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OPENSEQ.org

CENPL

ID: 1490375431 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 367 (267)
Sequences: 297 (188.7)
Seq/Len: 1.112
Nf(neff/√len): 11.5

Jackhmmer Results: (2016_04)
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: 1.112).

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 > 50% 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
163_L169_P1.9430.95
163_L172_L1.8990.95
162_P185_D1.8640.94
164_L169_P1.6410.87
169_P173_K1.6270.86
106_F176_I1.6210.86
180_L184_F1.6170.86
65_R107_E1.5680.83
132_Q135_L1.5560.83
176_I186_C1.5170.81
132_Q136_K1.4900.79
110_Y179_F1.4620.77
141_I147_L1.4460.76
135_L139_S1.4310.75
166_L169_P1.4260.74
164_L195_T1.4240.74
136_K139_S1.4150.74
163_L191_M1.4140.74
184_F198_L1.4090.73
173_K203_E1.4090.73
202_W245_G1.3950.72
164_L181_S1.3940.72
134_G138_T1.3940.72
108_I114_L1.3900.72
179_F205_W1.3770.71
36_G41_G1.3730.70
38_V41_G1.3240.66
144_P147_L1.3220.66
27_S103_G1.3120.65
250_S263_F1.3080.65
162_P169_P1.3080.65
172_L188_I1.3050.65
179_F189_S1.3010.64
141_I145_G1.2960.64
180_L224_T1.2750.62
26_L112_N1.2750.62
161_L185_D1.2590.61
40_R44_V1.2500.60
131_Q134_G1.2500.60
194_G255_I1.2490.60
164_L206_I1.2440.59
169_P193_L1.2420.59
169_P172_L1.2360.59
193_L197_R1.2320.58
111_E115_C1.2310.58
131_Q135_L1.2280.58
171_P191_M1.2190.57
131_Q136_K1.2130.56
93_D97_A1.2130.56
227_F236_D1.2110.56
203_E207_A1.2080.56
164_L223_L1.2050.56
78_D102_R1.2040.56
139_S145_G1.2030.55
134_G139_S1.2020.55
243_S253_V1.1990.55
6_H111_E1.1970.55
50_D76_T1.1920.54
11_L30_L1.1890.54
203_E211_L1.1860.54
37_D40_R1.1840.54
229_V243_S1.1810.53
5_T22_R1.1760.53
130_G133_D1.1660.52
167_R190_P1.1660.52
162_P184_F1.1600.51
140_S143_I1.1590.51
193_L227_F1.1550.51
36_G39_V1.1430.50
193_L203_E1.1410.50
135_L138_T1.1350.49
180_L188_I1.1280.48
144_P148_S1.1270.48
136_K140_S1.1220.48
89_S92_A1.1200.48
145_G149_E1.1170.47
135_L140_S1.1170.47
191_M249_K1.1160.47
161_L230_P1.1140.47
169_P181_S1.1140.47
178_D191_M1.1110.47
6_H11_L1.1070.46
3_F26_L1.1050.46
184_F188_I1.1030.46
40_R267_G1.1000.46
79_A91_A1.0990.46
164_L172_L1.0970.45
120_L169_P1.0970.45
186_C205_W1.0920.45
253_V256_P1.0910.45
39_V43_Q1.0900.45
64_I176_I1.0900.45
161_L184_F1.0900.45
170_A188_I1.0900.45
246_L251_I1.0880.45
161_L169_P1.0800.44
237_G251_I1.0780.44
242_P249_K1.0770.43
179_F202_W1.0760.43
112_N121_P1.0750.43
129_D153_R1.0740.43
220_D225_L1.0690.43
12_Y198_L1.0690.43
147_L152_S1.0660.42
141_I148_S1.0630.42
34_L57_G1.0540.41
145_G148_S1.0510.41
270_L273_S1.0510.41
126_Q129_D1.0500.41
41_G44_V1.0440.40
142_H145_G1.0440.40
140_S145_G1.0440.40
183_T252_D1.0410.40
141_I144_P1.0390.40
117_A120_L1.0360.40
180_L194_G1.0340.39
146_L150_S1.0340.39
172_L180_L1.0330.39
111_E117_A1.0310.39
119_L159_L1.0280.39
63_G77_D1.0270.39
42_V45_G1.0260.39
3_F22_R1.0260.39
130_G134_G1.0170.38
177_V190_P1.0160.38
43_Q46_L1.0140.38
140_S148_S1.0120.38
21_P63_G1.0110.37
171_P222_V1.0110.37
3_F62_V1.0110.37
171_P206_I1.0100.37
244_E259_E1.0090.37
187_R226_G1.0080.37
175_V206_I1.0080.37
180_L240_D1.0080.37
268_K273_S1.0070.37
231_S249_K1.0070.37
177_V183_T1.0060.37
131_Q137_S1.0060.37
2_T259_E1.0050.37
163_L193_L1.0050.37
159_L209_A1.0050.37
77_D80_D1.0040.37
211_L215_G1.0040.37
256_P259_E1.0030.37
31_R260_L1.0020.37
73_L265_R1.0010.37
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  
1iapA10.452335.40.971Contact Map
4je3A10.604927.20.972Contact Map
3ab3B20.425117.20.975Contact Map
3cx8B10.493212.10.976Contact Map
3vejA20.11177.50.979Contact Map
2z5eA20.15534.40.981Contact Map
2lnzA20.1093.90.981Contact Map
1hr8O40.02183.60.982Contact Map
3qxyA20.12263.40.982Contact Map
4hkcB10.01912.40.983Contact 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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