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cob 377 aa Cipangopaludina chinensis

ID: 1513628880 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 377 (329)
Sequences: 2342 (857.6)
Seq/Len: 7.119
Nf(neff/√len): 47.3

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: 7.119).

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
337_I350_G4.2171.00
119_L301_L4.1971.00
95_I124_T3.5901.00
222_H226_S2.9001.00
42_L194_T2.8031.00
270_Q339_S2.7871.00
127_V186_L2.6961.00
99_V121_L2.5991.00
58_G177_T2.3511.00
123_L193_M2.3471.00
126_A186_L2.3121.00
151_L165_V2.2741.00
26_S217_E2.2521.00
115_N301_L2.2511.00
122_F294_V2.1941.00
44_V83_V2.1761.00
124_T190_I2.1331.00
126_A151_L2.1251.00
53_S181_A2.1241.00
28_L225_Y2.0781.00
46_V191_V2.0311.00
50_F185_L1.9931.00
83_V240_F1.9441.00
159_K163_E1.8761.00
279_I292_A1.8521.00
90_A236_L1.8501.00
122_F126_A1.8441.00
37_L94_C1.8301.00
115_N119_L1.8111.00
104_Y324_F1.8111.00
40_L233_F1.7931.00
69_H73_D1.6941.00
240_F244_V1.6911.00
344_I348_W1.6741.00
302_I306_S1.6441.00
51_F54_M1.6261.00
57_I173_N1.6001.00
48_T83_V1.5801.00
130_L182_I1.5641.00
109_M307_N1.5290.99
116_V196_L1.5120.99
182_I186_L1.4990.99
103_V303_L1.4960.99
55_H69_H1.4960.99
118_V301_L1.4670.99
38_L95_I1.4650.99
102_G107_S1.4580.99
261_N264_V1.4540.99
115_N305_L1.4450.99
136_W176_L1.4400.99
112_Y115_N1.4340.99
337_I349_I1.4280.99
122_F297_V1.4080.99
182_I189_V1.4070.99
63_A66_S1.4070.99
333_I349_I1.4020.99
293_L296_S1.3890.99
112_Y203_E1.3850.99
341_P346_F1.3770.99
106_G109_M1.3710.99
99_V300_L1.3450.98
136_W164_W1.3380.98
138_Q142_W1.3380.98
118_V297_V1.3360.98
59_H62_L1.3230.98
242_F246_F1.3170.98
193_M196_L1.3140.98
30_I231_L1.2990.98
95_I99_V1.2970.98
324_F328_V1.2850.98
71_S82_I1.2830.98
291_I295_F1.2720.97
60_I63_A1.2560.97
201_L206_S1.2230.96
66_S70_I1.2040.96
348_W351_Q1.1920.96
192_V195_I1.1870.96
273_W276_L1.1840.95
295_F302_I1.1820.95
289_G338_G1.1800.95
82_I249_Q1.1640.95
181_A184_F1.1640.95
165_V182_I1.1610.95
255_E258_V1.1580.95
52_L70_I1.1400.94
101_R178_R1.1330.94
266_P269_I1.1270.94
190_I319_V1.1240.94
343_E346_F1.1230.94
127_V190_I1.1200.93
57_I62_L1.1200.93
160_M163_E1.1190.93
277_Y338_G1.1170.93
139_M142_W1.1170.93
164_W176_L1.1160.93
253_D270_Q1.1160.93
46_V80_I1.1140.93
70_I77_G1.1070.93
42_L46_V1.1040.93
129_F275_F1.1030.93
165_V294_V1.1000.93
118_V300_L1.0910.92
332_L352_V1.0900.92
29_S32_G1.0860.92
207_N313_S1.0860.92
91_F124_T1.0850.92
329_G333_I1.0840.92
66_S77_G1.0820.92
137_G256_N1.0810.92
48_T111_Y1.0790.92
116_V193_M1.0790.92
249_Q255_E1.0750.91
71_S81_R1.0750.91
36_S232_G1.0700.91
152_S162_V1.0670.91
255_E270_Q1.0650.91
85_A252_S1.0640.91
125_M275_F1.0630.91
143_G284_P1.0620.91
43_G191_V1.0620.91
130_L244_V1.0600.91
151_L161_L1.0570.90
90_A94_C1.0520.90
137_G164_W1.0490.90
35_G49_G1.0490.90
98_H117_G1.0440.90
155_P158_G1.0420.90
268_H341_P1.0410.90
127_V130_L1.0280.89
192_V196_L1.0270.89
177_T181_A1.0250.89
203_E328_V1.0240.89
59_H173_N1.0230.88
31_W56_Y1.0210.88
61_D189_V1.0210.88
199_L203_E1.0190.88
132_Y135_P1.0180.88
269_I277_Y1.0110.88
117_G197_H1.0080.88
58_G63_A1.0060.87
88_A223_V1.0060.87
60_I173_N1.0050.87
130_L179_F1.0030.87
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  
1pp9C20.97351000.047Contact Map
3cx5C20.99471000.06Contact Map
2qjyA60.99731000.061Contact Map
4ogqA10.55441000.409Contact Map
4ogqB10.39261000.754Contact Map
4gd3A20.413865.50.964Contact Map
1kqfC10.490753.30.967Contact Map
2kdrX10.07436.20.979Contact Map
2wdqC30.27593.70.981Contact Map
2bs2C20.334230.982Contact 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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