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T0805

ID: 1401901681 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 214 (205)
Sequences: 6025 (4460)
Seq/Len: 29.390
Nf(neff/√len): 311.5

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: 29.390).

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
28_P31_V4.3201.00
21_L25_K3.8481.00
34_E151_R3.6531.00
29_R57_E3.2101.00
35_C148_L2.9441.00
154_G192_T2.8251.00
29_R33_M2.7101.00
53_W140_A2.6831.00
25_K191_Y2.5961.00
52_Q210_H2.5591.00
145_C155_S2.5531.00
153_L191_Y2.4401.00
31_V153_L2.2361.00
21_L24_D2.2161.00
13_T149_R2.1491.00
31_V151_R2.1261.00
53_W115_L2.0851.00
54_V118_C2.0531.00
39_A144_F2.0081.00
37_E40_L1.9871.00
171_A183_Q1.9151.00
64_A173_V1.9051.00
148_L189_I1.8791.00
57_E212_N1.8631.00
169_K172_D1.8501.00
59_A63_K1.8191.00
7_V11_L1.8131.00
153_L189_I1.7971.00
118_C181_Y1.7701.00
9_E13_T1.7561.00
141_V185_G1.7281.00
61_K212_N1.7021.00
61_K64_A1.6351.00
35_C144_F1.6221.00
21_L193_Q1.5941.00
115_L144_F1.5811.00
38_L147_A1.5701.00
65_I170_V1.5661.00
7_V10_V1.5421.00
31_V191_Y1.5341.00
20_R188_P1.5341.00
33_M206_E1.5271.00
19_K193_Q1.5041.00
141_V187_L1.5031.00
203_L207_S1.4771.00
35_C189_I1.4561.00
36_L209_T1.4381.00
157_W185_G1.4291.00
139_P142_W1.4111.00
6_S9_E1.4030.99
63_K109_H1.3970.99
31_V34_E1.3910.99
55_F113_V1.3860.99
145_C157_W1.3850.99
59_A62_K1.3820.99
33_M37_E1.3590.99
35_C153_L1.3400.99
145_C187_L1.3210.99
205_A209_T1.3150.99
149_R154_G1.3140.99
118_C176_I1.3070.99
28_P191_Y1.3070.99
164_D169_K1.3060.99
32_L113_V1.3040.99
57_E211_W1.3010.99
58_D61_K1.2970.99
42_A143_S1.2970.99
55_F211_W1.2960.99
21_L191_Y1.2910.99
135_A138_F1.2900.99
27_V153_L1.2890.99
52_Q181_Y1.2750.99
113_V189_I1.2690.99
116_I183_Q1.2580.99
9_E12_T1.2570.99
30_D33_M1.2570.99
55_F209_T1.2420.98
168_H172_D1.2360.98
29_R211_W1.2300.98
27_V31_V1.2250.98
16_S156_C1.2170.98
148_L155_S1.2130.98
117_P141_V1.2090.98
54_V212_N1.1950.98
60_A64_A1.1820.98
12_T37_E1.1590.97
8_D34_E1.1540.97
68_V173_V1.1470.97
40_L208_V1.1300.97
117_P144_F1.1280.97
144_F187_L1.1250.97
26_P57_E1.1160.96
57_E113_V1.1140.96
38_L151_R1.1000.96
116_I174_L1.0810.95
120_K180_E1.0660.95
204_P207_S1.0660.95
142_W146_L1.0660.95
61_K173_V1.0640.95
11_L146_L1.0520.95
12_T41_Q1.0450.94
60_A63_K1.0450.94
27_V191_Y1.0230.93
8_D12_T1.0070.93
11_L143_S1.0050.93
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  
1bkjA20.79911000.232Contact Map
3eofA20.79441000.233Contact Map
3n2sA40.79911000.234Contact Map
1f5vA20.80371000.237Contact Map
1zchA10.80371000.244Contact Map
3of4A30.7851000.245Contact Map
3gr3A20.92061000.246Contact Map
4dn2A20.86921000.248Contact Map
1icrA20.80371000.248Contact Map
1noxA10.7851000.249Contact 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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