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T0839

ID: 1404241046 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 262 (252)
Sequences: 443 (268.4)
Seq/Len: 1.758
Nf(neff/√len): 16.9

HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.758).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
43_T82_G2.8701.00
202_S240_L2.3201.00
202_S244_Y2.0780.99
22_K35_H1.7780.96
32_K35_H1.7730.96
56_L59_Q1.7690.96
22_K34_K1.7190.95
166_T169_D1.6330.94
201_E205_I1.5980.93
177_L236_Q1.5960.93
20_I66_V1.5300.90
52_F93_N1.5110.90
71_A75_I1.4890.89
170_K173_Q1.4830.88
23_A35_H1.4580.87
22_K32_K1.4510.87
55_G59_Q1.4250.86
20_I59_Q1.4200.85
69_F73_I1.4170.85
206_Y242_K1.4140.85
116_I175_Q1.3910.84
157_G160_T1.3900.84
23_A34_K1.3890.83
119_Y123_L1.3700.82
32_K37_R1.3590.82
206_Y239_R1.3580.82
125_A131_K1.3440.81
20_I33_R1.3320.80
73_I193_S1.3320.80
20_I23_A1.3250.79
113_G117_R1.3170.79
52_F238_Y1.3150.79
79_L232_R1.3130.78
125_A172_D1.3060.78
75_I201_E1.2960.77
161_I168_Q1.2900.77
252_Y256_L1.2850.76
65_E103_G1.2730.75
255_S258_T1.2510.74
22_K37_R1.2460.73
112_Y116_I1.2430.73
47_K57_K1.2390.73
213_L216_M1.2360.72
216_M225_A1.2280.72
175_Q236_Q1.2200.71
52_F56_L1.2160.71
27_E232_R1.2110.70
16_L168_Q1.2070.70
203_Y233_Y1.1960.69
129_F192_I1.1960.69
116_I120_V1.1940.69
39_C44_W1.1920.68
33_R37_R1.1890.68
66_V94_R1.1820.67
76_H119_Y1.1820.67
16_L20_I1.1760.67
179_F232_R1.1730.67
34_K48_S1.1730.67
199_V205_I1.1720.66
119_Y122_F1.1530.65
58_V68_T1.1500.64
69_F194_A1.1470.64
209_I216_M1.1460.64
47_K108_G1.1440.64
216_M230_R1.1360.63
51_S54_A1.1340.63
164_L201_E1.1320.62
83_H126_K1.1300.62
35_H248_S1.1280.62
157_G165_M1.1250.62
165_M174_F1.1250.62
168_Q175_Q1.1230.62
36_V207_K1.1220.61
177_L180_S1.1190.61
115_L179_F1.1170.61
62_L247_C1.1150.61
40_I43_T1.1130.61
23_A27_E1.1080.60
199_V257_I1.1060.60
22_K25_S1.1050.60
171_I198_L1.1030.60
210_T233_Y1.1020.59
37_R244_Y1.1010.59
103_G117_R1.1010.59
65_E98_D1.1010.59
28_E195_L1.1010.59
37_R202_S1.0960.59
232_R236_Q1.0960.59
167_L177_L1.0960.59
168_Q181_H1.0890.58
32_K43_T1.0880.58
32_K38_S1.0870.58
97_I122_F1.0850.58
16_L55_G1.0840.58
206_Y243_F1.0810.57
256_L260_P1.0800.57
74_T236_Q1.0790.57
19_N35_H1.0780.57
113_G119_Y1.0780.57
116_I119_Y1.0770.57
66_V128_S1.0770.57
135_E149_K1.0760.57
144_E148_L1.0730.56
201_E230_R1.0700.56
33_R211_S1.0580.55
26_P62_L1.0570.55
30_A235_A1.0570.55
224_E228_P1.0530.54
40_I78_V1.0520.54
139_T149_K1.0490.54
49_S52_F1.0470.54
34_K37_R1.0470.54
35_H241_V1.0460.53
209_I233_Y1.0440.53
140_F143_E1.0430.53
24_T72_L1.0400.53
66_V82_G1.0370.53
19_N38_S1.0340.52
98_D127_L1.0320.52
166_T171_I1.0310.52
75_I101_S1.0290.52
91_M98_D1.0270.51
203_Y244_Y1.0270.51
31_P198_L1.0240.51
32_K42_Y1.0240.51
159_E163_D1.0220.51
74_T227_E1.0210.51
42_Y46_H1.0180.50
78_V257_I1.0170.50
62_L233_Y1.0160.50
218_S225_A1.0140.50
92_A178_I1.0140.50
59_Q258_T1.0130.50
31_P122_F1.0120.50
180_S185_I1.0100.50
69_F228_P1.0050.49
73_I229_L1.0030.49
82_G195_L1.0000.49
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (28Jun14)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
1hx8A20.87021000.337Contact Map
3zylA20.89691000.357Contact Map
3zymA30.88551000.368Contact Map
1eyhA10.538299.80.74Contact Map
1inzA10.522999.80.743Contact Map
3onkA10.507699.70.777Contact Map
4gzcA10.492499.60.786Contact Map
1xgwA10.503899.50.804Contact Map
1vdyA10.515398.70.863Contact Map
1x5bA10.587890.50.933Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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