PFRMAT AL
TARGET T0308 ARL6, Homo sapiens, 165 res
AUTHOR SAM-T99
REMARK Subject: T0308(database hits)
REMARK MIME-Version: 1.0
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REMARK 
REMARK The following are search results using the SAM-T99 method
REMARK for a sequence query against a database. If there
REMARK are no hits associated with this output, then your
REMARK score cutoff was too conservative.
REMARK 
REMARK Citation:  
REMARK   K. Karplus, C. Barrett, and R. Hughey,
REMARK   Hidden Markov Models for Detecting Remote Protein Homologies,
REMARK   Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. 
REMARK   http://www.cse.ucsc.edu/research/compbio/HMM-apps
REMARK --------------------------------------------------------
REMARK 
REMARK For questions or problems, please see the SAM-T99 FAQ at
REMARK 
REMARK http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html
REMARK 
REMARK or email us at sam-info@cse.ucsc.edu
REMARK 
REMARK 
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REMARK Content-type: text/plain; charset=us-ascii; name='t99-results-1149094084-28121.t99dbhits.txt'
REMARK Content-Disposition: attachment; filename="t99-results-1149094084-28121.t99dbhits.txt"
REMARK 
REMARK The E-value is an estimate of approximately  how many
REMARK sequences would score this well by chance in the database
REMARK searched.  For SAM-T99, E-values less than about 0.01 are
REMARK roughly equivalent, as sequences that score that well have
REMARK most likely already been included in the SAM-T99 multiple
REMARK alignment.
REMARK 
REMARK Database: PDB (updated Thu May 25 01:13:10 2006)
REMARK Score method: average
REMARK 
REMARK Summary of Database Hits:
REMARK                   Average               Target               Template     
REMARK SeqID       Reverse     EValue    Reverse     EValue    Reverse     EValue  SeqLabel
REMARK 2folA        -125.2  3.471e-50     -125.2   3.47e-50  ---------  ---------  :mol:protein length:191  Ras-related protein Rab-1A
REMARK 
REMARK 1yznA        -123.6  1.754e-49     -123.6   1.76e-49  ---------  ---------  :mol:protein length:185  GTP-binding protein YPT1  
REMARK 
REMARK 1hurB        -123.4  2.164e-49     -123.4   2.17e-49  ---------  ---------  :mol:protein length:180  HUMAN ADP-RIBOSYLATION FAC
REMARK 
REMARK 1r8qA        -123.4  2.164e-49     -123.4   2.17e-49  ---------  ---------  :mol:protein length:181  ADP-ribosylation factor 1 
REMARK 
REMARK 1r8qB        -123.4  2.164e-49     -123.4   2.17e-49  ---------  ---------  :mol:protein length:181  ADP-ribosylation factor 1 
REMARK 
REMARK 
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REMARK Content-type: text/plain; charset=us-ascii; name='t99-results-1149094084-28121.t99pairwise.casp.al'
REMARK Content-Disposition: attachment; filename="t99-results-1149094084-28121.t99pairwise.casp.al"
REMARK 
REMARK 
REMARK 
METHOD This pairwise alignment was produced using the SAM-T99 method
METHOD 
METHOD  ------------- Citations (SAM, SAM-T99, HMMs) -----------------
METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis:
METHOD   Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting
METHOD   remote protein homologies, Bioinformatics 14(10):846-856, 1999.
METHOD A. Krogh et al., Hidden Markov models in computational biology:
METHOD   Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
METHOD -------------
MODEL 1
PARENT 2folA
E 1    L 8
V 2    F 9
H 3    K 10
V 4    L 11
L 5    L 12
C 6    L 13
L 7    I 14
G 8    G 15
L 9    D 16
D 10    S 17
N 11    G 18
S 12    V 19
G 13    G 20
K 14    K 21
T 15    S 22
T 16    C 23
I 17    L 24
I 18    L 25
N 19    L 26
K 20    R 27
L 21    F 28
K 22    A 29
P 23    D 30
S 24    D 31
N 25    T 32
A 26    Y 33
S 28    T 34
Q 29    E 35
N 30    S 36
I 31    Y 37
L 32    I 38
P 33    S 39
T 34    T 40
I 35    I 41
G 36    G 42
F 37    V 43
S 38    D 44
I 39    F 45
E 40    I 50
K 41    E 51
F 42    L 52
K 43    D 53
S 44    G 54
S 45    K 55
S 46    T 56
L 47    I 57
S 48    K 58
F 49    L 59
T 50    Q 60
V 51    I 61
F 52    W 62
D 53    D 63
Y 68    Y 78
K 69    R 79
E 70    G 80
G 71    A 81
Q 72    H 82
A 73    G 83
I 74    I 84
I 75    I 85
F 76    V 86
V 77    V 87
I 78    Y 88
D 79    D 89
S 80    V 90
S 81    T 91
D 82    D 92
R 83    Q 93
L 84    E 94
R 85    S 95
M 86    F 96
V 87    N 97
V 88    N 98
A 89    V 99
K 90    K 100
E 91    Q 101
E 92    W 102
L 93    L 103
D 94    Q 104
T 95    E 105
L 96    I 106
L 97    D 107
N 98    R 108
H 99    Y 109
P 100    A 110
D 101    S 111
R 105    E 112
R 106    N 113
I 107    V 114
P 108    N 115
I 109    K 116
L 110    L 117
F 111    L 118
F 112    V 119
A 113    G 120
N 114    N 121
K 115    K 122
M 116    C 123
D 117    D 124
L 118    L 125
R 119    T 126
D 120    T 127
A 121    K 128
V 122    K 129
K 126    V 130
V 127    V 131
S 128    D 132
Q 129    Y 133
L 130    T 134
L 131    T 135
C 132    A 136
L 133    K 137
E 134    E 138
N 135    F 139
I 136    A 140
K 137    D 141
D 138    S 142
K 139    L 143
P 140    G 144
W 141    I 145
H 142    P 146
I 143    F 147
C 144    L 148
A 145    E 149
S 146    T 150
D 147    S 151
A 148    A 152
I 149    K 153
K 150    N 154
G 151    A 155
E 152    T 156
G 153    N 157
L 154    V 158
Q 155    E 159
E 156    Q 160
G 157    S 161
V 158    F 162
D 159    M 163
W 160    T 164
L 161    M 165
Q 162    A 166
D 163    A 167
Q 164    E 168
I 165    I 169
TER
END