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T0825

ID: 1403118694 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 205 (204)
Sequences: 33149 (23875.7)
Seq/Len: 162.495
Nf(neff/√len): 1671.6

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: 162.495).

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
41_H59_S2.9171.00
88_G101_A2.6641.00
47_G60_A2.6551.00
164_H182_S2.6351.00
129_G142_A2.5971.00
82_H100_S2.5811.00
25_V59_S2.4911.00
17_A50_F2.4281.00
123_H141_S2.3681.00
6_G19_A2.3521.00
17_A57_I2.3371.00
170_G183_A2.2931.00
66_V100_S2.2571.00
99_A132_F2.2391.00
140_A173_F2.1691.00
58_A98_I2.0711.00
107_V141_S2.0391.00
58_A91_F1.9711.00
100_S110_W1.9691.00
140_A180_I1.9321.00
148_V182_S1.9131.00
18_S28_W1.9071.00
8_A49_A1.8841.00
67_K78_T1.8831.00
99_A139_I1.8811.00
58_A68_L1.8631.00
26_K37_T1.8531.00
49_A90_A1.8181.00
90_A131_A1.7961.00
108_K119_T1.7731.00
141_S151_W1.7481.00
17_A27_L1.7321.00
67_K75_L1.7151.00
46_W62_D1.7051.00
92_S132_F1.6941.00
87_W103_D1.6901.00
51_S91_F1.6611.00
182_S192_W1.6581.00
99_A109_L1.6571.00
131_A172_A1.6431.00
128_W144_D1.6371.00
140_A150_L1.6181.00
17_A48_V1.6061.00
59_S69_W1.6041.00
5_W21_D1.5971.00
58_A89_V1.5831.00
142_A168_V1.5711.00
149_K160_T1.5601.00
181_A191_L1.5271.00
26_K34_L1.5131.00
169_W185_D1.5061.00
99_A130_V1.4791.00
61_S65_T1.4591.00
101_A127_V1.4241.00
19_A45_V1.3920.99
164_H184_S1.3790.99
41_H61_S1.3790.99
60_A86_V1.3770.99
133_S173_F1.3550.99
190_K201_T1.3540.99
11_P54_G1.3380.99
10_S14_Q1.3070.99
149_K157_L1.2710.99
20_S24_T1.2570.99
108_K116_L1.2390.98
123_H143_S1.2280.98
184_S188_T1.2230.98
40_G69_W1.2180.98
11_P50_F1.2150.98
140_A171_V1.2130.98
10_S50_F1.2010.98
90_A130_V1.1990.98
9_F16_I1.1940.98
82_H102_S1.1770.98
18_S26_K1.1550.97
19_A48_V1.1520.97
174_S179_T1.1460.97
142_A171_V1.1380.97
49_A89_V1.1360.97
8_A48_V1.1310.97
143_S147_T1.1140.96
93_P132_F1.1060.96
102_S106_T1.1010.96
134_P173_F1.0900.96
174_S178_Q1.0830.96
9_F30_R1.0780.95
131_A171_V1.0660.95
101_A130_V1.0600.95
52_P91_F1.0560.95
34_L37_T1.0470.94
75_L78_T1.0410.94
60_A89_V1.0240.93
164_H168_V1.0230.93
16_I30_R1.0140.93
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: (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  
2ymuA211000.087Contact Map
1vyhC1011000.105Contact Map
3mkqA311000.12Contact Map
3dwlC20.95121000.123Contact Map
3sfzA10.97561000.125Contact Map
1nr0A10.99511000.126Contact Map
4lg9A111000.132Contact Map
3w15A10.98541000.137Contact Map
3f3fA40.99511000.146Contact Map
3jroA111000.148Contact 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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