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T0845 120-448

ID: 1404751898 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 329 (300)
Sequences: 1741 (1380.5)
Seq/Len: 5.803
Nf(neff/√len): 79.7

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: 5.803).

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
142_D149_K2.8441.00
237_E285_S2.7851.00
194_E203_V2.5871.00
152_Y164_G2.5571.00
63_T70_Y2.5441.00
142_D151_K2.3811.00
111_D114_S2.3311.00
73_D76_T2.3311.00
246_S250_A2.1721.00
154_D157_E2.0901.00
107_I153_Y2.0621.00
56_Y71_I2.0081.00
186_K235_A2.0011.00
100_G112_L1.9971.00
128_F140_S1.9881.00
186_K239_E1.9711.00
15_N24_A1.9481.00
109_R121_K1.9401.00
243_Y288_L1.8681.00
131_S138_V1.8121.00
101_L138_V1.7691.00
160_A163_E1.7601.00
162_K209_F1.7481.00
292_Y301_K1.6791.00
138_V155_V1.6661.00
243_Y281_L1.6641.00
23_T159_I1.6591.00
92_L100_G1.6581.00
154_D161_A1.6531.00
246_S252_Y1.6491.00
54_K80_E1.6280.99
72_V79_Y1.5800.99
190_V207_N1.5740.99
150_V192_T1.5530.99
206_K212_E1.5410.99
235_A242_I1.5380.99
281_L288_L1.5260.99
243_Y307_K1.5160.99
254_Y261_S1.5150.99
48_I55_F1.5100.99
137_K209_F1.5100.99
81_N115_L1.5000.99
116_N210_T1.4880.99
18_D21_K1.4870.99
93_T133_I1.4750.99
311_V314_T1.4740.99
93_T131_S1.4550.99
154_D206_K1.4510.99
17_Y302_I1.4460.99
184_L207_N1.4440.99
125_L142_D1.4320.98
267_I270_E1.4100.98
56_Y100_G1.4090.98
44_D90_S1.3920.98
183_V233_M1.3870.98
204_K215_F1.3780.98
133_I155_V1.3770.98
242_I256_L1.3690.98
292_Y303_V1.3550.98
139_L152_Y1.3490.97
137_K161_A1.3400.97
159_I260_D1.3360.97
49_I53_G1.3340.97
255_I258_D1.3340.97
185_A236_S1.3310.97
83_A110_I1.3250.97
233_M242_I1.3140.97
68_H82_S1.3130.97
133_I138_V1.3070.97
50_H98_Q1.3030.97
79_Y82_S1.3010.97
109_R119_R1.3000.97
69_F92_L1.2970.97
24_A27_D1.2960.97
189_N240_N1.2930.96
261_S264_A1.2920.96
288_L307_K1.2850.96
304_V315_V1.2840.96
194_E201_N1.2790.96
243_Y309_G1.2790.96
119_R158_L1.2770.96
132_I182_F1.2700.96
55_F74_A1.2530.96
75_K156_N1.2460.95
139_L190_V1.2390.95
110_I117_N1.2350.95
70_Y79_Y1.2320.95
73_D114_S1.2270.95
53_G286_G1.2230.95
301_K314_T1.2200.95
149_K163_E1.2120.94
54_K71_I1.2120.94
109_R118_V1.2070.94
113_K156_N1.2040.94
274_S290_V1.1950.94
241_I287_E1.1950.94
94_I100_G1.1930.94
302_I317_C1.1920.94
45_S181_N1.1880.94
73_D111_D1.1870.94
185_A235_A1.1840.93
245_V279_L1.1820.93
184_L190_V1.1800.93
52_N239_E1.1770.93
14_F72_V1.1770.93
90_S129_Y1.1730.93
73_D80_E1.1720.93
23_T210_T1.1700.93
117_N120_I1.1660.93
96_N133_I1.1480.92
243_Y253_K1.1460.92
63_T68_H1.1430.92
56_Y112_L1.1430.92
150_V175_I1.1350.91
100_G138_V1.1350.91
23_T116_N1.1330.91
211_L214_V1.1310.91
70_Y82_S1.1280.91
80_E258_D1.1230.91
101_L158_L1.1230.91
203_V211_L1.1230.91
164_G205_I1.1200.91
237_E283_Q1.1180.91
240_N255_I1.1170.91
89_L102_V1.1060.90
85_V110_I1.1040.90
237_E281_L1.1030.90
12_G42_N1.1000.90
136_G240_N1.0930.89
123_E128_F1.0930.89
236_S243_Y1.0870.89
304_V313_H1.0790.88
52_N98_Q1.0720.88
207_N256_L1.0650.88
94_I112_L1.0560.87
151_K163_E1.0540.87
46_A55_F1.0520.87
236_S239_E1.0500.87
49_I185_A1.0460.86
150_V205_I1.0460.86
22_K287_E1.0380.86
95_L98_Q1.0350.85
99_Y118_V1.0310.85
102_V139_L1.0280.85
162_K210_T1.0260.85
14_F28_C1.0240.85
19_T289_Y1.0220.84
289_Y304_V1.0210.84
200_C217_N1.0080.83
91_G181_N1.0080.83
47_N92_L1.0080.83
49_I236_S1.0070.83
140_S153_Y1.0040.83
282_N289_Y1.0010.83
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: (05Jul14)
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  
3dsmA10.90271000.432Contact Map
3sbqA20.88751000.565Contact Map
3u4yA20.85711000.578Contact Map
1fwxA40.86321000.582Contact Map
2eceA10.90881000.592Contact Map
1l0qA40.85111000.606Contact Map
1mdaH20.86931000.61Contact Map
3vgzA40.820799.90.621Contact Map
1pbyB10.841999.90.624Contact Map
3c75H20.884599.90.625Contact 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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