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T0810 110-383

ID: 1402340605 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 274 (240)
Sequences: 1577 (1371.9)
Seq/Len: 6.571
Nf(neff/√len): 88.6

Jackhmmer Results: (2014_04_16)
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: 6.571).

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
85_V241_R4.5411.00
80_R107_R4.1271.00
107_R111_D3.9241.00
83_K111_D3.8261.00
93_A105_L2.8861.00
87_A240_L2.7741.00
157_F163_V2.7491.00
85_V244_Y2.6981.00
172_G192_W2.5691.00
237_P241_R2.5361.00
114_V254_T2.4031.00
84_E237_P2.2781.00
153_H187_T1.9971.00
142_F177_D1.9831.00
147_A151_G1.8871.00
124_C173_E1.8871.00
85_V237_P1.8591.00
212_L242_E1.8411.00
88_K113_H1.8321.00
118_H122_H1.8101.00
209_A213_A1.7881.00
63_V251_V1.7551.00
78_I233_A1.7391.00
120_I151_G1.7191.00
208_L212_L1.7141.00
80_R111_D1.6941.00
197_D200_R1.6631.00
93_A108_V1.6561.00
95_G120_I1.6271.00
204_N238_Q1.6251.00
215_V243_L1.6121.00
87_A250_V1.6071.00
59_R249_S1.6061.00
124_C171_Y1.5761.00
81_A233_A1.5680.99
81_A240_L1.5660.99
205_E238_Q1.5650.99
75_T227_D1.5500.99
141_T144_E1.5480.99
78_I236_M1.5430.99
109_A162_W1.5240.99
242_E245_N1.5220.99
76_D107_R1.4870.99
85_V240_L1.4730.99
208_L238_Q1.4670.99
180_A184_T1.4530.99
242_E246_R1.4510.99
203_S206_Q1.4430.99
230_R234_E1.4400.99
98_V155_A1.4320.99
105_L159_V1.4310.99
81_A236_M1.4230.99
155_A159_V1.4150.99
106_K110_A1.4020.99
193_N221_G1.3990.99
241_R245_N1.3910.98
211_V239_F1.3780.98
109_A160_L1.3730.98
195_E199_W1.3710.98
240_L250_V1.3660.98
79_L108_V1.3580.98
205_E209_A1.3510.98
169_F191_A1.3470.98
77_A234_E1.3400.98
240_L244_Y1.3290.98
150_R154_Q1.3200.98
236_M240_L1.3130.98
196_S225_F1.3110.98
145_A181_F1.3050.97
62_V215_V1.3030.97
87_A244_Y1.2750.97
154_Q158_D1.2650.97
60_K248_Y1.2640.97
70_P227_D1.2610.97
115_I156_V1.2530.96
66_F82_L1.2530.96
99_R155_A1.2450.96
145_A178_L1.2440.96
61_E249_S1.2410.96
105_L115_I1.2390.96
120_I155_A1.2390.96
62_V243_L1.2370.96
190_F253_L1.2240.96
235_I239_F1.2220.96
241_R244_Y1.1950.95
83_K88_K1.1810.95
247_G250_V1.1790.95
75_T79_L1.1790.95
66_F78_I1.1780.95
79_L111_D1.1660.94
119_S125_L1.1470.93
68_D227_D1.1440.93
108_V115_I1.1360.93
118_H226_H1.1210.92
62_V250_V1.1190.92
121_T148_E1.1150.92
222_I253_L1.1080.92
124_C139_N1.1050.92
146_A150_R1.1010.92
105_L108_V1.0970.91
65_T168_R1.0930.91
208_L235_I1.0840.91
64_L82_L1.0790.90
79_L107_R1.0790.90
117_S153_H1.0730.90
140_L144_E1.0710.90
76_D104_A1.0290.87
63_V253_L1.0260.87
74_Y233_A1.0250.87
126_G173_E1.0210.87
207_L235_I1.0210.87
156_V160_L1.0150.86
155_A158_D1.0140.86
98_V102_P1.0030.86
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: (07Jun14)
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  
2w3zA10.79561000.289Contact Map
2c1iA10.89421000.301Contact Map
1ny1A20.83941000.302Contact Map
2y8uA20.75551000.304Contact Map
2j13A10.74821000.307Contact Map
2cc0A20.70441000.307Contact Map
2iw0A10.7811000.324Contact Map
4m1bA20.7191000.328Contact Map
4l1gA40.76281000.332Contact Map
2vyoA10.72631000.333Contact 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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