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rnf144a

ID: 1504859966 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 292 (275)
Sequences: 373 (227.6)
Seq/Len: 1.356
Nf(neff/√len): 13.7

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: 1.356).

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
20_C23_C2.3190.99
226_H232_C2.0950.98
231_P234_N2.0220.98
105_D108_R1.9050.96
138_C156_C1.8540.96
143_C146_C1.8180.95
211_C214_C1.7820.94
38_C43_C1.7520.94
229_K232_C1.7150.93
20_C43_C1.7030.92
138_C143_C1.6950.92
199_A213_Y1.6860.92
228_D231_P1.6610.91
20_C38_C1.6590.91
141_E251_V1.6570.91
23_C38_C1.6340.90
268_L272_T1.6110.89
194_R199_A1.5820.88
65_C116_C1.5330.86
203_C206_C1.5290.86
31_Q48_K1.5260.85
206_C211_C1.5230.85
143_C156_C1.5230.85
23_C43_C1.5080.85
70_C232_C1.5000.84
162_I166_P1.4810.83
92_R96_L1.4800.83
227_Y232_C1.4780.83
60_E100_R1.4750.83
43_C46_C1.4680.82
206_C214_C1.4540.81
63_I139_R1.4450.81
226_H234_N1.4320.80
226_H231_P1.4310.80
203_C211_C1.4250.80
151_H156_C1.4000.78
185_C206_C1.3950.78
38_C46_C1.3920.77
117_Q205_N1.3890.77
146_C150_W1.3880.77
226_H230_G1.3550.75
203_C214_C1.3510.74
138_C146_C1.3500.74
222_F226_H1.3460.74
116_C146_C1.3300.73
116_C156_C1.3270.72
185_C211_C1.3040.71
185_C203_C1.3030.71
222_F227_Y1.2820.69
263_V270_L1.2740.68
225_I228_D1.2680.67
168_E173_F1.2660.67
243_V270_L1.2600.67
212_W215_L1.2590.67
20_C46_C1.2570.67
88_E168_E1.2570.67
185_C214_C1.2500.66
94_K99_E1.2370.65
238_H247_R1.2350.65
23_C46_C1.2290.64
226_H236_L1.2250.64
146_C156_C1.2120.62
170_S173_F1.2100.62
230_G236_L1.2050.62
198_C206_C1.2040.62
138_C151_H1.1980.61
138_C203_C1.1970.61
276_L282_C1.1950.61
183_K212_W1.1940.61
186_P206_C1.1920.60
198_C203_C1.1830.60
225_I231_P1.1770.59
244_I248_T1.1750.59
10_W14_L1.1710.58
254_F257_F1.1700.58
232_C236_L1.1650.58
278_C281_K1.1600.57
61_T76_L1.1570.57
109_T196_E1.1520.57
223_L226_H1.1470.56
186_P203_C1.1460.56
234_N238_H1.1400.55
111_C116_C1.1360.55
232_C238_H1.1350.55
263_V267_F1.1330.55
71_P139_R1.1330.55
50_Y54_L1.1300.54
200_Q209_A1.1260.54
11_D15_D1.1250.54
147_K157_P1.1230.54
171_A174_K1.1220.54
40_C199_A1.1190.53
232_C239_S1.1150.53
116_C138_C1.1140.53
228_D232_C1.1140.53
109_T144_S1.1120.53
198_C211_C1.1080.52
22_L42_F1.1030.52
271_A277_C1.1000.51
116_C143_C1.0990.51
263_V268_L1.0980.51
261_L264_A1.0960.51
186_P211_C1.0920.51
278_C283_S1.0890.50
54_L64_S1.0880.50
27_Y49_Q1.0850.50
197_G254_F1.0850.50
270_L275_V1.0780.49
45_L57_E1.0720.49
12_L15_D1.0720.49
231_P236_L1.0670.48
230_G233_R1.0630.48
102_V200_Q1.0600.47
166_P170_S1.0560.47
36_A39_Q1.0490.46
55_I190_V1.0490.46
262_L274_F1.0460.46
112_P201_M1.0460.46
82_E90_M1.0450.46
198_C214_C1.0430.46
109_T147_K1.0420.46
135_C197_G1.0390.45
242_S253_I1.0380.45
78_E94_K1.0370.45
229_K234_N1.0370.45
135_C156_C1.0350.45
258_G269_L1.0300.44
265_S268_L1.0300.44
228_D233_R1.0270.44
186_P214_C1.0270.44
265_S269_L1.0250.44
209_A216_E1.0240.44
16_P26_E1.0230.44
108_R119_V1.0200.43
35_I164_F1.0190.43
195_D212_W1.0170.43
194_R201_M1.0170.43
44_T84_M1.0150.43
199_A212_W1.0140.43
232_C240_R1.0140.43
226_H229_K1.0130.43
102_V105_D1.0090.42
272_T275_V1.0090.42
29_V48_K1.0080.42
168_E171_A1.0060.42
242_S248_T1.0050.42
156_C203_C1.0040.42
31_Q44_T1.0020.42
105_D200_Q1.0010.41
227_Y230_G1.0000.41
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  
4i1fA10.71581000.522Contact Map
5c1zA201000.525Contact Map
4k95A120.68151000.532Contact Map
5cawA201000.535Contact Map
4kblA20.82531000.562Contact Map
2m48A10.42811000.678Contact Map
4ljoA10.407599.70.8Contact Map
2ct7A10.284299.70.802Contact Map
1wimA10.321999.50.818Contact Map
3hcsA20.506899.10.854Contact 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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