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4pgr

ID: 1501760764 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 207 (203)
Sequences: 924 (903.8)
Seq/Len: 4.552
Nf(neff/√len): 63.4

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: 4.552).

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
12_L167_L3.7321.00
121_W165_Y3.0021.00
155_G197_N2.9561.00
107_G167_L2.6441.00
166_D190_D2.6351.00
163_I194_L2.2071.00
83_Y203_G2.1301.00
42_I46_A2.1131.00
107_G111_A2.0891.00
103_F191_F2.0101.00
124_L165_Y1.9831.00
189_L193_N1.9641.00
170_I187_L1.8971.00
135_G151_Y1.8641.00
131_L155_G1.8401.00
22_A188_Y1.8161.00
106_L164_L1.8161.00
117_L164_L1.7801.00
12_L107_G1.7411.00
168_N172_H1.6340.99
91_V202_F1.6230.99
124_L161_L1.6080.99
156_T194_L1.6010.99
159_F193_N1.5510.99
129_L133_V1.5410.99
149_M201_F1.5400.99
98_S202_F1.5400.99
98_S198_L1.5330.98
106_L160_S1.5220.98
76_L196_I1.5150.98
157_I161_L1.5080.98
18_T65_V1.5010.98
198_L202_F1.4990.98
110_G168_N1.4880.98
7_I11_I1.4650.98
80_V92_V1.4180.97
125_L129_L1.4010.97
4_K7_I1.3980.97
137_F141_S1.3930.97
197_N200_R1.3920.97
27_F31_F1.3900.97
14_V18_T1.3870.97
102_I198_L1.3840.97
101_V133_V1.3830.97
113_M168_N1.3490.96
123_F127_A1.3330.95
105_V129_L1.3130.95
153_V157_I1.2930.94
173_R183_M1.2790.94
49_I53_W1.2790.94
110_G118_S1.2680.94
109_I113_M1.2590.93
45_V48_I1.2470.93
180_I183_M1.2390.93
103_F163_I1.2320.92
95_A198_L1.2290.92
128_V132_A1.2180.92
113_M117_L1.2160.92
153_V201_F1.2030.91
103_F187_L1.1880.90
69_A73_G1.1870.90
159_F162_Y1.1630.89
79_I83_Y1.1600.89
190_D195_F1.1550.89
43_L48_I1.1540.89
154_I158_V1.1530.89
109_I112_K1.1440.88
93_L97_G1.1440.88
16_V104_A1.1430.88
118_S168_N1.1350.87
131_L158_V1.1330.87
152_S197_N1.1310.87
36_L39_P1.1250.87
159_F189_L1.1240.87
18_T69_A1.1220.87
158_V161_L1.1190.86
90_Y132_A1.1160.86
129_L132_A1.1150.86
146_A150_A1.0920.85
159_F166_D1.0890.84
94_E202_F1.0830.84
67_T71_V1.0810.84
14_V62_Y1.0760.83
159_F190_D1.0710.83
119_F123_F1.0660.83
145_S148_M1.0650.83
25_G70_F1.0600.82
193_N196_I1.0570.82
139_I157_I1.0520.81
25_G29_G1.0440.81
133_V137_F1.0430.81
170_I186_S1.0320.80
34_V38_L1.0280.79
63_A67_T1.0280.79
188_Y195_F1.0210.79
109_I115_K1.0200.79
96_F144_N1.0100.78
166_D189_L1.0040.77
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  
4pgrA10.99521000.004Contact Map
4i0uA100.28026.40.935Contact Map
4ev6A50.28996.40.935Contact Map
1r8hA60.14013.20.944Contact Map
3w9iA60.72463.10.945Contact Map
4dx5A30.77292.10.95Contact Map
3ne5A10.73911.80.951Contact Map
4b4aA10.64731.80.951Contact Map
3j9pD40.85991.50.953Contact Map
2xq2A10.77781.40.954Contact 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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