# 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 : LkR112 # VALUE PROT_NCHN : 1 # VALUE PROT_NRES : 140 # VALUE PROT_NALI : 97 # VALUE PROT_NFAR : 96 # VALUE PROT_NFAR50-5: 28 # VALUE PROT_NFAR40-5: 28 # VALUE PROT_NFAR30-5: 28 # VALUE PROT_NFAR5-5: 0 # # -------------------------------------------------------------------------------- # About the alignment: # # VALUE ALI_ORIG : LkR112.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 3 0 0 9 b e b e 2 0 96 10 9 8 9 11 13 15 17 24 28 2 R L L 0 0 104 0 42 2 4 0 4 b e b e 42 9 44 3 4 6 11 17 23 26 24 22 19 3 Q L H 2 0 110 0 56 4 5 1 2 b e b e 52 16 27 4 4 6 9 12 17 23 27 26 24 4 Y L H 3 0 0 0 0 0 5 2 2 b b b b 53 20 23 22 22 21 22 22 20 18 15 12 10 5 M L H 2 0 0 0 0 1 5 2 2 b b b b 50 23 22 27 25 22 22 20 18 15 12 10 8 6 K L H 3 0 114 0 56 3 5 2 2 b e b e 54 21 21 5 6 8 11 15 20 24 26 24 21 7 M L H 1 0 56 0 30 1 4 2 2 b e b i 42 28 25 13 13 15 18 21 22 22 20 18 15 8 V L L 0 0 0 0 0 1 3 2 4 b b b b 30 26 39 26 25 23 22 19 16 12 10 8 7 9 R L L 5 0 104 0 42 3 1 1 7 b e b e 14 15 68 6 6 9 13 19 23 26 24 20 16 10 P L L 5 0 76 0 56 2 1 1 7 b e b e 16 11 72 9 10 11 13 16 20 24 25 23 21 11 F L L 7 0 11 0 6 1 0 1 8 b b b b 8 10 80 18 20 23 23 21 17 14 12 12 12 12 D L L 6 0 68 0 42 2 0 1 8 b e b e 7 12 79 11 11 13 16 19 23 25 23 18 14 13 F L E 3 0 0 0 0 2 1 6 2 b b b b 11 60 27 27 26 22 20 17 15 11 8 5 4 14 V L E 7 0 0 0 0 6 0 8 1 b b b b 6 83 10 35 29 19 15 12 10 8 5 3 2 15 I L E 7 0 0 0 0 8 0 8 0 b b b b 8 84 8 41 34 20 13 9 7 5 3 1 0 16 I L E 7 0 0 0 0 9 1 8 0 b b b b 11 82 7 43 34 19 13 9 6 4 2 1 0 17 V L E 5 0 0 0 0 6 1 7 0 b b b b 20 75 10 38 32 20 15 12 9 6 4 2 1 18 A L E 3 0 0 0 0 6 2 6 1 b b b b 28 67 12 36 30 21 16 13 11 8 5 3 2 19 L L E 3 0 0 0 0 6 2 6 1 b b b b 32 66 12 36 30 20 15 12 9 7 5 3 2 20 I L E 3 0 0 0 0 4 2 5 1 b b b b 31 65 13 32 28 22 18 15 12 10 7 5 3 21 L L E 2 0 0 0 0 3 3 5 1 b b b b 34 55 19 30 27 22 19 17 15 12 10 8 6 22 G L E 0 0 0 0 0 1 3 3 3 b b b b 32 37 33 26 24 21 20 19 18 16 15 13 12 23 S L L 1 0 0 0 0 1 2 2 4 b b b b 30 26 49 24 23 20 20 19 18 17 14 12 10 24 F L L 1 0 0 0 0 1 2 3 4 b b b b 24 32 46 24 23 21 20 19 18 17 15 13 11 25 L L L 0 0 0 0 0 1 1 3 4 b b b b 20 39 45 27 25 22 21 19 17 14 11 9 7 26 P L E 0 0 0 0 0 1 1 4 3 b b b b 17 48 39 25 24 21 20 18 17 16 13 11 9 27 L L E 4 0 0 0 0 3 1 6 2 b b b b 15 65 21 31 29 23 20 16 14 11 8 6 4 28 L L E 6 0 0 0 0 4 0 7 1 b b b b 9 77 13 33 29 22 18 15 12 10 7 4 3 29 L L E 7 0 0 0 0 3 0 8 0 b b b b 7 84 8 31 28 21 18 15 13 10 7 4 3 30 F L E 7 0 0 0 0 4 0 8 0 b b b b 4 86 7 33 29 22 18 15 12 8 5 3 2 31 S L E 8 0 26 0 20 1 0 8 0 b e b i 4 89 7 18 17 18 21 22 22 18 14 9 6 32 V L E 6 0 0 0 0 2 0 8 1 b b b b 5 80 14 27 25 22 20 19 16 12 9 6 5 33 A L E 4 0 31 0 30 2 0 7 2 b e b i 5 69 24 13 14 16 19 22 23 22 18 14 10 34 E L E 1 0 81 0 42 2 1 5 4 b e b e 10 50 40 9 11 13 17 20 23 24 22 17 14 35 A L L 1 0 31 0 30 0 1 3 5 b e b i 11 35 53 11 12 13 16 18 21 21 21 20 19 36 K L L 3 0 184 0 90 3 1 2 6 b e b e 11 28 60 2 2 3 6 10 15 22 27 32 33 37 N L L 6 0 141 0 90 2 0 1 8 b e b e 7 12 80 6 6 8 11 14 17 20 23 26 27 38 T L L 8 0 127 0 90 2 0 0 8 b e b e 5 7 87 5 5 7 10 13 17 21 23 27 28 39 G L L 8 0 75 0 90 2 0 0 9 b e b e 3 6 88 6 6 7 10 13 17 20 24 27 28 40 D L L 6 0 68 0 42 1 0 1 8 b e b e 3 16 79 6 7 9 13 17 20 23 22 21 18 41 E L E 1 0 58 0 30 2 0 5 4 b e b i 3 57 40 13 14 15 19 21 22 21 18 14 10 42 V L E 6 0 0 0 0 1 0 8 1 b b b b 1 83 14 26 24 22 21 19 16 11 7 4 2 43 V L E 8 0 0 0 0 3 0 9 0 b b b b 2 90 5 30 27 22 20 18 15 10 5 2 1 44 A L E 8 0 0 0 0 7 0 9 0 b b b b 1 91 4 38 30 16 13 12 10 7 4 2 1 45 I L E 9 0 0 0 0 4 0 9 0 b b b b 1 93 3 32 27 18 16 15 13 9 6 3 2 46 I L E 8 0 0 0 0 6 0 9 0 b b b b 1 92 4 39 32 21 16 13 10 6 3 2 1 47 S L E 6 0 39 0 30 2 0 8 1 b e b i 1 82 13 15 15 17 20 23 24 21 16 10 7 48 Q L E 2 0 59 0 30 2 0 6 3 b e b i 2 62 33 12 13 16 19 22 24 23 19 15 13 49 N L L 7 0 113 0 72 2 0 1 8 b e b e 2 11 84 6 6 7 10 14 19 22 25 26 25 50 G L L 7 0 35 0 42 1 0 1 8 b e b e 3 10 84 12 12 13 16 18 21 22 21 19 18 51 K L L 0 0 114 0 56 3 0 4 5 b e b e 3 43 48 4 5 6 9 13 18 23 25 24 22 52 V L E 6 0 42 0 30 1 0 8 1 b e b i 2 83 16 15 14 14 18 20 21 20 16 11 8 53 I L E 8 0 0 0 0 1 0 9 0 b b b b 1 89 8 26 24 21 20 19 16 12 8 4 3 54 R L E 8 0 74 0 30 3 0 9 0 b e b i 1 91 6 9 10 13 18 23 26 25 19 12 7 55 E L E 8 0 58 0 30 3 0 9 0 b e b i 2 91 7 8 10 12 18 21 24 23 19 12 7 56 I L E 7 0 0 0 0 0 0 8 1 b b b b 1 86 12 25 25 24 24 21 17 11 7 4 2 57 P L E 6 0 57 0 42 3 0 8 1 b e b e 2 84 15 7 8 10 14 19 23 26 25 20 16 58 L L E 4 0 0 0 0 2 0 7 2 b b b b 3 72 26 29 26 23 20 17 15 11 8 5 5 59 T L E 0 0 59 0 42 2 0 4 4 b e b e 4 48 47 9 10 12 16 20 23 24 22 19 16 60 G L L 4 0 75 0 90 1 0 2 7 b e b e 5 23 72 7 7 9 12 15 18 20 22 24 25 61 H L L 6 0 165 0 90 1 0 1 7 b e b e 5 16 79 6 7 9 12 16 20 22 24 25 26 62 K L L 6 0 184 0 90 3 0 1 7 b e b e 5 17 79 1 2 3 6 10 16 23 28 33 34 63 G L L 6 0 60 0 72 3 0 1 8 b e b e 4 14 79 5 5 6 9 12 17 22 26 29 29 64 N L L 4 0 65 0 42 0 0 2 7 b e b e 4 23 72 5 6 8 12 16 20 24 24 23 21 65 E L E 0 0 81 0 42 2 0 4 4 b e b e 4 49 48 9 10 12 16 19 22 23 21 17 14 66 Q L E 5 0 59 0 30 2 0 7 2 b e b i 2 76 22 10 11 13 17 20 23 22 19 14 10 67 F L E 7 0 0 0 0 1 0 8 1 b b b b 1 87 10 28 27 25 23 19 14 9 5 3 2 68 T L E 8 0 42 0 30 3 0 9 0 b e b i 2 92 6 11 12 14 19 23 25 23 17 11 6 69 I L E 8 0 0 0 0 3 0 9 0 b b b b 1 90 8 32 28 23 19 17 14 9 6 3 2 70 K L E 6 0 86 0 42 3 0 7 1 b e b e 2 80 19 5 6 9 14 20 26 27 23 17 12 71 G L E 0 0 25 0 30 0 0 4 4 b e b i 3 48 48 14 15 16 18 20 21 21 20 18 17 72 K L L 5 0 184 0 90 2 0 2 7 b e b e 4 20 76 3 4 5 9 13 18 23 26 29 30 73 G L L 7 0 75 0 90 3 0 1 8 b e b e 4 10 85 4 4 5 8 11 16 21 25 30 32 74 A L L 7 0 44 0 42 0 0 1 8 b e b e 3 14 84 9 10 11 14 17 21 22 22 21 20 75 Q L L 2 0 83 0 42 2 0 3 6 b e b e 3 37 62 8 8 10 14 17 21 24 24 20 17 76 Y L E 4 0 44 0 20 2 0 7 2 b e b i 3 71 26 16 18 21 24 25 22 18 12 8 6 77 N L E 7 0 31 0 20 0 0 8 1 b e b i 2 85 12 19 18 17 19 21 21 18 13 8 5 78 L L E 8 0 0 0 0 2 0 9 0 b b b b 2 89 6 29 26 21 20 18 15 11 7 3 2 79 M L E 8 0 0 0 0 6 0 9 0 b b b b 1 92 5 38 32 20 16 13 10 6 4 2 1 80 E L E 8 0 58 0 30 2 0 9 0 b e b i 1 90 8 13 14 16 20 22 24 22 17 11 8 81 V L E 5 0 0 0 0 3 0 7 2 b b b b 1 77 23 30 28 23 20 18 15 11 7 5 4 82 D L L 2 0 68 0 42 1 0 3 6 b e b e 1 39 63 4 5 7 11 16 22 25 25 22 19 83 G L L 7 0 60 0 72 1 0 0 8 b e b e 2 8 87 8 8 9 12 15 19 22 23 25 25 84 E L L 6 0 108 0 56 2 0 1 8 b e b e 3 14 80 6 7 9 12 16 20 23 24 24 24 85 R L E 2 0 104 0 42 2 0 5 3 b e b e 4 58 37 7 8 11 15 19 23 24 22 18 14 86 I L E 7 0 0 0 0 3 0 8 1 b b b b 1 85 13 33 29 23 20 16 12 8 5 3 2 87 R L E 8 0 74 0 30 3 0 8 0 b e b i 2 89 8 8 9 12 18 22 25 24 18 11 6 88 I L E 8 0 0 0 0 3 0 8 0 b b b b 2 89 8 32 28 22 19 17 14 10 6 3 2 89 K L E 5 0 86 0 42 3 0 7 2 b e b e 2 75 22 5 6 8 13 18 24 26 22 16 12 90 E L E 0 0 81 0 42 1 0 5 4 b e b e 3 49 45 10 11 14 17 20 22 23 22 20 18 91 D L L 5 0 117 0 72 2 0 1 7 b e b e 4 19 74 6 7 8 12 15 18 20 22 25 25 92 N L L 6 0 141 0 90 2 0 1 8 b e b e 4 15 81 4 5 6 9 13 18 22 26 29 30 93 S L L 8 0 15 0 12 1 0 0 8 b b b i 3 8 88 18 19 21 22 22 20 17 14 12 11 94 P L L 7 0 97 0 72 2 0 0 8 b e b e 8 6 83 7 8 9 12 15 18 21 23 25 24 95 D L L 7 0 117 0 72 0 0 0 8 b e b e 9 9 80 8 9 10 13 17 20 21 22 23 23 96 Q L L 1 0 59 0 30 1 1 3 5 b e b i 10 36 54 11 12 14 17 20 22 22 20 17 15 97 V L E 3 0 0 0 0 1 0 6 3 b b b b 5 66 32 28 27 23 22 19 15 11 8 5 4 98 G L E 5 0 0 0 0 2 0 7 2 b b b b 5 74 22 27 24 21 20 19 18 15 11 7 5 99 V L E 5 0 0 0 0 3 0 7 2 b b b b 6 73 20 30 27 22 20 17 15 12 9 6 5 100 K L E 3 0 86 0 42 2 0 6 2 b e b e 5 65 29 8 9 11 14 18 22 24 23 19 15 101 M L E 1 0 56 0 30 0 0 5 3 b e b i 9 52 40 14 14 15 18 20 21 21 20 18 16 102 G L L 0 0 25 0 30 0 0 4 4 b e b i 7 45 50 15 14 14 17 19 21 21 20 18 16 103 W L E 2 0 68 0 30 1 0 5 3 b e b i 6 61 35 14 15 16 19 21 22 21 19 17 15 104 K L E 4 0 61 0 30 1 0 6 2 b e b i 7 68 28 13 13 13 16 19 21 21 19 15 12 105 S L E 0 0 54 0 42 0 0 4 4 b e b e 7 50 44 11 12 13 15 18 20 21 21 20 19 106 K L L 5 0 147 0 72 2 0 2 7 b e b e 5 23 73 3 4 6 10 14 19 23 25 27 27 107 A L L 7 0 95 0 90 4 0 0 8 b e b e 5 9 86 4 4 5 7 10 15 20 26 31 34 108 G L L 8 0 60 0 72 1 0 0 8 b e b e 3 8 89 9 9 10 13 15 19 21 23 24 24 109 D L L 4 0 68 0 42 2 0 2 7 b e b e 3 25 71 10 11 13 16 19 22 23 21 18 15 110 T L E 4 0 28 0 20 1 0 7 2 b e b i 3 72 27 17 17 16 19 21 21 19 15 10 7 111 I L E 7 0 0 0 0 5 0 8 1 b b b b 2 87 10 35 29 20 17 15 13 10 8 5 3 112 V L E 8 0 0 0 0 5 0 8 0 b b b b 2 89 8 34 28 19 17 15 13 9 7 4 3 113 C L E 5 0 0 0 0 6 0 7 2 b b b b 2 79 21 37 31 21 16 13 11 8 5 3 2 114 L L L 1 0 0 0 0 3 0 4 5 b b b b 2 43 58 33 29 24 21 18 14 10 6 3 2 115 P L L 6 0 0 0 0 0 0 1 7 b b b b 3 17 79 23 22 20 20 20 19 18 16 14 12 116 H L L 6 0 55 0 30 1 0 1 7 b e b i 6 16 76 15 16 18 21 23 24 23 19 16 14 117 K L E 1 0 61 0 30 2 0 5 3 b e b i 6 56 38 12 13 16 20 23 24 23 20 15 13 118 V L E 6 0 0 0 0 4 0 8 1 b b b b 3 82 13 33 29 21 18 15 13 9 6 3 2 119 F L E 8 0 0 0 0 3 0 9 0 b b b b 3 91 4 29 25 20 19 18 16 12 9 5 3 120 V L E 8 0 0 0 0 8 0 9 0 b b b b 1 91 4 41 33 19 13 10 8 5 3 2 1 121 E L E 8 0 58 0 30 3 0 9 0 b e b i 1 92 4 10 11 13 18 21 24 22 17 11 6 122 I L E 8 0 0 0 0 5 0 9 0 b b b b 2 88 7 35 30 22 18 15 12 8 5 3 2 123 K L E 4 0 86 0 42 2 0 7 2 b e b e 2 74 25 5 6 8 12 17 23 25 24 19 16 124 S L L 2 0 39 0 30 0 0 3 5 b e b i 3 39 59 13 14 15 18 19 20 19 18 17 15 125 T L L 5 0 59 0 42 0 0 1 7 b e b e 6 19 72 7 8 10 14 18 21 23 23 23 23 126 Q L L 5 0 142 0 72 1 1 1 7 b e b e 11 15 72 5 6 9 13 16 20 23 24 25 25 127 K L L 5 0 184 0 90 3 1 1 7 b e b e 16 12 69 2 3 4 7 10 16 21 26 31 32 128 D L L 6 0 117 0 72 2 1 0 7 b e b e 15 9 75 4 5 7 11 15 19 22 24 26 26 129 S L L 6 0 93 0 72 2 1 0 8 b e b e 13 6 77 5 6 8 12 15 18 21 24 26 26 130 K L L 5 0 147 0 72 3 1 0 7 b e b e 15 8 72 2 3 5 8 11 16 21 25 28 28 131 D L L 6 0 117 0 72 1 1 0 8 b e b e 10 8 78 7 8 10 13 16 19 21 21 23 22 132 P L L 7 0 97 0 72 1 0 0 8 b e b e 9 6 82 6 7 9 13 16 19 20 21 23 23 133 D L L 7 0 117 0 72 2 1 0 8 b e b e 11 5 83 5 6 7 10 13 18 21 24 26 26 134 T L L 5 0 42 0 30 1 1 1 7 b e b i 15 11 73 12 13 15 17 19 20 20 19 16 14 135 D L L 4 0 68 0 42 1 1 2 6 b e b e 11 24 64 13 13 14 17 19 21 22 21 18 16 136 L L E 1 0 0 0 0 0 0 5 3 b b b b 6 55 37 24 22 21 21 20 18 15 12 9 8 137 I L E 3 0 0 0 0 1 0 6 2 b b b b 4 65 28 24 22 19 19 20 19 17 14 12 10 138 V L E 0 0 0 0 0 0 0 5 4 b b b b 3 51 45 23 22 21 21 20 19 17 13 10 8 139 P L L 3 0 97 0 72 2 0 3 6 b e b e 4 30 66 6 6 8 11 14 16 19 20 24 24 140 N L L 9 0 141 0 90 7 0 0 9 b e b e 2 2 94 2 2 3 4 6 10 14 19 32 39