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T0814 23-419 -force run

ID: 1405039972 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 397 (391)
Sequences: 231 (205.3)
Seq/Len: 0.591
Nf(neff/√len): 10.4

Jackhmmer Results: (2014_04_16)
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: 0.591).

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
326_N333_E5.9341.00
60_N64_T4.0741.00
138_E388_R3.4941.00
255_D347_Y3.0981.00
380_R387_D2.6870.99
145_A375_I2.6630.99
164_F375_I2.4240.97
112_S138_E2.3800.96
268_D370_Q2.2410.95
52_Y129_I2.0970.92
323_M334_K2.0620.91
305_S322_K2.0240.90
173_I180_L1.9840.88
374_S392_V1.8900.85
44_G52_Y1.8860.85
119_V130_F1.8820.84
135_S389_L1.8760.84
60_N386_Y1.8380.83
189_R192_N1.8160.81
249_N293_H1.7400.77
222_E370_Q1.7320.77
18_V40_I1.7130.76
90_G323_M1.7000.75
18_V132_A1.6960.75
58_H66_S1.6810.74
307_Y321_S1.6460.72
238_V252_L1.6450.72
222_E270_D1.6280.71
376_Y389_L1.6280.71
18_V38_I1.6220.70
318_D321_S1.5700.67
381_P384_A1.5300.64
181_K380_R1.5290.64
66_S176_P1.5160.63
135_S376_Y1.5110.62
222_E268_D1.4960.61
197_L215_L1.4590.58
40_I132_A1.4530.58
180_L207_I1.4480.57
231_N290_Y1.4460.57
112_S162_V1.4340.56
143_I377_V1.4320.56
72_E385_R1.4200.55
180_L377_V1.4200.55
141_V171_F1.4110.54
41_N284_D1.3990.53
258_R363_E1.3930.53
275_I304_G1.3560.50
223_Y322_K1.3530.50
270_D370_Q1.3480.49
185_Y190_R1.3440.49
219_A367_Y1.3440.49
70_P78_Q1.3330.48
254_T295_T1.3250.47
154_D159_H1.3180.47
111_V288_D1.3170.47
129_I143_I1.3090.46
185_Y376_Y1.3070.46
191_D377_V1.3040.46
313_F321_S1.2940.45
100_L117_I1.2790.44
16_L40_I1.2560.42
149_G156_N1.2510.42
307_Y322_K1.2480.41
184_V325_Y1.2460.41
160_Q371_N1.2460.41
44_G117_I1.2440.41
140_V219_A1.2430.41
57_V118_Q1.2380.41
277_C280_C1.2240.39
248_Y367_Y1.2150.39
31_A308_L1.2140.39
173_I179_D1.2100.38
54_Y104_N1.2080.38
30_I38_I1.2070.38
60_N387_D1.2030.38
338_L343_Y1.2020.38
149_G229_L1.1910.37
234_N238_V1.1900.37
109_F262_T1.1870.37
56_V158_S1.1780.36
54_Y76_G1.1780.36
131_T214_N1.1770.36
308_L336_V1.1700.35
71_I265_Y1.1690.35
72_E287_A1.1670.35
75_N108_Q1.1660.35
329_T333_E1.1630.35
294_F338_L1.1580.35
228_F290_Y1.1580.35
321_S336_V1.1560.34
230_S288_D1.1540.34
194_V238_V1.1510.34
119_V287_A1.1470.34
185_Y374_S1.1420.33
95_Y191_D1.1330.33
161_Q216_I1.1300.32
52_Y130_F1.1280.32
296_L362_I1.1280.32
182_I279_D1.1270.32
84_D99_R1.1260.32
166_I391_G1.1230.32
193_A196_D1.1190.32
44_G190_R1.1190.32
33_G144_S1.1160.32
55_N86_A1.1130.31
261_G295_T1.1130.31
8_V39_E1.1120.31
144_S338_L1.1090.31
143_I375_I1.1090.31
293_H343_Y1.1070.31
62_D168_N1.1050.31
171_F379_Y1.1050.31
15_T173_I1.1020.31
145_A164_F1.0990.30
13_I322_K1.0980.30
166_I254_T1.0940.30
176_P181_K1.0930.30
225_R342_S1.0860.29
229_L342_S1.0850.29
18_V227_E1.0840.29
224_R363_E1.0840.29
166_I377_V1.0840.29
105_D166_I1.0790.29
102_L109_F1.0780.29
154_D347_Y1.0770.29
79_G111_V1.0750.29
85_F181_K1.0730.29
116_A184_V1.0720.29
16_L229_L1.0670.28
344_N381_P1.0630.28
164_F182_I1.0630.28
135_S385_R1.0610.28
223_Y276_R1.0610.28
191_D348_L1.0590.28
165_N240_N1.0590.28
116_A256_Y1.0570.28
64_T324_G1.0530.27
73_Y136_V1.0500.27
67_Q381_P1.0490.27
76_G104_N1.0470.27
119_V202_I1.0460.27
258_R347_Y1.0440.27
32_L115_Y1.0410.27
291_I335_A1.0400.26
306_V336_V1.0370.26
15_T169_K1.0350.26
223_Y315_N1.0340.26
143_I393_T1.0340.26
191_D353_G1.0320.26
64_T328_E1.0320.26
146_S163_S1.0310.26
16_L223_Y1.0290.26
109_F230_S1.0280.26
381_P388_R1.0260.26
54_Y265_Y1.0250.26
99_R337_L1.0210.25
13_I52_Y1.0210.25
60_N212_N1.0170.25
145_A169_K1.0150.25
60_N380_R1.0140.25
227_E266_D1.0120.25
32_L140_V1.0020.24
192_N377_V1.0010.24
13_I44_G1.0000.24
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: (05Jul14)
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  
4aefA20.284696.30.954Contact Map
2qlvB20.2166960.955Contact Map
4aeeA20.3023960.956Contact Map
2lu3A10.26295.60.957Contact Map
1ac0A10.246994.80.959Contact Map
1z0nA30.216693.80.961Contact Map
4cfeB20.229291.90.963Contact Map
2z0bA60.26288.40.966Contact Map
1m7xA40.302370.70.972Contact Map
1ea9C20.312358.60.974Contact 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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