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VV_TRAP_LARGE

ID: 1515979586 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 429 (414)
Sequences: 20978 (11466.3)
Seq/Len: 50.671
Nf(neff/√len): 563.5

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: 50.671).

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
102_L182_C3.6361.00
127_R133_D3.5361.00
388_P391_T3.4191.00
320_N364_N3.3441.00
299_Q303_D3.0681.00
311_N314_V3.0561.00
71_S263_G2.9081.00
81_F85_M2.5621.00
300_M304_Y2.4421.00
391_T394_R2.4271.00
101_S118_L2.4151.00
229_G235_F2.3951.00
290_W294_R2.3741.00
184_A406_V2.3641.00
95_H186_M2.3381.00
76_E80_N2.2911.00
89_I92_S2.2701.00
390_H394_R2.2691.00
214_K218_L2.2611.00
269_R273_N2.2521.00
81_F84_S2.2171.00
270_E273_N2.2141.00
347_A357_F2.1891.00
67_H270_E2.1821.00
188_M402_P2.1671.00
300_M303_D2.1241.00
260_T263_G2.0991.00
166_S169_A2.0951.00
401_V405_I2.0791.00
397_L401_V2.0771.00
134_D391_T2.0631.00
95_H190_Y2.0151.00
71_S266_E2.0141.00
71_S270_E2.0071.00
348_S354_P2.0051.00
415_Q422_E1.9911.00
262_T266_E1.9901.00
25_I284_G1.9891.00
67_H70_N1.9721.00
46_Q294_R1.8841.00
415_Q419_L1.8811.00
296_Q299_Q1.8781.00
320_N411_A1.8761.00
71_S267_I1.8681.00
325_F329_F1.8631.00
323_L339_L1.8541.00
326_L335_L1.8281.00
179_I183_V1.8261.00
303_D306_L1.8021.00
156_L359_V1.7511.00
187_V191_F1.7081.00
303_D307_S1.7041.00
67_H71_S1.6991.00
415_Q418_L1.6931.00
68_L252_G1.6891.00
67_H271_T1.6631.00
97_N140_T1.6631.00
315_L350_V1.6511.00
304_Y307_S1.6291.00
169_A422_E1.6261.00
408_A412_V1.6031.00
181_C403_L1.5761.00
115_A381_V1.5681.00
169_A172_L1.5581.00
160_G167_I1.5461.00
290_W293_A1.5401.00
310_E314_V1.5331.00
321_L325_F1.5231.00
191_F194_K1.5091.00
262_T265_V1.5081.00
188_M192_I1.5031.00
217_F221_M1.4891.00
418_L422_E1.4801.00
250_F254_V1.4641.00
116_G380_V1.4611.00
335_L365_L1.4591.00
98_I189_S1.4341.00
46_Q290_W1.4321.00
64_L268_L1.4241.00
77_R81_F1.4221.00
169_A355_V1.4221.00
168_G172_L1.4040.99
163_S344_V1.3950.99
159_Y358_G1.3880.99
304_Y308_I1.3830.99
173_A417_T1.3820.99
111_A377_A1.3780.99
419_L422_E1.3740.99
51_I283_M1.3690.99
183_V187_V1.3640.99
73_G76_E1.3610.99
317_L408_A1.3560.99
9_G12_G1.3550.99
190_Y194_K1.3510.99
331_E334_A1.3450.99
266_E270_E1.3290.99
405_I409_L1.3290.99
205_S208_E1.3240.99
409_L413_F1.3240.99
316_L411_A1.3170.99
211_T214_K1.3130.99
138_G395_G1.3100.99
28_A291_I1.3070.99
389_F393_T1.3050.99
18_M23_S1.3040.99
413_F416_I1.3030.99
222_T247_Y1.2960.99
266_E269_R1.2830.99
340_V361_A1.2790.99
184_A402_P1.2760.99
28_A287_V1.2650.99
47_M287_V1.2620.99
186_M190_Y1.2510.99
112_L380_V1.2480.99
315_L347_A1.2450.98
185_L403_L1.2440.98
123_I385_G1.2420.98
102_L178_G1.2420.98
70_N76_E1.2420.98
315_L319_I1.2350.98
410_V417_T1.2300.98
409_L416_I1.2300.98
103_L107_M1.2290.98
46_Q49_G1.2280.98
319_I343_L1.2230.98
382_S389_F1.2220.98
150_V178_G1.2150.98
137_G392_L1.2130.98
101_S114_D1.2110.98
344_V348_S1.2040.98
169_A421_P1.2000.98
80_N215_E1.1970.98
133_D391_T1.1900.98
320_N360_M1.1890.98
176_I416_I1.1880.98
125_S128_D1.1810.98
81_F213_F1.1780.98
412_V415_Q1.1780.98
138_G142_A1.1770.98
292_V297_L1.1720.98
171_F175_A1.1710.98
302_A306_L1.1700.97
317_L321_L1.1700.97
387_I392_L1.1660.97
176_I180_L1.1600.97
23_S27_V1.1540.97
370_L400_L1.1540.97
137_G385_G1.1520.97
172_L420_L1.1470.97
227_I231_F1.1410.97
90_T194_K1.1410.97
263_G266_E1.1370.97
42_F45_Q1.1280.97
151_P160_G1.1260.97
148_P366_M1.1260.97
41_N45_Q1.1220.97
61_F241_A1.1190.96
21_G284_G1.1110.96
210_F213_F1.1030.96
158_I333_L1.1030.96
298_P302_A1.0990.96
319_I347_A1.0920.96
124_K128_D1.0900.96
113_A116_G1.0880.96
68_L245_S1.0820.96
67_H267_I1.0810.95
395_G398_P1.0800.95
175_A179_I1.0790.95
221_M225_I1.0760.95
137_G381_V1.0730.95
187_V190_Y1.0700.95
353_D356_H1.0630.95
289_G338_L1.0620.95
115_A377_A1.0610.95
106_G114_D1.0590.95
65_T244_S1.0590.95
104_F114_D1.0570.95
26_F30_V1.0550.95
31_F291_I1.0550.95
251_L255_V1.0540.95
398_P402_P1.0460.94
72_A252_G1.0440.94
77_R80_N1.0440.94
77_R216_A1.0430.94
336_L365_L1.0410.94
211_T215_E1.0340.94
120_Q124_K1.0330.94
281_M285_V1.0300.94
364_N411_A1.0300.94
119_G384_V1.0280.94
360_M411_A1.0280.94
328_T400_L1.0280.94
135_F195_K1.0260.94
210_F214_K1.0240.93
322_L326_L1.0200.93
98_I185_L1.0130.93
176_I419_L1.0120.93
222_T248_A1.0110.93
98_I143_S1.0110.93
378_L393_T1.0070.93
160_G170_L1.0040.93
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  
4f35D40.91141000.411Contact Map
4r1iA20.96971000.593Contact Map
4r0cA4099.90.615Contact Map
4pd6A10.790217.10.956Contact Map
3qe7A10.447612.60.959Contact Map
2kncA10.121210.80.96Contact Map
3giaA10.45226.50.964Contact Map
2nq2A20.41265.40.965Contact Map
2m67A10.18654.60.966Contact Map
4g1uA20.41033.90.968Contact 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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