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rhom

ID: 1487972735 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 303 (280)
Sequences: 856 (675.5)
Seq/Len: 3.057
Nf(neff/√len): 40.4

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: 3.057).

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
131_A184_V3.2901.00
166_G192_A3.1771.00
127_M167_V3.0481.00
79_S140_L2.5971.00
231_A247_F2.4111.00
294_F298_F2.2601.00
195_G254_G2.2391.00
174_S246_S2.2291.00
82_E140_L2.1851.00
126_Y171_S1.9691.00
167_V189_G1.7700.99
83_L136_I1.7680.99
110_F114_P1.7290.99
79_S143_Q1.6430.98
139_N186_A1.6430.98
139_N187_S1.6360.98
130_H135_H1.6250.98
82_E143_Q1.5720.97
228_M231_A1.5370.96
123_F126_Y1.5260.96
106_L109_P1.5040.96
169_A256_A1.5040.96
84_A88_Y1.4870.96
130_H250_H1.4720.95
105_I109_P1.4220.94
30_M33_D1.4180.94
142_M190_V1.4040.93
163_Y186_A1.3970.93
183_L246_S1.3900.93
109_P114_P1.3580.92
183_L186_A1.3450.91
188_G249_A1.3370.91
119_E122_R1.3340.91
143_Q163_Y1.3220.90
106_L110_F1.3220.90
108_S111_I1.3200.90
135_H187_S1.3170.90
82_E126_Y1.3150.90
285_Y288_C1.3120.90
223_I228_M1.3090.90
82_E163_Y1.3000.89
108_S112_Y1.2750.88
140_L143_Q1.2730.88
163_Y188_G1.2620.87
23_E26_E1.2580.87
162_V196_G1.2550.87
147_G196_G1.2540.87
142_M191_Y1.2520.87
77_S81_A1.2420.86
168_I172_L1.2300.86
26_E29_K1.2290.85
191_Y231_A1.2160.85
129_V184_V1.2160.85
22_E26_E1.2130.84
130_H187_S1.2010.84
35_G38_D1.2000.84
142_M146_L1.1930.83
22_E25_E1.1930.83
78_I164_L1.1880.83
283_A286_L1.1820.82
74_F160_G1.1730.82
163_Y189_G1.1720.82
79_S82_E1.1710.82
189_G196_G1.1690.81
109_P112_Y1.1680.81
82_E127_M1.1660.81
31_R34_G1.1540.80
79_S195_G1.1540.80
274_K277_R1.1480.80
201_V205_F1.1460.80
133_V137_L1.1450.79
28_E35_G1.1430.79
227_D231_A1.1420.79
171_S188_G1.1360.79
25_E29_K1.1330.78
128_L164_L1.1330.78
105_I110_F1.1310.78
52_W55_P1.1310.78
221_I225_V1.1290.78
107_E110_F1.1240.78
139_N250_H1.1230.78
135_H250_H1.1200.77
183_L189_G1.1190.77
28_E31_R1.1170.77
85_V89_Y1.1170.77
165_A193_L1.1110.77
108_S114_P1.1090.76
89_Y129_V1.1070.76
24_L27_E1.1050.76
167_V246_S1.0980.75
45_V49_V1.0930.75
146_L160_G1.0880.74
21_K24_L1.0880.74
82_E123_F1.0830.74
25_E31_R1.0810.74
173_A252_A1.0800.74
24_L30_M1.0790.74
273_L277_R1.0760.73
21_K28_E1.0720.73
34_G40_A1.0710.73
143_Q190_V1.0660.72
27_E31_R1.0620.72
132_G184_V1.0600.72
124_I168_I1.0600.72
56_E59_R1.0560.71
168_I171_S1.0550.71
139_N183_L1.0510.71
222_L226_L1.0510.71
50_S55_P1.0400.70
174_S183_L1.0360.69
160_G164_L1.0340.69
147_G252_A1.0340.69
106_L111_I1.0270.68
24_L28_E1.0260.68
164_L278_F1.0250.68
187_S253_G1.0250.68
278_F281_A1.0240.68
132_G158_R1.0210.68
185_G253_G1.0190.67
30_M38_D1.0190.67
167_V174_S1.0180.67
31_R35_G1.0180.67
123_F262_Y1.0150.67
123_F143_Q1.0140.67
186_A189_G1.0110.66
187_S250_H1.0100.66
272_L277_R1.0090.66
80_L225_V1.0090.66
269_D274_K1.0080.66
277_R291_F1.0080.66
132_G191_Y1.0010.65
151_E158_R1.0000.65
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  
2nr9A10.63371000.494Contact Map
4njnA10.60071000.496Contact Map
2xovA10.59741000.511Contact Map
4zw9A1043.50.945Contact Map
4j05A20.590840.40.946Contact Map
1pw4A10.663424.70.952Contact Map
3wdoA10.217822.90.953Contact Map
2wswA10.742620.20.954Contact Map
4m64A40.075918.70.955Contact Map
2kogA10.280518.40.955Contact 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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