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ID: 1501094728 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 264 (187)
Sequences: 196 (104.5)
Seq/Len: 1.048
Nf(neff/√len): 7.6

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: 1.048).

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
240_G252_A2.8031.00
219_Y242_H1.9730.95
112_H168_R1.8000.92
173_T257_R1.7220.89
156_V241_M1.6870.88
100_T132_G1.6380.86
216_T243_V1.6090.84
119_P230_G1.5810.83
223_T242_H1.5740.82
108_M116_A1.5360.80
171_I255_L1.5240.79
120_T153_I1.5160.79
85_F89_V1.5050.78
128_I136_E1.4800.77
148_G169_P1.4330.73
186_N190_Y1.4130.72
119_P208_L1.4030.71
138_L159_K1.3870.70
166_D223_T1.3790.69
84_G234_C1.3710.69
148_G243_V1.3650.68
78_C94_R1.3550.67
92_A232_I1.3350.66
113_D163_K1.3250.65
242_H247_G1.3200.64
256_K259_Y1.3160.64
98_T105_E1.3110.63
111_V241_M1.2880.61
110_G164_F1.2860.61
79_G85_F1.2690.60
78_C85_F1.2580.59
168_R171_I1.2570.59
197_V204_G1.2520.58
107_T135_V1.2340.57
193_M233_T1.2320.56
172_P191_P1.2290.56
223_T227_Q1.2210.55
87_Y170_H1.1990.53
99_A153_I1.1970.53
230_G247_G1.1960.53
137_V143_L1.1830.52
78_C141_K1.1790.51
204_G253_A1.1790.51
213_T253_A1.1760.51
148_G216_T1.1760.51
117_V241_M1.1730.51
119_P243_V1.1720.51
162_E250_G1.1690.50
152_E244_G1.1670.50
197_V213_T1.1420.48
151_L164_F1.1380.48
153_I200_V1.1320.47
219_Y250_G1.1320.47
108_M233_T1.1300.47
93_K102_S1.1300.47
156_V198_G1.1290.47
79_G160_R1.1280.47
153_I238_V1.1260.46
114_N163_K1.1220.46
219_Y223_T1.1180.46
80_C92_A1.1150.45
125_G137_V1.1140.45
85_F94_R1.1130.45
186_N199_A1.1080.45
179_N182_V1.1050.44
209_G221_F1.1050.44
153_I205_Y1.1030.44
204_G208_L1.1010.44
196_P237_K1.1000.44
99_A108_M1.0950.44
80_C262_Q1.0930.43
95_N111_V1.0930.43
221_F244_G1.0910.43
230_G244_G1.0890.43
90_A97_V1.0860.43
79_G100_T1.0800.42
130_V174_Q1.0790.42
107_T185_V1.0770.42
161_S243_V1.0750.42
194_Y237_K1.0690.41
180_D196_P1.0680.41
159_K236_G1.0580.40
181_G234_C1.0570.40
116_A164_F1.0550.40
111_V114_N1.0550.40
242_H245_G1.0540.40
156_V166_D1.0510.40
119_P152_E1.0470.39
78_C116_A1.0420.39
113_D232_I1.0410.39
152_E166_D1.0410.39
170_H183_L1.0400.39
160_R195_V1.0400.39
213_T246_N1.0370.38
187_T225_A1.0320.38
232_I262_Q1.0310.38
100_T263_N1.0310.38
109_L242_H1.0230.37
90_A98_T1.0220.37
235_T246_N1.0210.37
84_G97_V1.0180.37
100_T103_K1.0140.36
110_G122_A1.0140.36
85_F92_A1.0120.36
208_L215_R1.0060.36
165_R227_Q1.0030.35
114_N119_P1.0010.35
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  
3q3yA20.68561000.471Contact Map
3qzrA20.68181000.478Contact Map
1cqqA10.68181000.491Contact Map
2b0fA10.68941000.501Contact Map
3zveA10.69321000.509Contact Map
2ijd120.69321000.511Contact Map
4dcdA10.6971000.556Contact Map
2bhgA20.65531000.584Contact Map
2halA10.66671000.646Contact Map
1lvmA20.704599.30.87Contact 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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