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T0826 1-220

ID: 1403946945 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 220 (212)
Sequences: 556 (444.8)
Seq/Len: 2.623
Nf(neff/√len): 30.5

Jackhmmer Results: (2014_04_16)
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: 2.623).

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
131_G135_A3.1601.00
82_L138_Y2.8461.00
79_P139_I2.7011.00
62_N162_S2.5011.00
52_T177_Y2.3181.00
15_L138_Y2.1401.00
79_P135_A2.0801.00
103_M106_N2.0661.00
91_Q118_L2.0251.00
173_Q177_Y1.9800.99
79_P138_Y1.9380.99
92_E99_F1.9190.99
87_A127_I1.8980.99
22_Y27_L1.8880.99
49_F177_Y1.7950.99
59_F165_C1.7730.98
91_Q99_F1.7610.98
19_L78_I1.6780.98
23_S65_F1.6730.97
188_T198_G1.6660.97
152_L160_A1.6380.97
104_L203_K1.5730.96
174_Y178_A1.5500.96
63_F163_F1.5050.95
100_N103_M1.4960.94
151_E155_R1.4880.94
31_F185_K1.4620.93
62_N158_L1.4600.93
129_C136_L1.4380.93
80_L84_I1.4360.93
76_V79_P1.3510.89
23_S172_L1.3290.88
94_F138_Y1.3280.88
63_F159_A1.3220.88
136_L140_A1.3060.87
31_F198_G1.3050.87
108_L203_K1.2900.86
31_F57_L1.2850.86
49_F173_Q1.2840.86
24_S58_F1.2810.86
179_S183_N1.2680.85
20_S27_L1.2630.84
71_P75_K1.2610.84
212_I215_T1.2600.84
178_A182_R1.2540.84
99_F214_Y1.2350.83
137_A217_L1.2100.81
140_A144_K1.2020.80
89_S126_W1.2020.80
23_S184_N1.1930.79
21_L58_F1.1840.79
179_S182_R1.1840.79
146_R151_E1.1670.77
11_G14_A1.1670.77
170_A183_N1.1360.75
22_Y69_A1.1330.74
55_V125_L1.1310.74
68_I77_L1.1300.74
31_F192_V1.1290.74
99_F123_Y1.1260.74
75_K79_P1.1250.74
180_F195_N1.1200.73
60_L161_V1.1130.73
95_F110_T1.1100.72
16_I163_F1.1060.72
93_I192_V1.1050.72
174_Y181_F1.1040.72
43_G46_A1.0940.71
48_I51_Y1.0940.71
91_Q214_Y1.0930.71
104_L200_G1.0880.70
156_L160_A1.0840.70
95_F153_L1.0790.69
194_S199_A1.0790.69
126_W130_L1.0740.69
19_L138_Y1.0730.69
145_Y151_E1.0730.69
132_V164_L1.0700.68
91_Q123_Y1.0690.68
24_S27_L1.0680.68
174_Y182_R1.0680.68
30_A93_I1.0670.68
100_N106_N1.0650.68
192_V198_G1.0630.67
70_L73_V1.0620.67
103_M182_R1.0620.67
86_A161_V1.0610.67
31_F35_V1.0610.67
174_Y191_I1.0580.67
86_A131_G1.0520.66
54_P177_Y1.0460.66
164_L167_L1.0450.66
128_V132_V1.0390.65
12_S155_R1.0380.65
119_I124_V1.0370.65
95_F103_M1.0200.63
85_S196_F1.0180.63
63_F166_A1.0170.62
214_Y217_L1.0090.62
179_S218_D1.0070.61
71_P190_L1.0060.61
153_L161_V1.0040.61
31_F53_M1.0020.61
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: (21Jun14)
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  
4a82A40.92732.90.969Contact Map
1fmeA10.10452.90.969Contact Map
2yevB20.51362.90.969Contact Map
2pfcA10.23642.60.97Contact Map
3qf4A10.93642.60.97Contact Map
3b60A40.91822.40.97Contact Map
3b5xA20.93182.20.971Contact Map
2a65A10.595520.972Contact Map
4gycB10.25451.70.973Contact Map
3ddlA20.47731.70.973Contact 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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