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NanR

ID: 1517101784 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 263 (232)
Sequences: 14272 (9565.9)
Seq/Len: 61.517
Nf(neff/√len): 628.0

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: 61.517).

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
152_A230_R4.3621.00
137_R238_D3.7351.00
50_G53_E3.3571.00
233_D236_E3.2801.00
159_S223_I2.9101.00
43_M48_E2.8781.00
123_H186_P2.6301.00
43_M64_F2.5141.00
58_E69_R2.3361.00
130_F134_S2.3231.00
37_E78_A2.2441.00
150_L178_V2.2361.00
147_Q184_G2.1861.00
41_E82_K2.1821.00
129_L246_N2.0941.00
36_V65_F2.0841.00
141_E234_P2.0691.00
228_A236_E2.0641.00
126_Q138_Y2.0481.00
144_T147_Q2.0421.00
36_V67_V2.0161.00
86_Q96_S2.0091.00
155_L226_V1.9401.00
181_E189_M1.9001.00
176_H222_H1.8461.00
148_I230_R1.8441.00
236_E240_A1.8201.00
227_D231_R1.7281.00
30_K38_E1.7271.00
221_Q247_S1.6851.00
137_R234_P1.6581.00
87_I93_A1.6491.00
178_V181_E1.6491.00
238_D242_Q1.6431.00
127_L191_I1.6431.00
223_I227_D1.6351.00
39_E43_M1.6111.00
177_R193_V1.5961.00
154_A171_S1.5931.00
61_L72_V1.5821.00
152_A226_V1.5561.00
137_R235_D1.5511.00
164_N167_A1.5451.00
133_S242_Q1.5401.00
42_Q46_R1.5381.00
129_L249_S1.5211.00
224_A240_A1.5121.00
153_K157_I1.4971.00
88_N91_E1.4931.00
134_S137_R1.4931.00
157_I174_D1.4861.00
143_A232_H1.4791.00
152_A156_E1.4721.00
179_L229_I1.4721.00
133_S238_D1.4681.00
143_A148_I1.4581.00
231_R236_E1.4481.00
239_R243_S1.4401.00
136_V237_A1.4331.00
35_M39_E1.4291.00
180_A192_H1.3810.99
129_L242_Q1.3650.99
37_E82_K1.3590.99
221_Q244_H1.3550.99
150_L181_E1.3420.99
183_P189_M1.3410.99
60_E64_F1.3380.99
190_A194_A1.3270.99
157_I171_S1.3180.99
59_R63_A1.3070.99
148_I226_V1.3030.99
170_R174_D1.2950.99
147_Q182_I1.2830.99
128_R132_E1.2760.99
135_L180_A1.2710.99
155_L223_I1.2690.99
39_E65_F1.2650.99
129_L133_S1.2640.99
234_P238_D1.2440.98
134_S238_D1.2350.98
76_L85_V1.2210.98
39_E42_Q1.2170.98
123_H185_N1.2050.98
222_H244_H1.1980.98
235_D239_R1.1840.98
136_V140_A1.1750.98
140_A237_A1.1730.98
148_I232_H1.1730.98
133_S137_R1.1680.97
175_F226_V1.1660.97
172_D222_H1.1630.97
159_S219_Y1.1540.97
136_V241_L1.1480.97
154_A178_V1.1440.97
177_R181_E1.1430.97
236_E239_R1.1400.97
143_A229_I1.1380.97
174_D178_V1.1350.97
225_I241_L1.1340.97
143_A182_I1.1270.97
54_Q94_R1.1270.97
31_K34_E1.1260.97
126_Q185_N1.1230.97
143_A147_Q1.1130.96
224_A243_S1.1060.96
172_D176_H1.0990.96
126_Q142_H1.0990.96
30_K35_M1.0980.96
122_A253_H1.0940.96
224_A236_E1.0910.96
74_E77_A1.0880.96
226_V230_R1.0850.96
43_M65_F1.0810.95
88_N94_R1.0780.95
49_F95_V1.0770.95
123_H187_I1.0760.95
220_Q224_A1.0750.95
85_V93_A1.0750.95
122_A249_S1.0680.95
242_Q246_N1.0670.95
57_S60_E1.0670.95
88_N92_R1.0660.95
132_E176_H1.0660.95
187_I198_W1.0640.95
151_L178_V1.0570.95
249_S253_H1.0550.95
167_A170_R1.0550.95
150_L153_K1.0410.94
140_A234_P1.0340.94
91_E94_R1.0300.94
149_D153_K1.0290.94
156_E160_Q1.0280.94
140_A229_I1.0270.94
178_V182_I1.0230.93
86_Q94_R1.0170.93
176_H244_H1.0150.93
225_I240_A1.0110.93
152_A227_D1.0080.93
37_E41_E1.0030.93
228_A233_D1.0000.92
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  
4p96A20.88591000.327Contact Map
3c7jA20.88211000.331Contact Map
3sxyA20.76051000.333Contact Map
2di3A20.85551000.336Contact Map
4p9fA20.79851000.351Contact Map
3ihuA20.76811000.352Contact Map
2hs5A10.77951000.353Contact Map
1hw1A20.85551000.36Contact Map
3ic7A20.422199.80.624Contact Map
3by6A50.475399.80.624Contact 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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