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bv1 -force run

ID: 1513453782 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 252 (252)
Sequences: 189 (94.5)
Seq/Len: 0.750
Nf(neff/√len): 6.0

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: 0.750).

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
59_N105_L2.2060.96
139_V247_Y1.9540.91
111_Q163_S1.8530.88
78_T81_R1.7830.85
61_F223_G1.7790.85
3_S31_A1.6390.78
75_T84_R1.6090.76
219_N223_G1.5440.72
59_N67_L1.5290.71
24_V131_I1.4910.68
78_T119_P1.4650.66
123_I193_L1.4210.62
23_S204_Y1.4160.62
66_V123_I1.4090.61
81_R215_R1.3970.61
13_S21_R1.3890.60
140_G211_S1.3790.59
41_V78_T1.3730.59
78_T88_N1.3560.57
30_A35_A1.3520.57
6_N46_Q1.3480.56
17_S61_F1.3400.56
10_R28_Y1.3380.56
114_T123_I1.3350.55
100_R174_I1.3340.55
6_N178_T1.3310.55
16_V34_Y1.3250.54
17_S22_T1.3230.54
161_N246_T1.3080.53
167_A193_L1.3020.53
5_S68_S1.2970.52
51_F131_I1.2910.52
182_V191_I1.2900.51
22_T46_Q1.2890.51
220_G228_N1.2790.51
222_Y228_N1.2790.51
17_S23_S1.2730.50
60_Q93_Y1.2690.50
12_Q196_T1.2610.49
76_F116_M1.2540.48
73_L118_G1.2420.47
12_Q22_T1.2420.47
51_F202_K1.2420.47
17_S49_P1.2390.47
3_S6_N1.2390.47
22_T53_T1.2380.47
27_S209_S1.2360.47
31_A121_S1.2240.46
182_V189_L1.2230.46
13_S41_V1.2220.46
21_R209_S1.2220.46
119_P167_A1.2200.45
35_A42_V1.2150.45
7_T45_S1.2150.45
64_E240_A1.2130.45
3_S10_R1.2080.44
28_Y48_A1.2070.44
3_S21_R1.2050.44
178_T193_L1.2040.44
29_G120_I1.2040.44
6_N79_Y1.2000.44
17_S28_Y1.1980.44
36_R72_A1.1960.43
19_V27_S1.1950.43
33_G131_I1.1920.43
10_R22_T1.1880.43
58_E70_N1.1810.42
28_Y223_G1.1790.42
30_A33_G1.1780.42
236_W242_S1.1740.42
120_I167_A1.1710.41
63_P66_V1.1670.41
12_Q41_V1.1660.41
17_S40_N1.1530.40
42_V56_V1.1510.40
6_N40_N1.1490.40
167_A188_T1.1420.39
6_N17_S1.1300.38
35_A56_V1.1300.38
4_T241_Q1.1270.38
13_S119_P1.1260.38
131_I151_L1.1150.37
29_G240_A1.1130.37
39_P211_S1.1090.36
13_S29_G1.1070.36
77_V86_V1.1070.36
73_L142_S1.1050.36
4_T140_G1.1030.36
12_Q46_Q1.1020.36
9_C30_A1.0970.35
10_R196_T1.0940.35
27_S30_A1.0920.35
24_V43_L1.0900.35
67_L178_T1.0870.35
23_S211_S1.0850.34
28_Y41_V1.0850.34
119_P163_S1.0830.34
79_Y82_Y1.0780.34
6_N21_R1.0750.34
189_L215_R1.0730.33
71_S123_I1.0720.33
24_V204_Y1.0640.33
128_S150_A1.0630.33
56_V232_V1.0620.33
21_R28_Y1.0620.33
79_Y193_L1.0610.33
201_N205_N1.0610.33
43_L193_L1.0600.32
7_T246_T1.0580.32
55_R185_Q1.0570.32
49_P172_Y1.0560.32
82_Y214_E1.0550.32
43_L52_T1.0540.32
152_F171_R1.0520.32
17_S21_R1.0500.32
7_T49_P1.0430.31
139_V214_E1.0420.31
3_S13_S1.0420.31
10_R19_V1.0420.31
81_R119_P1.0390.31
10_R21_R1.0390.31
22_T33_G1.0380.31
23_S209_S1.0380.31
21_R33_G1.0370.31
29_G114_T1.0360.31
66_V78_T1.0350.31
193_L196_T1.0340.31
18_H52_T1.0330.30
82_Y90_T1.0290.30
137_P153_G1.0270.30
13_S196_T1.0260.30
119_P209_S1.0150.29
19_V61_F1.0130.29
17_S30_A1.0070.29
73_L83_V1.0040.28
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  
3i6uA20.3694.10.981Contact Map
4xt1A10.07543.40.982Contact Map
2xk0A10.26982.40.983Contact Map
2ixkA20.52382.20.983Contact Map
3ukxC10.09132.10.984Contact Map
3llpA20.30951.70.985Contact Map
2eqrA10.24211.60.985Contact Map
4hdqC10.01981.40.985Contact Map
1ep0A10.50791.40.985Contact Map
1hcwA10.08731.30.986Contact 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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