PFRMAT AL
TARGET T0277 1wj8, Thermus thermophilus
AUTHOR SAM-T99
REMARK --simple mime boundary
REMARK Content-type: text/plain; charset=us-ascii
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-Disposition: attachment; filename="t99-results-1092457647-13393.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 Aug 12 04:13:29 2004)
REMARK Score method: average
REMARK
REMARK Summary of Database Hits:
REMARK Average Target Template
REMARK SeqID Reverse EValue Reverse EValue Reverse EValue SeqLabel
REMARK 1jogB -81.06 3.541e-31 -81.06 3.6e-31 --------- --------- :mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK
REMARK 1jogC -81.06 3.541e-31 -81.06 3.6e-31 --------- --------- :mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK
REMARK 1jogD -81.06 3.541e-31 -81.06 3.6e-31 --------- --------- :mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK
REMARK 1jogA -78.84 3.261e-30 -81.06 3.6e-31 -76.62 3e-29 :mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK
REMARK
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REMARK
REMARK
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REMARK >T0277 1wj8, Thermus thermophilus
REMARK MASLARAVERLKAALERPKDEFIRDSAIQRFEFTFELAWKTLKTFLELQG
REMARK LEARSPRAAIRGAFQVGLLPEDPFWLEMLELRNLTNHTYDEALAERIYAE
REMARK LPKALERFQELLRRLEEP-a
REMARK >1jogB mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK xxtdklnLNVLDAAFYSLEQTVVQISDrnwfdxqpsivqDTLIAGAIQKF
REMARK EFVYELSLKXXKRQLQQDAIntddiGAYGFKDILREALRFGLIGDXSKWV
REMARK AYRDXRNITSHTYDQEKAXAVYAQIDDFLIESSFLLEQLRQRNqyd
REMARK
REMARK
REMARK >T0277 1wj8, Thermus thermophilus
REMARK MASLARAVERLKAALERPKDEFIRDSAIQRFEFTFELAWKTLKTFLELQG
REMARK LEARSPRAAIRGAFQVGLLPEDPFWLEMLELRNLTNHTYDEALAERIYAE
REMARK LPKALERFQELLRRLEEP-a
REMARK >1jogC mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK xxtdklnLNVLDAAFYSLEQTVVQISDrnwfdxqpsivqDTLIAGAIQKF
REMARK EFVYELSLKXXKRQLQQDAIntddiGAYGFKDILREALRFGLIGDXSKWV
REMARK AYRDXRNITSHTYDQEKAXAVYAQIDDFLIESSFLLEQLRQRNqyd
REMARK
REMARK
REMARK >T0277 1wj8, Thermus thermophilus
REMARK MASLARAVERLKAALERPKDEFIRDSAIQRFEFTFELAWKTLKTFLELQG
REMARK LEARSPRAAIRGAFQVGLLPEDPFWLEMLELRNLTNHTYDEALAERIYAE
REMARK LPKALERFQELLRRLEEP-a
REMARK >1jogD mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK xxtdklnLNVLDAAFYSLEQTVVQISDrnwfdxqpsivqDTLIAGAIQKF
REMARK EFVYELSLKXXKRQLQQDAIntddiGAYGFKDILREALRFGLIGDXSKWV
REMARK AYRDXRNITSHTYDQEKAXAVYAQIDDFLIESSFLLEQLRQRNqyd
REMARK
REMARK
REMARK >T0277 1wj8, Thermus thermophilus
REMARK MASLARAVERLKAALERPKDEFIRDSAIQRFEFTFELAWKTLKTFLELQG
REMARK LEARSPRAAIRGAFQVGLLPEDPFWLEMLELRNLTNHTYDEALAERIYAE
REMARK LPKALERFQELLRRLEEP-a
REMARK >1jogA mol:protein-het length:146 Hypothetical Protein Hi0074
REMARK xxtdklnLNVLDAAFYSLEQTVVQISDrnwfdxqpsivqDTLIAGAIQKF
REMARK EFVYELSLKXXKRQLQQDAIntddiGAYGFKDILREALRFGLIGDXSKWV
REMARK AYRDXRNITSHTYDQEKAXAVYAQIDDFLIESSFLLEQLRQRNqyd
REMARK
REMARK --simple mime boundary
REMARK Content-type: text/plain; charset=us-ascii; name='t99-results-1092457647-13393.t99pairwise.casp.al'
REMARK Content-Disposition: attachment; filename="t99-results-1092457647-13393.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 1jogB
M 1 L 8
A 2 N 9
S 3 V 10
L 4 L 11
A 5 D 12
R 6 A 13
A 7 A 14
V 8 F 15
E 9 Y 16
R 10 S 17
L 11 L 18
K 12 E 19
A 13 Q 20
A 14 T 21
L 15 V 22
E 16 V 23
R 17 Q 24
P 18 I 25
K 19 S 26
D 20 D 27
E 21 D 40
F 22 T 41
I 23 L 42
R 24 I 43
D 25 A 44
S 26 G 45
A 27 A 46
I 28 I 47
Q 29 Q 48
R 30 K 49
F 31 F 50
E 32 E 51
F 33 F 52
T 34 V 53
F 35 Y 54
E 36 E 55
L 37 L 56
A 38 S 57
W 39 L 58
K 40 K 59
T 41 X 60
L 42 X 61
K 43 K 62
T 44 R 63
F 45 Q 64
L 46 L 65
E 47 Q 66
L 48 Q 67
Q 49 D 68
G 50 A 69
L 51 I 70
E 52 G 76
A 53 A 77
R 54 Y 78
S 55 G 79
P 56 F 80
R 57 K 81
A 58 D 82
A 59 I 83
I 60 L 84
R 61 R 85
G 62 E 86
A 63 A 87
F 64 L 88
Q 65 R 89
V 66 F 90
G 67 G 91
L 68 L 92
L 69 I 93
P 70 G 94
E 71 D 95
D 72 X 96
P 73 S 97
F 74 K 98
W 75 W 99
L 76 V 100
E 77 A 101
M 78 Y 102
L 79 R 103
E 80 D 104
L 81 X 105
R 82 R 106
N 83 N 107
L 84 I 108
T 85 T 109
N 86 S 110
H 87 H 111
T 88 T 112
Y 89 Y 113
D 90 D 114
E 91 Q 115
A 92 E 116
L 93 K 117
A 94 A 118
E 95 X 119
R 96 A 120
I 97 V 121
Y 98 Y 122
A 99 A 123
E 100 Q 124
L 101 I 125
P 102 D 126
K 103 D 127
A 104 F 128
L 105 L 129
E 106 I 130
R 107 E 131
F 108 S 132
Q 109 S 133
E 110 F 134
L 111 L 135
L 112 L 136
R 113 E 137
R 114 Q 138
L 115 L 139
E 116 R 140
E 117 Q 141
TER
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