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T0805

ID: 1401903394 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 214 (206)
Sequences: 816 (634)
Seq/Len: 3.961
Nf(neff/√len): 44.2

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: 3.961).

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
34_E151_R3.7941.00
154_G192_T2.7501.00
52_Q210_H2.7431.00
169_K172_D2.5181.00
153_L191_Y2.4011.00
13_T149_R2.4001.00
20_R188_P2.3901.00
7_V11_L2.3151.00
35_C148_L2.2641.00
148_L155_S2.2631.00
145_C155_S2.1751.00
21_L25_K2.1631.00
29_R33_M2.1561.00
35_C189_I2.1471.00
148_L189_I2.0941.00
59_A62_K1.9551.00
11_L143_S1.9501.00
65_I170_V1.9051.00
59_A63_K1.8821.00
145_C157_W1.8691.00
205_A209_T1.8421.00
53_W140_A1.7700.99
176_I179_D1.7560.99
149_R154_G1.7410.99
29_R57_E1.7130.99
32_L189_I1.6460.99
61_K64_A1.6260.99
21_L24_D1.6120.99
27_V153_L1.6020.99
37_E40_L1.5910.98
64_A173_V1.5800.98
44_T51_W1.5480.98
171_A183_Q1.5380.98
31_V151_R1.5150.98
31_V153_L1.5120.98
164_D169_K1.5080.98
25_K191_Y1.4880.97
35_C153_L1.4810.97
27_V191_Y1.4740.97
35_C144_F1.4740.97
7_V10_V1.4340.96
144_F189_I1.4260.96
141_V187_L1.4220.96
10_V152_G1.4180.96
68_V173_V1.3880.96
61_K173_V1.3540.95
33_M206_E1.3350.94
8_D151_R1.3340.94
8_D38_L1.3230.94
31_V34_E1.3130.93
203_L207_S1.3000.93
26_P59_A1.2910.93
38_L151_R1.2800.92
52_Q181_Y1.2670.92
6_S9_E1.2610.92
141_V185_G1.2460.91
69_Y170_V1.2450.91
49_Q202_R1.2280.90
30_D33_M1.2180.90
34_E38_L1.2150.89
60_A63_K1.2060.89
39_A43_P1.2050.89
60_A64_A1.1940.88
32_L36_L1.1900.88
40_L208_V1.1880.88
53_W208_V1.1880.88
66_A77_L1.1810.88
19_K195_I1.1780.87
107_H110_R1.1760.87
139_P185_G1.1710.87
11_L42_A1.1710.87
5_L150_S1.1690.87
144_F155_S1.1650.87
41_Q200_A1.1580.86
36_L55_F1.1180.83
28_P31_V1.1110.83
170_V173_V1.1100.83
146_L150_S1.1070.83
69_Y186_L1.0840.81
29_R211_W1.0690.80
137_L184_G1.0670.79
20_R156_C1.0570.78
132_S182_S1.0570.78
20_R190_A1.0510.78
9_E13_T1.0500.78
14_T190_A1.0450.77
115_L144_F1.0440.77
45_G159_T1.0410.77
43_P51_W1.0380.77
76_Y81_A1.0360.76
63_K67_D1.0280.76
67_D207_S1.0250.75
36_L209_T1.0160.75
154_G157_W1.0120.74
47_N202_R1.0090.74
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: (29May14)
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  
3gr3A20.92061000.347Contact Map
2h0uA10.78041000.356Contact Map
3of4A30.91121000.368Contact Map
2wzvA20.92061000.37Contact Map
1icrA20.92061000.371Contact Map
2hayA40.92061000.372Contact Map
3gagA40.93461000.373Contact Map
1vfrA20.93461000.374Contact Map
1noxA10.91591000.375Contact Map
3eo8A60.92061000.375Contact 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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