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beta -force run

ID: 1411433541 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 261 (253)
Sequences: 199 (171.8)
Seq/Len: 0.787
Nf(neff/√len): 10.8

Jackhmmer Results: (2014_04_16)
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: 0.787).

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
62_E84_R2.0490.94
43_Q67_P1.7480.85
81_G85_I1.7310.84
31_R41_D1.5840.76
108_I160_A1.5690.75
156_M162_L1.5490.73
51_A63_I1.4990.70
86_I108_I1.4980.70
66_F76_V1.4770.68
31_R37_G1.4460.66
239_T242_E1.4450.66
50_V62_E1.4420.66
83_S156_M1.4370.65
198_N201_T1.4270.64
238_L243_A1.3910.61
123_M127_R1.3810.61
86_I153_H1.3770.60
126_C149_R1.3640.59
244_V247_L1.3480.58
57_N64_Y1.3450.58
126_C147_P1.3410.57
147_P155_A1.3410.57
5_L9_A1.3340.57
86_I160_A1.3340.57
47_L53_Q1.3190.55
238_L242_E1.3150.55
172_K175_A1.3050.54
43_Q47_L1.3010.54
78_G117_I1.2910.53
241_A244_V1.2840.52
22_D26_L1.2760.52
8_L11_K1.2680.51
208_L211_A1.2540.50
80_D168_G1.2520.50
149_R158_Q1.2510.49
147_P161_R1.2420.49
69_K73_I1.2390.48
121_E126_C1.2370.48
94_G164_F1.2340.48
188_R193_D1.2320.48
157_I165_G1.2130.46
185_T190_P1.2100.46
203_Q206_N1.2100.46
201_T247_L1.2080.46
179_V182_T1.1970.45
47_L59_W1.1970.45
57_N152_R1.1930.44
94_G163_A1.1850.44
6_A16_V1.1800.43
35_F47_L1.1730.43
239_T250_L1.1730.43
79_V154_K1.1690.42
97_F152_R1.1660.42
225_S230_R1.1640.42
33_T73_I1.1580.41
239_T243_A1.1550.41
184_Y193_D1.1520.41
30_L67_P1.1390.40
80_D161_R1.1350.40
47_L63_I1.1330.39
238_L250_L1.1310.39
79_V162_L1.1310.39
202_M214_K1.1260.39
224_C247_L1.1230.39
67_P73_I1.1210.38
57_N156_M1.1210.38
65_A73_I1.1170.38
47_L54_Y1.1150.38
208_L250_L1.1140.38
79_V83_S1.1080.37
33_T55_G1.1060.37
154_K175_A1.1060.37
181_N195_T1.1040.37
121_E158_Q1.0990.37
123_M151_L1.0980.37
106_C110_R1.0900.36
222_P230_R1.0890.36
82_W149_R1.0870.36
245_K249_F1.0860.36
50_V53_Q1.0850.35
164_F174_E1.0830.35
97_F151_L1.0810.35
4_A18_M1.0800.35
33_T44_F1.0800.35
105_T120_T1.0790.35
141_G145_S1.0790.35
155_A161_R1.0780.35
205_I208_L1.0760.35
83_S152_R1.0730.35
17_G42_A1.0670.34
96_D107_R1.0650.34
51_A60_T1.0640.34
67_P72_G1.0640.34
80_D167_A1.0620.34
9_A18_M1.0620.34
92_F119_V1.0620.34
197_V201_T1.0610.34
5_L8_L1.0610.34
79_V163_A1.0600.34
157_I161_R1.0580.33
7_T14_E1.0570.33
54_Y65_A1.0550.33
157_I175_A1.0540.33
5_L10_G1.0510.33
94_G110_R1.0480.33
153_H157_I1.0440.32
67_P154_K1.0440.32
105_T126_C1.0430.32
47_L66_F1.0420.32
62_E125_E1.0390.32
39_A159_C1.0370.32
97_F104_C1.0370.32
82_W153_H1.0360.32
100_D147_P1.0360.32
124_D148_K1.0350.32
232_I236_S1.0330.31
47_L77_V1.0320.31
10_G14_E1.0310.31
6_A10_G1.0310.31
154_K174_E1.0310.31
50_V84_R1.0300.31
141_G144_Q1.0280.31
110_R116_P1.0270.31
142_P157_I1.0260.31
184_Y187_E1.0260.31
68_D76_V1.0250.31
61_K78_G1.0230.31
68_D153_H1.0220.31
51_A102_E1.0200.30
201_T221_L1.0190.30
161_R170_Y1.0190.30
35_F85_I1.0190.30
74_V78_G1.0170.30
53_Q62_E1.0150.30
49_I53_Q1.0120.30
50_V57_N1.0080.30
91_Q106_C1.0080.30
23_P26_L1.0080.30
35_F148_K1.0070.30
241_A247_L1.0040.29
80_D85_I1.0040.29
47_L168_G1.0040.29
183_A186_A1.0010.29
44_F146_H1.0000.29
154_K158_Q1.0000.29
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: (17Jul14)
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  
3si9A40.743334.70.953Contact Map
3rhiA40.325730.20.954Contact Map
2vc6A20.739526.60.955Contact Map
1owfA10.34126.10.955Contact Map
4i7wA20.739525.40.956Contact Map
3na8A40.72824.40.956Contact Map
2ehhA40.75121.90.957Contact Map
4icnA20.747120.10.958Contact Map
2wkjA40.735618.90.958Contact Map
1xkyA40.731818.30.958Contact 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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