PFRMAT AL 
TARGET T0065 
AUTHOR 6795-8227-6214 
REMARK CASP3 Prediction by Michael Bass on 8/17/98 
METHOD AmgenThread.  Gapped alignments with no end penalties. 
METHOD Uses residue-based statistical potentials.  Specific 
METHOD potentials include exposed surface area, inter-residue 
METHOD distance-dependent contacts, and backbone dihedral 
METHOD angle preferences.  The search database is against the 
METHOD Hobohm PDB-SELECT list, Oct 97, at the 45% identity or 
METHOD less level containing 1,247 structures. 
METHOD This is an automatic prediction method. 
REMARK Results from database search: 
REMARK Sequence "t0065" has a significant match 
REMARK pdb1yrn_A     6.834     0.320    13.403  MOLECULE: MATING-TYPE PROTEIN A-1; 
REMARK                                          SCOP: Alpha; DNA-binding 3-helical bundle 
REMARK pdb1fxd       5.781     0.279    15.981  FERREDOXIN II 
REMARK                                          SCOP: A+B; Ferredoxin-like 
REMARK pdb6ins_E     4.763     0.240     7.362  INSULIN (PEPTIDE-LINKED, 29B - 1A, DES-30B) 
REMARK                                          SCOP: Small; Insulin-like 
REMARK pdb1lea       4.610     0.234     6.112  LEXA REPRESSOR DNA BINDING DOMAIN 
REMARK                                          SCOP: Alpha; DNA-binding 3-helical bundle 
REMARK pdb1mjc       4.413     0.226     7.272  MAJOR COLD SHOCK PROTEIN 7.4 (CSPA (CS 7.4)) OF 
REMARK                                          SCOP: Beta; OB-fold 
REMARK pdb1wfb_A     4.376     0.225     9.807  ANTIFREEZE PROTEIN ISOFORM HPLC6 (-180 DEGREES C) 
REMARK                                          SCOP: Peptides; Antifreeze polypeptide HPLC-6 
REMARK pdb1cei       4.174     0.217     7.868  MOLECULE: COLICIN E7 IMMUNITY PROTEIN; 
REMARK                                          SCOP: Alpha; Acyl carrier protein 
REMARK pdb1lfb       4.055     0.212    12.146  TRANSCRIPTION FACTOR LFB1 (HOMEODOMAIN) 
REMARK                                          SCOP: Alpha; DNA-binding 3-helical bundle 
REMARK pdb1aik_N     3.717     0.199    11.360  MOLECULE: HIV-1 GP41 GLYCOPROTEIN; 
REMARK pdb1r69       3.661     0.197     5.896  434 REPRESSOR (AMINO-TERMINAL DOMAIN) (R1-69) 
REMARK                                          SCOP: Alpha; lambda repressor-like DNA-binding domains 
REMARK pdb1cse_I     3.659     0.197    -0.026  SUBTILISIN CARLSBERG (E.C.3.4.21.62) (COMMERCIAL PRODUCT 
MODEL  1 
REMARK Sequence alignment follows: 
REMARK t0065        ........MKNAKQEHFELDQEWVELMVEAKEANISPEEIRKYLLLNKKS 
REMARK                      |: | .:|#.||.: .: |:|  . ||:.| |. ||.::  : 
REMARK pdb1yrn_A    ISPQARAFLEQVFRRKQSLNSKEKEEVAK..KCGITPLQVRVWFINKRMR 
REMARK  
REMARK t0065        AHPGPAARSHTVNPF 
REMARK                              
REMARK pdb1yrn_A    S.............. 
REMARK  
PARENT 1yrn_A 
M B1  L 85 
K B2  E 86 
N B3  Q 87 
A B4  V 88 
K B5  F 89 
Q B6  R 90 
E B7  R 91 
H B8  K 92 
F B9  Q 93 
E B10  S 94 
L B11  L 95 
D B12  N 96 
Q B13  S 97 
E B14  K 98 
W B15  E 99 
V B16  K 100 
E B17  E 101 
L B18  E 102 
M B19  V 103 
V B20  A 104 
E B21  K 105 
E B24  K 106 
A B25  C 107 
N B26  G 108 
I B27  I 109 
S B28  T 110 
P B29  P 111 
E B30  L 112 
E B31  Q 113 
I B32  V 114 
R B33  R 115 
K B34  V 116 
Y B35  W 117 
L B36  F 118 
L B37  I 119 
L B38  N 120 
N B39  K 121 
K B40  R 122 
K B41  M 123 
S B42  R 124 
A B43  S 125 
TER 
END 
