
PFRMAT AL
TARGET T0096
AUTHOR 7574-7279-4773
REMARK CASP4 Prediction by Michael Bass on 9/8/2000
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 a set of PDB structures sharing 45% identity or
METHOD less level containing 2,205 structures.
METHOD This is an automatic prediction method.
REMARK Results from database search:
REMARK Sequence "t0096n" has a significant match
REMARK pdb1lea       8.255     0.330    14.145  LEXA REPRESSOR DNA BINDING DOMAIN
REMARK                                          SCOP: Alpha; DNA/RNA-binding 3-helical bundle
REMARK pdb1qbj_A     8.091     0.324    23.084  MOLECULE: DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE
REMARK                                          SCOP: Alpha; DNA/RNA-binding 3-helical bundle
REMARK pdb1hst_A     6.727     0.277    11.320  HISTONE H5 (GLOBULAR DOMAIN)
REMARK                                          SCOP: Alpha; DNA/RNA-binding 3-helical bundle
REMARK pdb1b72_B     6.397     0.266    13.275  MOLECULE: HOMEOBOX PROTEIN HOX-B1;
REMARK                                          SCOP: Alpha; DNA/RNA-binding 3-helical bundle
REMARK pdb1nkl       6.281     0.262    11.710  MOLECULE: NK-LYSIN;
REMARK                                          SCOP: Alpha; Saposin
REMARK pdb1cy5_A     6.251     0.261     6.720  MOLECULE: APOPTOTIC PROTEASE ACTIVATING FACTOR 1;
REMARK                                          SCOP: Alpha; DEATH domain
REMARK pdb1ay7_B     5.592     0.238    12.648  MOLECULE: GUANYL-SPECIFIC RIBONUCLEASE SA;
REMARK                                          SCOP: A/B; Barstar (barnase inhibitor)
REMARK pdb5icb       5.445     0.233     8.177  MOLECULE: CALBINDIN D9K;
REMARK                                          SCOP: Alpha; EF Hand-like
REMARK pdb1rzl       5.376     0.230     2.992  MOLECULE: NONSPECIFIC LIPID TRANSFER PROTEIN;
REMARK                                          SCOP: Alpha; Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
REMARK pdb1smt_A     5.164     0.223    13.732  MOLECULE: TRANSCRIPTIONAL REPRESSOR SMTB;
REMARK                                          SCOP: Alpha; DNA/RNA-binding 3-helical bundle
REMARK
REMARK Results from database search:
REMARK Sequence "t0096c" has a significant match
REMARK pdb1or3_A     5.980     0.215     8.395  MOLECULE: APOLIPOPROTEIN E;
REMARK                                          SCOP: Alpha; Four-helical up-and-down bundle
REMARK pdb2a0b       5.254     0.193    11.543  MOLECULE: HPT DOMAIN;
REMARK                                          SCOP: Alpha; Four-helical up-and-down bundle
REMARK pdb1cpq       4.913     0.183    15.697  MOLECULE: CYTOCHROME C';
REMARK                                          SCOP: Alpha; Four-helical up-and-down bundle
REMARK pdb2abk       4.819     0.181     4.755  MOLECULE: ENDONUCLEASE III;
REMARK                                          SCOP: Alpha; DNA-glycosylase
REMARK pdb1eca       4.785     0.180    10.191  HEMOGLOBIN (ERYTHROCRUORIN, AQUO MET)
REMARK                                          SCOP: Alpha; Globin-like
REMARK pdb1rl6_A     4.585     0.174     3.991  MOLECULE: RIBOSOMAL PROTEIN L6;
REMARK                                          SCOP: A+B; Ribosomal protein L6
REMARK pdb1a6m       4.560     0.173     3.634  MOLECULE: MYOGLOBIN;
REMARK                                          SCOP: Alpha; Globin-like
REMARK pdb1qcz_A     4.382     0.168     5.111  MOLECULE: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE;
REMARK                                          SCOP: A/B; Flavodoxin-like
REMARK pdb1gdj       4.297     0.165    10.615  LEGHEMOGLOBIN (DEOXY)
REMARK                                          SCOP: Alpha; Globin-like
REMARK pdb1fvk_A     4.172     0.162     8.355  MOLECULE: DISULFIDE BOND FORMATION PROTEIN;
REMARK                                          SCOP: 65-128: Alpha; Disulphide-bond formation facilitator (DSBA), insertion domain
REMARK                                          SCOP: 1-64: A/B; Thioredoxin fold
MODEL  1
REMARK Sequence alignment follows:
REMARK t0096n          1 MVIKAQSPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGV.TRTTLR
REMARK                          |  #  . ||: | ..:###|. :| | || |  || ..  |:
REMARK pdb1lea         1 .....MKALTARQQEVFDLIRDHISQTGMPPTRA.EIAQRLGFRSPNAAE
REMARK 
REMARK t0096n         50 EVLQRLARDGWLTIQHGKPTKVNNFWETSGL
REMARK                   | |::|:: |||:.  |:  #|. #||    
REMARK pdb1lea        45 EHLKALARKGVIEIVSGASRGIRLLQEE...
REMARK 
PARENT 1lea
Q 6  M 1
S 7  K 2
P 8  A 3
A 9  L 4
G 10  T 5
F 11  A 6
A 12  R 7
E 13  Q 8
E 14  Q 9
Y 15  E 10
I 16  V 11
I 17  F 12
E 18  D 13
S 19  L 14
I 20  I 15
W 21  R 16
N 22  D 17
N 23  H 18
R 24  I 19
F 25  S 20
P 26  Q 21
P 27  T 22
G 28  G 23
T 29  M 24
I 30  P 25
L 31  P 26
P 32  T 27
A 33  R 28
E 34  A 29
E 36  E 30
L 37  I 31
S 38  A 32
E 39  Q 33
L 40  R 34
I 41  L 35
G 42  G 36
V 43  F 37
T 44  S 39
R 45  P 40
T 46  N 41
T 47  A 42
L 48  A 43
R 49  E 44
E 50  E 45
V 51  H 46
L 52  L 47
Q 53  K 48
R 54  A 49
L 55  L 50
A 56  A 51
R 57  R 52
D 58  K 53
G 59  G 54
W 60  V 55
L 61  I 56
T 62  E 57
I 63  I 58
Q 64  V 59
H 65  S 60
G 66  G 61
K 67  A 62
P 68  S 63
T 69  R 64
K 70  G 65
V 71  I 66
N 72  R 67
N 73  L 68
F 74  L 69
W 75  Q 70
E 76  E 71
TER
REMARK Sequence alignment follows:
REMARK t0096c          1 ...............WETSGL.NILETLARLDHESVPQLIDNLLS.VRTN
REMARK                                  ||.:|  :| |.|.:|| |:||:.|: |#. ::.|
REMARK pdb2a0b         1 SKSEALLDIPMLEQYLELVGPKLITDGLAVFE.KMMPGYVSVLESNLTAQ
REMARK 
REMARK t0096c         34 ISTIFIRTAFRQHPDKAQEV.LATANEVADHADAFAE..LDYNIFRGLAF
REMARK                      . |..::|| .:.| |: | :: |.:|:||   :  |:#:| . |  
REMARK pdb2a0b        50 DKKG.IVEEGHKIKGAAGSVGLRHLQQLGQQIQSPDLPAWEDNVGEWIEE
REMARK 
REMARK t0096c         81 ASGNPIYGLILNGMKGLYTRIGRHYFANPEARSLALGFYHKLSALCSEGA
REMARK                   |: :  .  ||: || |  :                              
REMARK pdb2a0b        99 MKEE..WRHDVEVLKAWVAKAT............................
REMARK 
REMARK t0096c        131 HDQVYETVRRYGHESGEIWHRMQKNLPGDLAIQGR
REMARK                                                      
REMARK pdb2a0b       119 ...................................
REMARK 
PARENT 2a0b
T 77  L 674
S 78  V 675
G 79  G 676
L 80  P 677
N 81  L 679
I 82  I 680
L 83  T 681
E 84  D 682
T 85  G 683
L 86  L 684
A 87  A 685
R 88  V 686
L 89  F 687
D 90  E 688
E 92  K 689
S 93  M 690
V 94  M 691
P 95  P 692
Q 96  G 693
L 97  Y 694
I 98  V 695
D 99  S 696
N 100  V 697
L 101  L 698
L 102  E 699
S 103  S 700
V 104  L 702
R 105  T 703
T 106  A 704
N 107  Q 705
I 108  D 706
S 109  K 707
T 110  K 708
I 111  G 709
I 113  I 710
R 114  V 711
T 115  E 712
A 116  E 713
F 117  G 714
R 118  H 715
Q 119  K 716
H 120  I 717
P 121  K 718
D 122  G 719
K 123  A 720
A 124  A 721
Q 125  G 722
E 126  S 723
V 127  V 724
L 128  L 726
A 129  R 727
T 130  H 728
A 131  L 729
N 132  Q 730
E 133  Q 731
V 134  L 732
A 135  G 733
D 136  Q 734
H 137  Q 735
A 138  I 736
D 139  Q 737
A 140  S 738
F 141  P 739
A 142  D 740
E 143  L 741
L 144  W 744
D 145  E 745
Y 146  D 746
N 147  N 747
I 148  V 748
F 149  G 749
R 150  E 750
G 151  W 751
L 152  I 752
A 153  E 753
F 154  E 754
A 155  M 755
S 156  K 756
G 157  E 757
N 158  E 758
Y 161  W 759
G 162  R 760
L 163  H 761
I 164  D 762
L 165  V 763
N 166  E 764
G 167  V 765
M 168  L 766
K 169  K 767
G 170  A 768
L 171  W 769
Y 172  V 770
T 173  A 771
R 174  K 772
I 175  A 773
G 176  T 774
TER
END


