OPENSEQ.org
5pp1ag_2

ID: 1516100265 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 314 (286)
Sequences: 3936 (2304.4)
Seq/Len: 13.762
Nf(neff/√len): 136.3

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: 13.762).

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
149_R205_E5.3631.00
29_R306_D4.3201.00
25_G299_D3.2801.00
168_D182_K3.2231.00
7_S32_E3.0341.00
9_V66_P2.8191.00
26_L305_C2.7091.00
25_G302_G2.6201.00
220_Q303_P2.6181.00
145_L280_V2.5541.00
25_G28_A2.4711.00
252_D256_R2.4341.00
31_H309_I2.3801.00
218_D307_A2.3171.00
34_Y66_P2.2931.00
263_L266_T2.2711.00
214_V246_I2.2631.00
247_S250_V2.2571.00
271_K281_L2.2091.00
303_P306_D2.1491.00
248_D251_K2.1331.00
299_D302_G2.1161.00
214_V270_I2.0801.00
221_V255_V2.0751.00
115_E124_S2.0591.00
18_H289_F1.9961.00
219_D259_K1.9641.00
115_E125_P1.9391.00
9_V36_F1.8971.00
26_L33_P1.8821.00
217_I222_I1.8631.00
249_E252_D1.8581.00
220_Q255_V1.8541.00
273_G277_N1.8451.00
273_G279_R1.8031.00
31_H305_C1.8021.00
29_R302_G1.7791.00
207_L279_R1.7291.00
216_V255_V1.6741.00
155_D158_A1.6611.00
229_T242_E1.6491.00
29_R309_I1.6331.00
210_D227_I1.5901.00
68_A308_L1.5721.00
163_H169_C1.5701.00
158_A161_R1.5611.00
120_A311_Q1.5551.00
211_D228_V1.5551.00
216_V258_A1.5531.00
208_T274_A1.5371.00
257_A268_M1.5351.00
248_D252_D1.5241.00
21_S293_E1.5151.00
25_G29_R1.5141.00
148_P205_E1.5101.00
140_L280_V1.4911.00
168_D184_E1.4821.00
151_L162_F1.4801.00
251_K255_V1.4711.00
258_A266_T1.4681.00
216_V221_V1.4681.00
269_D282_E1.4421.00
113_R138_A1.4341.00
212_V244_I1.4341.00
159_V203_F1.4311.00
146_P277_N1.4271.00
222_I303_P1.4251.00
214_V221_V1.4091.00
23_T35_V1.3850.99
7_S67_A1.3680.99
8_I31_H1.3670.99
293_E299_D1.3620.99
137_L147_V1.3620.99
150_S204_Q1.3610.99
153_T159_V1.3570.99
62_Q65_R1.3520.99
7_S34_Y1.3510.99
264_R307_A1.3300.99
302_G306_D1.3230.99
217_I304_L1.3170.99
293_E296_A1.2960.99
216_V254_C1.2930.99
12_G19_V1.2920.99
257_A280_V1.2880.99
218_D310_A1.2850.99
253_Q280_V1.2700.99
184_E188_L1.2580.99
180_T235_R1.2570.99
256_R260_L1.2550.99
130_N285_A1.2400.98
25_G305_C1.2370.98
224_A292_F1.2360.98
219_D255_V1.2260.98
10_V23_T1.2100.98
9_V69_V1.2070.98
307_A311_Q1.2010.98
145_L257_A1.1850.98
211_D239_E1.1820.98
8_I305_C1.1780.98
228_V238_E1.1780.98
170_I182_K1.1740.98
6_T31_H1.1720.98
161_R165_E1.1690.97
28_A302_G1.1640.97
8_I26_L1.1610.97
37_D40_R1.1590.97
54_A110_V1.1510.97
250_V270_I1.1490.97
246_I251_K1.1440.97
250_V278_Y1.1380.97
293_E301_C1.1330.97
146_P256_R1.1240.97
48_S51_E1.1230.97
221_V258_A1.1230.97
115_E118_G1.1210.97
140_L257_A1.1110.96
120_A308_L1.1100.96
24_E28_A1.1070.96
182_K206_L1.1030.96
32_E67_A1.0990.96
168_D185_A1.0960.96
220_Q251_K1.0930.96
145_L253_Q1.0910.96
22_V304_L1.0790.95
69_V114_W1.0760.95
270_I278_Y1.0750.95
253_Q270_I1.0710.95
265_Y304_L1.0690.95
257_A261_V1.0620.95
169_C183_L1.0560.95
10_V19_V1.0520.95
71_L127_A1.0520.95
137_L202_C1.0420.94
209_G271_K1.0330.94
255_V259_K1.0260.94
27_R33_P1.0210.93
307_A310_A1.0190.93
227_I242_E1.0170.93
23_T27_R1.0150.93
122_Y304_L1.0150.93
171_Y203_F1.0050.93
149_R166_V1.0020.92
218_D311_Q1.0010.92
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  
3vpbA40.84711000.47Contact Map
4iwxA10.88851000.475Contact Map
1gsaA10.8791000.507Contact Map
3vpdA20.84711000.514Contact Map
2p0aA20.85031000.541Contact Map
1pk8A80.88541000.56Contact Map
2q7dA20.85671000.564Contact Map
3t7aA10.84711000.567Contact Map
1i7nA20.88221000.568Contact Map
3r5xA40.85351000.576Contact 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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