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T0826 1-220

ID: 1403945944 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 220 (213)
Sequences: 571 (456.1)
Seq/Len: 2.681
Nf(neff/√len): 31.3

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: 2.681).

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_A3.0931.00
79_P139_I2.8331.00
62_N162_S2.6321.00
82_L138_Y2.6001.00
52_T177_Y2.3901.00
79_P135_A2.1031.00
59_F165_C2.1021.00
15_L138_Y2.0571.00
103_M106_N2.0421.00
91_Q118_L2.0051.00
22_Y27_L1.9850.99
87_A127_I1.9290.99
173_Q177_Y1.9280.99
49_F177_Y1.9120.99
92_E99_F1.9000.99
79_P138_Y1.8830.99
91_Q99_F1.8130.99
151_E155_R1.7630.98
23_S65_F1.6960.98
188_T198_G1.6760.98
19_L78_I1.6400.97
104_L203_K1.6330.97
108_L203_K1.6110.97
129_C136_L1.5420.96
152_L160_A1.5260.95
100_N103_M1.4500.93
136_L140_A1.4420.93
174_Y178_A1.4270.93
94_F138_Y1.3590.90
20_S27_L1.3450.89
62_N158_L1.3450.89
31_F185_K1.3380.89
31_F198_G1.3230.88
63_F163_F1.3140.88
170_A183_N1.3140.88
76_V79_P1.3050.87
11_G14_A1.3030.87
24_S58_F1.3010.87
71_P75_K1.2990.87
104_L200_G1.2890.86
128_V132_V1.2820.86
63_F159_A1.2750.86
95_F153_L1.2690.85
75_K79_P1.2570.85
31_F35_V1.2490.84
103_M182_R1.2430.84
145_Y151_E1.2340.83
99_F214_Y1.2050.81
89_S126_W1.2050.81
59_F169_I1.2040.81
91_Q214_Y1.1990.80
49_F173_Q1.1930.80
86_A131_G1.1790.79
10_L18_F1.1770.79
140_A144_K1.1750.79
80_L84_I1.1740.79
48_I51_Y1.1740.79
204_Y208_K1.1660.78
179_S183_N1.1640.78
190_L195_N1.1630.78
16_I163_F1.1620.78
93_I192_V1.1530.77
21_L58_F1.1390.76
23_S172_L1.1330.75
192_V198_G1.1310.75
95_F110_T1.1240.74
115_S119_I1.1090.73
11_G84_I1.1080.73
43_G46_A1.1050.72
63_F216_Q1.1050.72
86_A161_V1.1030.72
63_F166_A1.0980.72
30_A93_I1.0980.72
22_Y69_A1.0940.71
68_I77_L1.0800.70
31_F192_V1.0790.70
174_Y181_F1.0790.70
23_S184_N1.0590.68
9_K144_K1.0540.67
31_F53_M1.0540.67
33_A120_T1.0460.66
55_V77_L1.0460.66
31_F57_L1.0460.66
100_N106_N1.0450.66
24_S27_L1.0450.66
103_M114_E1.0430.66
91_Q123_Y1.0360.65
179_S182_R1.0310.65
92_E134_P1.0300.65
90_Y203_K1.0270.64
126_W130_L1.0270.64
108_L175_Q1.0270.64
161_V164_L1.0200.63
127_I132_V1.0150.63
32_F35_V1.0140.63
55_V125_L1.0130.63
60_L161_V1.0100.62
180_F195_N1.0090.62
69_A207_W1.0090.62
70_L73_V1.0080.62
132_V164_L1.0070.62
10_L14_A1.0060.62
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  
2hi2A10.30452.60.969Contact Map
4httA20.25452.40.97Contact Map
4b4aA10.25452.30.97Contact Map
4a82A40.909120.971Contact Map
1fmeA10.10451.80.972Contact Map
2r7rA10.24091.70.972Contact Map
2m7gA10.27731.60.973Contact Map
4gycB10.25451.60.973Contact Map
4humA10.84551.50.973Contact Map
2a65A10.61.50.973Contact 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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