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OPENSEQ.org

av1_cp -force run

ID: 1512071973 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 256 (256)
Sequences: 186 (49)
Seq/Len: 0.727
Nf(neff/√len): 3.1

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: 0.727).

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
213_Q228_M1.9010.89
146_T154_E1.8100.86
138_F180_R1.8050.86
29_T32_A1.7830.85
5_P8_I1.7080.81
5_P9_V1.6900.80
153_G158_M1.5900.74
8_I12_T1.5240.69
172_H213_Q1.4850.67
232_A235_H1.4840.66
111_V114_V1.4400.63
68_C75_Q1.3690.57
129_K190_Q1.3680.57
8_I30_R1.3320.54
5_P30_R1.3140.53
71_P75_Q1.3140.53
27_Y30_R1.3090.52
18_R21_L1.3070.52
232_A236_A1.3060.52
130_N133_N1.2930.51
6_A14_A1.2800.50
187_T192_G1.2780.50
57_R60_R1.2750.49
138_F168_V1.2700.49
5_P10_I1.2700.49
180_R185_T1.2700.49
6_A10_I1.2590.48
147_D154_E1.2420.46
8_I14_A1.2300.45
13_P18_R1.2260.45
8_I27_Y1.2250.45
118_G133_N1.2240.45
158_M199_V1.2240.45
155_V168_V1.2220.45
7_D13_P1.2170.44
27_Y34_P1.2150.44
187_T205_V1.2140.44
104_R112_K1.2140.44
151_D155_V1.2100.44
191_Y207_N1.2050.43
119_K122_M1.2040.43
185_T194_K1.1980.43
182_W208_Y1.1960.43
78_E181_K1.1930.42
210_V214_Q1.1920.42
169_K177_Q1.1890.42
129_K193_A1.1850.42
180_R204_R1.1850.42
219_Y225_N1.1840.42
6_A16_K1.1810.41
192_G207_N1.1780.41
8_I13_P1.1710.41
237_S240_V1.1690.40
69_E72_C1.1630.40
102_T107_K1.1580.39
81_H90_M1.1560.39
207_N210_V1.1560.39
148_K190_Q1.1530.39
14_A30_R1.1520.39
211_Y214_Q1.1510.39
83_V88_K1.1510.39
187_T193_A1.1500.39
151_D154_E1.1500.39
68_C72_C1.1470.39
72_C75_Q1.1470.39
7_D12_T1.1450.38
138_F172_H1.1450.38
221_N225_N1.1450.38
129_K191_Y1.1430.38
68_C71_P1.1420.38
10_I16_K1.1350.38
171_M182_W1.1340.38
2_S8_I1.1290.37
82_D85_H1.1280.37
8_I16_K1.1240.37
47_R63_D1.1230.37
134_N159_F1.1220.37
8_I29_T1.1220.37
94_D98_G1.1180.36
68_C94_D1.1180.36
141_R144_R1.1170.36
7_D11_S1.1150.36
190_Q193_A1.1150.36
128_S190_Q1.1150.36
103_H108_R1.1110.36
138_F159_F1.1110.36
171_M213_Q1.1100.36
56_Y63_D1.1090.36
10_I34_P1.1070.35
2_S12_T1.1050.35
22_N25_S1.1050.35
147_D200_K1.1040.35
65_P72_C1.1000.35
14_A29_T1.0980.35
79_S90_M1.0980.35
5_P24_D1.0960.35
171_M228_M1.0940.34
138_F198_L1.0940.34
7_D18_R1.0940.34
150_Q179_L1.0940.34
172_H228_M1.0930.34
174_D177_Q1.0920.34
129_K192_G1.0920.34
243_T249_Y1.0870.34
112_K121_W1.0810.33
119_K132_T1.0810.33
245_K249_Y1.0810.33
12_T18_R1.0790.33
48_P52_K1.0790.33
58_M101_L1.0750.33
240_V243_T1.0740.33
27_Y39_T1.0720.33
63_D82_D1.0720.33
44_W47_R1.0710.33
50_N79_S1.0700.33
71_P98_G1.0670.32
34_P39_T1.0670.32
187_T190_Q1.0650.32
60_R63_D1.0640.32
181_K185_T1.0590.32
103_H107_K1.0500.31
64_V82_D1.0490.31
83_V111_V1.0470.31
231_M234_T1.0460.31
57_R82_D1.0450.31
148_K159_F1.0450.31
229_L232_A1.0440.31
209_V212_N1.0420.30
33_V36_V1.0420.30
160_D165_T1.0410.30
68_C74_V1.0360.30
5_P14_A1.0350.30
74_V94_D1.0350.30
146_T171_M1.0350.30
14_A55_I1.0350.30
88_K111_V1.0330.30
60_R82_D1.0300.30
121_W133_N1.0300.30
72_C85_H1.0280.29
24_D39_T1.0280.29
57_R63_D1.0260.29
81_H88_K1.0260.29
187_T191_Y1.0240.29
101_L180_R1.0240.29
230_Y236_A1.0240.29
159_F198_L1.0220.29
120_I135_V1.0210.29
9_V24_D1.0200.29
121_W130_N1.0190.29
56_Y60_R1.0170.29
112_K118_G1.0140.29
154_E171_M1.0130.28
112_K133_N1.0120.28
147_D151_D1.0110.28
247_R251_Y1.0110.28
109_F127_K1.0040.28
124_E127_K1.0020.28
47_R52_K1.0020.28
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  
3kbyA20.21889.20.985Contact Map
2e3xA10.21485.10.987Contact Map
2knpA10.1254.50.987Contact Map
2dw0A20.21484.50.987Contact Map
3zucA10.20314.30.987Contact Map
3k7nA10.22663.90.987Contact Map
3k7lA10.24613.80.987Contact Map
1a9xA40.23443.30.988Contact Map
1co7I10.03523.20.988Contact Map
3ezqA80.394530.988Contact 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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