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T0831 109-352 Tp831 -force run

ID: 1407214509 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 244 (240)
Sequences: 64 (52.3)
Seq/Len: 0.267
Nf(neff/√len): 3.4

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: 0.267).

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
125_R238_L1.7290.53
214_G225_K1.7100.52
116_I197_I1.6450.48
125_R185_W1.6200.46
193_S221_F1.6080.45
35_W227_E1.5830.44
39_I42_A1.5510.42
59_I86_L1.4870.38
197_I217_S1.4450.35
94_N210_F1.4440.35
32_S143_F1.4240.34
22_H26_R1.3980.33
61_S225_K1.3950.32
41_R117_E1.3840.32
123_H156_K1.3800.31
226_K232_H1.3780.31
239_R242_V1.3650.31
78_D107_L1.3470.30
7_V14_L1.3380.29
100_V128_R1.3300.29
89_Q123_H1.3150.28
237_A241_R1.3060.27
45_F116_I1.2960.27
126_P214_G1.2890.27
46_T214_G1.2870.27
36_L143_F1.2850.26
229_K235_W1.2820.26
123_H244_A1.2770.26
11_Q18_Q1.2700.26
8_A12_Q1.2690.26
17_V116_I1.2640.25
12_Q16_P1.2640.25
197_I219_D1.2630.25
191_E228_Y1.2600.25
195_K242_V1.2500.25
56_R184_L1.2460.24
86_L212_D1.2420.24
125_R232_H1.2400.24
163_E168_D1.2370.24
40_H222_E1.2340.24
34_W191_E1.2200.23
191_E227_E1.2200.23
100_V222_E1.2180.23
151_F191_E1.2170.23
202_K227_E1.2170.23
55_V242_V1.2150.23
81_G200_F1.2120.23
16_P23_E1.2060.23
136_F193_S1.2060.23
62_N100_V1.1950.22
97_Q227_E1.1900.22
85_L91_E1.1860.22
125_R136_F1.1860.22
78_D221_F1.1820.22
23_E163_E1.1770.21
105_K180_T1.1740.21
98_K195_K1.1700.21
113_R232_H1.1680.21
55_V149_K1.1670.21
100_V198_L1.1670.21
56_R181_T1.1660.21
191_E214_G1.1660.21
85_L195_K1.1610.21
59_I116_I1.1570.20
113_R143_F1.1480.20
8_A97_Q1.1470.20
13_A17_V1.1440.20
102_E116_I1.1400.20
128_R195_K1.1360.20
229_K240_N1.1310.19
151_F158_Q1.1290.19
16_P20_T1.1260.19
125_R226_K1.1260.19
213_E228_Y1.1230.19
16_P19_Q1.1160.19
124_L229_K1.1090.18
34_W227_E1.1070.18
38_V55_V1.1030.18
54_R89_Q1.1020.18
225_K239_R1.0990.18
158_Q167_E1.0980.18
131_L244_A1.0960.18
92_E101_R1.0920.18
8_A11_Q1.0860.18
27_K239_R1.0860.18
125_R131_L1.0860.18
37_N40_H1.0840.18
7_V243_S1.0810.17
38_V244_A1.0810.17
35_W194_M1.0780.17
76_F142_L1.0770.17
166_I169_E1.0770.17
55_V179_T1.0740.17
86_L146_Y1.0730.17
51_L146_Y1.0730.17
5_T11_Q1.0720.17
88_T117_E1.0720.17
149_K181_T1.0710.17
155_V199_S1.0690.17
194_M225_K1.0660.17
38_V144_T1.0640.17
21_I177_A1.0570.17
11_Q222_E1.0520.16
89_Q124_L1.0510.16
12_Q19_Q1.0500.16
56_R224_W1.0500.16
63_Y141_E1.0500.16
125_R231_L1.0490.16
39_I226_K1.0450.16
196_A224_W1.0450.16
104_V237_A1.0410.16
173_V218_M1.0400.16
13_A20_T1.0370.16
23_E244_A1.0350.16
97_Q197_I1.0330.16
8_A16_P1.0330.16
11_Q32_S1.0320.16
136_F231_L1.0300.16
78_D84_F1.0260.15
54_R136_F1.0220.15
123_H136_F1.0190.15
136_F242_V1.0170.15
147_E183_G1.0170.15
123_H132_N1.0170.15
136_F171_G1.0170.15
184_L242_V1.0170.15
50_E144_T1.0140.15
51_L189_E1.0140.15
116_I159_T1.0130.15
58_E94_N1.0100.15
19_Q22_H1.0090.15
38_V43_I1.0020.15
123_H126_P1.0010.15
125_R240_N1.0000.15
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: (17Jul14)
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  
3ghgC40.44677.30.966Contact Map
4kblA20.49596.60.967Contact Map
3ghgA40.42216.20.967Contact Map
2zihA40.3325.10.968Contact Map
1m1jC20.43854.90.969Contact Map
2xb0X10.24594.70.969Contact Map
2higA20.18444.60.969Contact Map
1pehA10.13524.30.97Contact Map
4aycA10.54513.90.97Contact Map
1deqA40.35253.50.971Contact 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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