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T0858

ID: 1451377329 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 494 (433)
Sequences: 1295 (959.7)
Seq/Len: 2.991
Nf(neff/√len): 46.1

HHblits Results: (2015_06)
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: 2.991).

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
179_C246_L5.3741.00
428_A448_N3.8771.00
262_G305_Y3.8621.00
79_M365_I3.3631.00
262_G266_K3.1191.00
214_F231_V3.0641.00
220_A223_A3.0111.00
152_E224_E2.9831.00
215_V268_A2.8261.00
75_Q447_E2.7651.00
143_I209_D2.7191.00
325_H368_W2.6901.00
478_Y488_Y2.6791.00
212_T264_Q2.6631.00
265_M270_L2.6141.00
457_L488_Y2.5631.00
365_I424_V2.4431.00
219_Q268_A2.4091.00
102_R162_E2.3201.00
119_S426_P2.3181.00
108_E410_R2.3061.00
322_L367_N2.2891.00
125_I214_F2.2761.00
448_N452_T2.2571.00
78_T429_V2.2391.00
208_Q260_A2.2341.00
222_K227_D2.2291.00
86_I121_I2.1781.00
266_K304_Q2.1471.00
76_Y430_R2.1411.00
175_A232_T2.1281.00
334_L371_G2.1061.00
208_Q264_Q2.0751.00
428_A450_D2.0741.00
428_A452_T2.0531.00
313_N338_T2.0511.00
74_E432_A2.0161.00
216_K220_A1.9901.00
101_D104_A1.9821.00
258_K299_D1.9340.99
457_L467_I1.9330.99
143_I212_T1.9280.99
173_I373_I1.9160.99
72_P431_I1.9010.99
107_T111_S1.8970.99
107_T166_I1.8870.99
125_I174_A1.8800.99
116_F418_A1.8480.99
441_I457_L1.8360.99
264_Q268_A1.8330.99
103_H162_E1.8250.99
208_Q212_T1.8240.99
215_V264_Q1.7810.99
80_D332_E1.7590.99
75_Q429_V1.7340.99
480_V486_T1.7030.98
464_S479_D1.6750.98
231_V274_I1.6470.98
176_P234_Q1.6430.98
157_L226_I1.5880.97
172_V226_I1.5770.97
94_L378_M1.5750.97
212_T215_V1.5470.97
71_N74_E1.5410.96
255_D259_T1.5380.96
238_L277_F1.5230.96
218_I228_I1.5030.96
431_I447_E1.5030.96
445_A455_F1.4970.96
323_N326_Q1.4910.95
276_A296_I1.4870.95
106_L163_I1.4850.95
148_L220_A1.4740.95
425_K428_A1.4730.95
130_F379_L1.4590.95
462_E483_K1.4540.95
248_M253_Q1.4490.94
181_K189_T1.4400.94
161_K224_E1.4300.94
431_I453_Y1.4290.94
425_K448_N1.4260.94
258_K301_A1.4190.94
276_A306_L1.4170.94
310_A336_T1.4040.93
79_M82_F1.3900.93
311_Y333_L1.3890.93
103_H107_T1.3850.93
148_L224_E1.3840.92
82_F365_I1.3790.92
469_V476_F1.3790.92
212_T268_A1.3760.92
418_A422_S1.3570.91
98_K101_D1.3570.91
215_V219_Q1.3450.91
275_Y310_A1.3440.91
298_E328_Y1.3410.91
219_Q270_L1.3390.91
454_A489_R1.3370.91
332_E370_K1.3240.90
174_A217_W1.3200.90
210_Y214_F1.3180.90
177_W184_K1.3130.90
257_V306_L1.2990.89
172_V228_I1.2980.89
455_F490_W1.2970.89
111_S117_G1.2960.89
376_N379_L1.2940.89
257_V262_G1.2730.88
123_I228_I1.2690.87
273_K307_A1.2620.87
176_P214_F1.2580.87
98_K406_K1.2530.87
322_L326_Q1.2520.86
374_V417_I1.2510.86
480_V484_S1.2480.86
104_A108_E1.2470.86
138_C143_I1.2380.86
174_A228_I1.2330.85
82_F421_S1.2320.85
237_P314_Y1.2310.85
364_T369_C1.2210.85
217_W221_F1.2190.84
307_A332_E1.2150.84
423_V487_S1.2140.84
69_T470_S1.2140.84
464_S482_G1.2080.84
262_G302_A1.2040.83
358_E458_I1.2020.83
219_Q269_G1.1900.82
216_K219_Q1.1830.82
476_F488_Y1.1810.82
265_M272_T1.1730.81
203_N206_Y1.1700.81
94_L105_F1.1700.81
455_F469_V1.1610.80
123_I217_W1.1530.80
137_C151_E1.1510.79
116_F422_S1.1460.79
89_S379_L1.1440.79
232_T278_D1.1410.79
335_F338_T1.1400.79
429_V432_A1.1360.78
151_E221_F1.1360.78
264_Q267_A1.1340.78
433_T443_C1.1300.78
94_L102_R1.1290.78
86_I160_L1.1270.77
441_I480_V1.1260.77
262_G304_Q1.1230.77
107_T114_D1.1220.77
162_E165_A1.1200.77
88_G124_S1.1160.76
124_S128_S1.1140.76
171_K426_P1.1130.76
86_I163_I1.1090.76
257_V305_Y1.1080.76
378_M400_I1.1070.76
120_Y371_G1.1040.75
136_T189_T1.1040.75
118_F374_V1.1020.75
297_Y309_A1.1020.75
178_T184_K1.1010.75
281_Y321_L1.0990.75
84_A397_A1.0990.75
378_M408_I1.0950.74
110_F163_I1.0940.74
178_T181_K1.0930.74
197_W200_G1.0910.74
67_T468_T1.0880.74
399_D411_N1.0870.74
254_R258_K1.0860.74
164_L226_I1.0840.73
250_W295_K1.0810.73
125_I217_W1.0790.73
127_C244_A1.0750.73
76_Y431_I1.0750.73
80_D171_K1.0660.72
339_S395_Y1.0640.71
149_Q152_E1.0630.71
311_Y369_C1.0600.71
109_T118_F1.0530.70
117_G425_K1.0510.70
116_F423_V1.0500.70
296_I306_L1.0500.70
148_L152_E1.0490.70
307_A331_K1.0440.69
125_I231_V1.0440.69
254_R299_D1.0380.69
124_S244_A1.0370.69
76_Y432_A1.0370.69
130_F376_N1.0360.69
420_L424_V1.0350.68
355_E483_K1.0270.68
362_L420_L1.0260.67
121_I170_I1.0260.67
294_G327_A1.0260.67
110_F121_I1.0210.67
256_F263_P1.0140.66
260_A263_P1.0130.66
364_T372_V1.0130.66
401_N407_T1.0120.66
308_G379_L1.0100.66
95_L155_Y1.0090.66
94_L162_E1.0060.65
424_V456_V1.0030.65
265_M271_S1.0000.65
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  
2nt0A40.96761000.136Contact Map
2wnwA20.88461000.283Contact Map
3clwA60.82591000.321Contact Map
4ccdA10.75711000.327Contact Map
4qawA80.72671000.398Contact Map
4uqdA101000.42Contact Map
4fmvA10.72061000.425Contact Map
2y24A10.71661000.432Contact Map
4m29A10.73681000.744Contact Map
1w91A80.76111000.763Contact 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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