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RNF

ID: 1504827218 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 442 (167)
Sequences: 1101 (638.3)
Seq/Len: 6.593
Nf(neff/√len): 49.4

HHblits Results: (2016_02)
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: 6.593).

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
55_F62_L3.8771.00
51_I73_V3.3971.00
52_H66_K2.7641.00
112_A116_E2.0301.00
56_G66_K1.9681.00
112_A117_F1.9641.00
116_E119_D1.7941.00
59_Q62_L1.7611.00
59_Q63_A1.6881.00
113_N117_F1.6741.00
55_F66_K1.6021.00
52_H70_L1.5730.99
44_A73_V1.5310.99
104_I127_R1.4190.99
108_F120_L1.3760.98
12_L80_K1.3670.98
87_Q127_R1.3560.98
87_Q140_P1.3460.98
84_F87_Q1.3220.98
155_A158_L1.3190.98
22_L84_F1.2900.97
55_F59_Q1.2840.97
154_F158_L1.2680.97
148_S151_R1.2640.97
40_V47_E1.2600.97
71_Q75_S1.2450.96
154_F157_C1.2430.96
106_S110_S1.2400.96
65_R68_L1.2390.96
104_I108_F1.2310.96
6_V9_C1.2240.96
104_I116_E1.2220.96
5_Y9_C1.2090.95
140_P143_S1.2040.95
63_A66_K1.1840.95
37_V88_L1.1770.95
19_V23_Q1.1750.95
149_D152_A1.1690.94
48_E70_L1.1680.94
40_V84_F1.1670.94
39_E51_I1.1650.94
102_L106_S1.1630.94
12_L38_E1.1620.94
16_V105_C1.1520.94
20_K23_Q1.1510.94
156_R162_L1.1500.94
156_R159_E1.1250.93
16_V109_L1.1080.92
58_M62_L1.1040.92
130_G133_T1.0960.91
48_E74_Q1.0940.91
146_I150_H1.0920.91
149_D153_E1.0890.91
153_E157_C1.0880.91
20_K106_S1.0850.91
55_F102_L1.0850.91
138_L141_I1.0830.91
33_L84_F1.0810.91
19_V101_H1.0800.91
140_P144_S1.0660.90
21_A34_Q1.0650.90
44_A77_Y1.0640.90
70_L124_L1.0480.89
101_H121_G1.0480.89
114_K119_D1.0480.89
111_L116_E1.0440.88
56_G59_Q1.0400.88
155_A159_E1.0350.88
75_S78_E1.0250.87
30_I124_L1.0250.87
157_C160_P1.0230.87
31_A53_A1.0210.87
147_A150_H1.0140.86
152_A155_A1.0120.86
77_Y87_Q1.0090.86
153_E156_R1.0090.86
108_F116_E1.0070.86
157_C165_G1.0050.86
100_V104_I1.0040.86
148_S152_A1.0010.86
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: (06Aug15)
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  
4nqjA30.380198.50.923Contact Map
4ltbA20.364398.30.928Contact Map
4tn3A20.68197.30.942Contact Map
3okqA10.280596.40.948Contact Map
4m3lA40.135795.90.95Contact Map
4kblA20.289694.20.955Contact Map
4cg4A6090.90.96Contact Map
4cfgA20.296488.30.962Contact Map
1i84S20.1131830.964Contact Map
2dfsA20.27647.10.972Contact 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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