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PilT

ID: 1513372479 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 363 (346)
Sequences: 7160 (4368.2)
Seq/Len: 20.694
Nf(neff/√len): 234.8

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: 20.694).

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
119_L263_A3.4871.00
157_I193_A3.1351.00
122_L262_R3.1121.00
117_N147_Y2.9821.00
288_T313_Y2.9771.00
273_V332_S2.9671.00
94_A155_H2.9641.00
159_I189_A2.9331.00
233_S236_Q2.6791.00
128_L227_S2.6521.00
272_R279_I2.6331.00
130_T229_L2.5491.00
150_R170_K2.5121.00
324_D328_R2.4941.00
294_L306_M2.4721.00
90_R163_I2.4191.00
52_L95_A2.4141.00
293_N297_E2.2441.00
34_D271_K2.2341.00
233_S304_P2.1971.00
120_A144_V2.1231.00
108_E117_N2.1221.00
265_I284_I2.0811.00
321_V325_Y2.0671.00
106_T109_E2.0521.00
78_G101_P2.0501.00
287_A292_R2.0211.00
85_N196_E1.9821.00
319_D340_A1.9791.00
20_H197_D1.9771.00
82_F97_F1.9631.00
279_I330_I1.9561.00
154_D200_I1.9461.00
118_K286_I1.9401.00
206_M215_A1.9061.00
94_A175_N1.8841.00
141_L202_L1.8411.00
11_M16_A1.8161.00
287_A295_I1.8071.00
7_F19_L1.7951.00
129_V140_T1.7901.00
116_L144_V1.7871.00
322_I336_A1.7851.00
9_K13_D1.7791.00
291_V303_I1.7681.00
87_Y177_R1.7611.00
64_F93_I1.7561.00
238_I261_I1.7411.00
34_D153_Y1.7281.00
206_M227_S1.7281.00
100_I165_F1.7171.00
316_M324_D1.7101.00
294_L299_K1.6911.00
206_M212_I1.6741.00
16_A31_L1.6631.00
86_Y95_A1.6521.00
317_S320_D1.6501.00
272_R330_I1.6461.00
285_L315_M1.6261.00
30_R197_D1.6221.00
321_V324_D1.6191.00
121_L147_Y1.6111.00
299_K302_Q1.5931.00
271_K335_E1.5921.00
201_I218_A1.5891.00
146_D150_R1.5891.00
141_L226_F1.5781.00
154_D172_C1.5781.00
323_M327_N1.5731.00
127_I224_V1.5671.00
212_I244_V1.5631.00
209_R213_A1.5451.00
82_F99_I1.5401.00
10_L14_T1.5281.00
281_A325_Y1.5171.00
103_K109_E1.5121.00
11_M19_L1.5101.00
335_E338_I1.5081.00
25_N48_L1.4741.00
89_E175_N1.4481.00
84_V97_F1.4371.00
26_P37_R1.4371.00
213_A217_E1.4331.00
4_L51_M1.4271.00
185_S188_N1.4271.00
290_A313_Y1.4201.00
149_N156_I1.4111.00
308_Q320_D1.4101.00
146_D170_K1.4081.00
288_T306_M1.4030.99
20_H30_R1.3940.99
68_G88_K1.3850.99
190_L214_L1.3690.99
37_R40_Y1.3640.99
326_L336_A1.3600.99
53_Y61_I1.3500.99
302_Q305_S1.3420.99
191_R208_D1.3390.99
279_I325_Y1.3320.99
306_M310_G1.3310.99
127_I263_A1.3210.99
331_I335_E1.3210.99
130_T231_T1.3160.99
133_T198_P1.3150.99
119_L127_I1.3060.99
150_R153_Y1.3060.99
107_V143_A1.2930.99
63_R67_E1.2830.99
57_P60_I1.2820.99
193_A201_I1.2790.99
331_I336_A1.2760.99
62_K66_E1.2610.99
148_A226_F1.2530.99
159_I179_L1.2490.99
94_A157_I1.2480.99
177_R193_A1.2380.98
326_L333_P1.2370.98
235_A285_L1.2360.98
69_E183_T1.2340.98
159_I193_A1.2320.98
32_H272_R1.2310.98
64_F183_T1.2280.98
29_I38_I1.2210.98
327_N330_I1.2200.98
124_K262_R1.2190.98
126_L225_V1.2190.98
268_T318_L1.2180.98
112_L282_T1.2120.98
147_Y151_M1.2050.98
148_A200_I1.2020.98
14_T36_Q1.2010.98
306_M313_Y1.1930.98
105_K109_E1.1840.98
245_F276_P1.1840.98
212_I241_I1.1810.98
33_G278_R1.1770.98
49_R53_Y1.1730.98
282_T316_M1.1710.98
187_A210_E1.1680.97
153_Y171_N1.1500.97
12_V80_A1.1400.97
208_D211_T1.1280.97
107_V117_N1.1270.97
217_E243_D1.1250.97
19_L29_I1.1230.97
111_G280_V1.1160.96
325_Y330_I1.1150.96
189_A193_A1.1130.96
108_E147_Y1.1110.96
37_R152_R1.0910.96
15_G32_H1.0880.96
28_L37_R1.0880.96
85_N96_A1.0810.95
316_M321_V1.0770.95
257_L261_I1.0760.95
11_M29_I1.0630.95
264_V285_L1.0630.95
262_R292_R1.0610.95
64_F182_H1.0600.95
270_F331_I1.0590.95
133_T223_H1.0570.95
155_H175_N1.0550.95
270_F335_E1.0460.94
258_S295_I1.0420.94
8_F82_F1.0380.94
297_E302_Q1.0370.94
16_A29_I1.0360.94
59_E276_P1.0360.94
237_T264_V1.0310.94
179_L183_T1.0300.94
22_S28_L1.0260.94
114_Q316_M1.0160.93
61_I183_T1.0160.93
285_L291_V1.0150.93
130_T237_T1.0150.93
44_N47_E1.0060.93
323_M326_L1.0020.92
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  
2ewvA10.94211000.266Contact Map
3jvvA30.92841000.283Contact Map
4ksrA301000.329Contact Map
4phtA30.8761000.342Contact Map
1p9rA10.87331000.374Contact Map
2eyuA20.67771000.477Contact Map
2oap120.94211000.532Contact Map
4ihqA30.93661000.563Contact Map
2gzaA30.78241000.609Contact Map
4bloA120.691599.90.714Contact 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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