93 1 3 10 12 15 20 24 26 24 19 12 7 101 C L H 8 0 0 0 0 5 9 0 0 b b b b 91 1 5 35 30 21 17 14 11 7 4 2 1 102 A L H 8 0 0 0 0 2 9 0 0 b b b b 91 0 5 28 25 20 19 17 15 12 9 7 5 103 E L H 7 0 108 0 56 5 9 0 0 b e b e 87 0 9 2 3 4 7 11 16 24 30 29 27 104 R L H 7 0 104 0 42 3 8 0 1 b e b e 85 1 10 6 8 11 16 21 25 27 24 19 15 105 C L H 3 0 0 0 0 1 6 0 3 b b b b 63 1 30 28 27 25 24 21 15 11 7 5 4 106 D L H 0 0 91 0 56 2 5 0 4 b e b e 51 1 47 8 8 10 13 16 20 24 25 24 23 107 G L L 4 0 75 0 90 4 2 0 7 b e b e 27 1 73 2 3 5 8 12 15 19 23 30 33 108 D L L 4 0 117 0 72 1 2 0 7 b e b e 24 1 73 4 5 7 11 15 20 23 25 26 26 109 E L L 3 0 108 0 56 3 3 0 6 b e b e 29 2 63 4 5 7 10 15 19 23 25 25 25 110 P L H 3 0 97 0 72 3 6 0 3 b e b e 63 1 31 4 5 7 10 13 17 22 27 28 27 111 L L H 6 0 32 0 20 1 8 0 1 b e b i 77 1 16 12 13 15 18 21 21 20 17 13 10 112 E L H 7 0 58 0 30 1 8 0 1 b e b i 87 1 10 16 16 17 20 21 22 20 16 11 8 113 R L H 8 0 104 0 42 3 9 0 0 b e b e 91 0 5 5 5 8 11 16 21 25 25 19 15 114 E L H 9 0 58 0 30 3 9 0 0 b e b i 94 1 4 8 9 13 17 21 24 24 19 12 7 115 C L H 8 0 0 0 0 7 9 0 0 b b b b 93 1 4 40 33 20 15 12 9 6 4 2 1 116 A L H 8 0 0 0 0 2 9 0 0 b b b b 93 0 4 28 25 20 19 17 15 12 8 5 3 117 G L H 9 0 35 0 42 3 9 0 0 b e b e 95 0 3 6 6 8 12 16 22 27 27 20 14 118 A L H 9 0 0 0 0 2 9 0 0 b b b b 94 0 3 27 24 19 18 18 16 13 9 6 4 119 C L H 9 0 0 0 0 8 9 0 0 b b b b 95 0 3 42 33 18 13 9 6 4 2 1 0 120 R L H 9 0 104 0 42 4 9 0 0 b e b e 95 0 3 5 5 8 12 17 23 27 24 17 11 121 R L H 9 0 104 0 42 3 9 0 0 b e b e 94 0 3 7 8 12 17 22 26 27 22 14 9 122 F L H 9 0 0 0 0 7 9 0 0 b b b b 94 0 3 40 32 19 14 10 7 5 3 2 1 123 V L H 9 0 0 0 0 0 9 0 0 b b b b 95 0 2 23 21 19 21 22 20 16 11 7 4 124 E L H 9 0 108 0 56 7 9 0 0 b e b e 93 0 3 2 2 3 6 10 18 28 34 31 26 125 A L H 8 0 21 0 20 2 9 0 0 b e b i 92 1 3 13 14 17 22 26 26 23 17 11 7 126 C L H 8 0 0 0 0 8 9 0 0 b b b b 89 1 6 41 33 20 14 10 6 4 3 2 1 127 R L H 8 0 74 0 30 3 9 0 0 b e b i 88 1 6 9 10 14 19 24 26 26 21 15 10 128 P L H 6 0 122 0 90 4 8 0 1 b e b e 83 1 14 2 3 3 5 8 12 19 27 32 34 129 L L H 4 0 32 0 20 1 7 0 2 b e b i 72 3 25 18 19 20 22 23 21 19 16 13 12 130 L L L 2 0 19 0 12 0 3 0 5 b b b i 37 4 57 19 19 21 22 22 19 17 14 12 12 131 P L L 7 0 122 0 90 5 1 0 8 b e b e 13 2 83 2 2 4 6 9 13 18 23 31 36 132 A L L 9 0 95 0 90 7 0 0 9 b e b e 2 2 94 5 5 5 6 7 8 10 14 29 36