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T0825

ID: 1403122556 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 205 (204)
Sequences: 5550 (4448.4)
Seq/Len: 27.206
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: 27.206).

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
25_V59_S2.4241.00
66_V100_S2.3881.00
107_V141_S2.1641.00
148_V182_S2.1481.00
82_H100_S2.0191.00
123_H141_S1.9761.00
41_H59_S1.9551.00
67_K78_T1.8921.00
99_A139_I1.8731.00
190_K201_T1.8141.00
164_H182_S1.7841.00
17_A57_I1.7711.00
149_K160_T1.7481.00
26_K37_T1.7401.00
108_K119_T1.7171.00
140_A173_F1.7091.00
17_A50_F1.7081.00
140_A180_I1.6871.00
6_G19_A1.6871.00
58_A98_I1.6691.00
88_G101_A1.6331.00
56_T97_T1.5961.00
99_A132_F1.5801.00
47_G60_A1.5761.00
129_G142_A1.5531.00
128_W144_D1.5191.00
157_L198_L1.4941.00
49_A90_A1.4781.00
55_Q96_Q1.4741.00
170_G183_A1.4481.00
58_A91_F1.4451.00
34_L75_L1.4341.00
67_K75_L1.4010.99
90_A131_A1.3980.99
75_L116_L1.3880.99
87_W103_D1.3850.99
131_A172_A1.3740.99
74_Q115_Q1.3660.99
116_L157_L1.3550.99
143_S147_T1.3500.99
11_P54_G1.3490.99
8_A49_A1.3470.99
5_W21_D1.3440.99
20_S24_T1.3380.99
97_T138_T1.3270.99
46_W62_D1.3190.99
33_Q74_Q1.3150.99
34_L116_L1.3100.99
138_T179_T1.3060.99
77_Q118_Q1.3060.99
52_P95_G1.3000.99
15_T56_T1.2930.99
118_Q159_Q1.2890.99
50_F91_F1.2730.99
140_A150_L1.2650.99
137_Q178_Q1.2600.99
61_S65_T1.2530.99
36_Q118_Q1.2460.98
111_N152_N1.2400.98
156_Q197_Q1.2390.98
121_T162_T1.2390.98
56_T138_T1.2120.98
58_A89_V1.2110.98
82_H86_V1.2050.98
102_S106_T1.2030.98
18_S22_D1.2000.98
9_F50_F1.1970.98
80_T121_T1.1950.98
36_Q77_Q1.1930.98
96_Q137_Q1.1880.98
99_A130_V1.1780.98
97_T179_T1.1610.97
134_P177_G1.1580.97
41_H45_V1.1570.97
159_Q200_Q1.1510.97
82_H104_D1.1470.97
149_K157_L1.1470.97
33_Q156_Q1.1330.97
190_K198_L1.1290.97
14_Q55_Q1.1280.97
152_N193_N1.1270.97
14_Q96_Q1.1240.97
29_N70_N1.1240.97
34_L157_L1.1240.97
91_F132_F1.1210.97
72_N195_N1.1150.96
31_N113_N1.1130.96
75_L157_L1.1120.96
34_L198_L1.1100.96
33_Q197_Q1.0890.96
184_S188_T1.0880.96
123_H143_S1.0880.96
15_T97_T1.0780.95
123_H145_D1.0740.95
164_H184_S1.0720.95
140_A171_V1.0710.95
74_Q156_Q1.0690.95
77_Q200_Q1.0660.95
26_K34_L1.0650.95
70_N111_N1.0650.95
77_Q159_Q1.0640.95
112_R153_R1.0640.95
55_Q178_Q1.0550.95
108_K116_L1.0550.95
115_Q197_Q1.0510.94
30_R71_R1.0490.94
162_T203_T1.0430.94
9_F30_R1.0430.94
75_L198_L1.0400.94
123_H127_V1.0400.94
115_Q156_Q1.0370.94
132_F173_F1.0350.94
9_F132_F1.0320.94
15_T138_T1.0280.94
50_F173_F1.0260.94
128_W169_W1.0240.93
55_Q137_Q1.0230.93
169_W185_D1.0120.93
56_T179_T1.0090.93
58_A68_L1.0080.93
181_A191_L1.0060.93
14_Q137_Q1.0030.93
76_L117_L1.0010.92
74_Q197_Q1.0000.92
116_L198_L1.0000.92
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: (14Jun14)
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  
1vyhC1011000.211Contact Map
1nr0A10.99511000.212Contact Map
2ymuA211000.214Contact Map
3sfzA10.97561000.221Contact Map
3w15A10.98541000.228Contact Map
3f3fA40.99511000.232Contact Map
4lg9A111000.245Contact Map
3mkqA311000.251Contact Map
3j65q10.99511000.257Contact Map
3zwlB20.99511000.261Contact 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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