GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0858

ID: 1405537830 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 494 (447)
Sequences: 662 (535.1)
Seq/Len: 1.481
Nf(neff/√len): 25.3

HHblits Results: (2013_03)
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: 1.481).

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_L4.7401.00
262_G305_Y4.0901.00
428_A448_N3.8461.00
214_F231_V3.1501.00
457_L488_Y2.9451.00
220_A223_A2.7861.00
143_I209_D2.6741.00
79_M365_I2.6151.00
215_V268_A2.6041.00
262_G266_K2.4421.00
478_Y488_Y2.3831.00
212_T264_Q2.2410.99
152_E224_E2.2060.99
86_I121_I2.1870.99
325_H368_W2.1860.99
428_A452_T2.1700.99
75_Q447_E2.1640.99
265_M270_L2.1430.99
448_N452_T2.0720.98
334_L371_G2.0610.98
322_L367_N2.0390.98
101_D104_A2.0380.98
208_Q260_A2.0050.98
258_K301_A2.0020.98
157_L226_I1.9970.98
258_K299_D1.9730.98
125_I174_A1.9370.97
208_Q264_Q1.9020.97
216_K220_A1.8810.97
176_P234_Q1.8770.97
138_C143_I1.8720.97
125_I214_F1.8120.96
175_A232_T1.8070.96
107_T166_I1.8030.96
98_K406_K1.7990.95
181_K197_W1.7870.95
102_R162_E1.7800.95
108_E410_R1.7740.95
119_S426_P1.7680.95
177_W184_K1.7540.95
480_V486_T1.7470.94
212_T215_V1.7320.94
266_K304_Q1.7280.94
75_Q429_V1.7070.93
364_T372_V1.6870.93
143_I212_T1.6560.92
173_I373_I1.6390.92
428_A450_D1.6380.92
78_T429_V1.6220.91
469_V476_F1.5640.89
248_M253_Q1.5570.89
441_I457_L1.5450.88
313_N338_T1.5120.87
222_K227_D1.5100.86
215_V264_Q1.5040.86
103_H162_E1.5010.86
106_L163_I1.4880.85
425_K428_A1.4780.85
254_R299_D1.4740.85
86_I160_L1.4730.85
445_A455_F1.4690.84
74_E432_A1.4550.84
423_V487_S1.4480.83
76_Y430_R1.4480.83
148_L152_E1.4450.83
264_Q268_A1.4440.83
172_V226_I1.4380.83
130_F379_L1.4350.82
366_N444_S1.4340.82
149_Q152_E1.4310.82
107_T114_D1.4270.82
88_G124_S1.4180.81
255_D259_T1.4060.81
402_N407_T1.4030.80
365_I424_V1.3890.79
110_F163_I1.3820.79
185_V203_N1.3740.78
94_L105_F1.3640.78
203_N206_Y1.3630.78
116_F418_A1.3630.78
464_S479_D1.3600.77
86_I163_I1.3570.77
431_I453_Y1.3540.77
219_Q268_A1.3520.77
455_F490_W1.3420.76
257_V262_G1.3420.76
476_F488_Y1.3410.76
208_Q212_T1.3330.75
237_P314_Y1.3310.75
219_Q269_G1.3270.75
107_T111_S1.3270.75
111_S117_G1.3200.74
161_K224_E1.3170.74
148_L220_A1.3170.74
455_F469_V1.3170.74
136_T197_W1.3020.73
94_L378_M1.2910.72
79_M82_F1.2880.72
76_Y431_I1.2870.72
212_T268_A1.2820.71
250_W295_K1.2760.71
82_F421_S1.2730.71
217_W221_F1.2720.70
376_N379_L1.2710.70
118_F374_V1.2660.70
322_L326_Q1.2570.69
218_I228_I1.2570.69
374_V397_A1.2480.68
256_F263_P1.2450.68
176_P214_F1.2370.67
185_V200_G1.2360.67
238_L277_F1.2290.67
124_S244_A1.2240.66
466_K479_D1.2120.65
130_F376_N1.2110.65
87_T385_P1.2100.65
123_I228_I1.2080.65
46_L49_D1.2020.64
275_Y310_A1.1950.63
109_T397_A1.1890.63
89_S130_F1.1870.63
462_E483_K1.1810.62
40_Y423_V1.1790.62
402_N405_Y1.1740.61
425_K448_N1.1720.61
355_E483_K1.1700.61
431_I447_E1.1670.61
148_L224_E1.1630.60
418_A422_S1.1620.60
77_Q430_R1.1500.59
232_T278_D1.1490.59
123_I217_W1.1440.58
361_A398_V1.1410.58
41_T53_D1.1400.58
80_D332_E1.1370.58
37_V55_V1.1340.57
276_A296_I1.1340.57
94_L102_R1.1280.57
172_V228_I1.1210.56
374_V417_I1.1190.56
260_A263_P1.1150.56
280_N394_C1.1140.55
431_I441_I1.1130.55
257_V306_L1.1110.55
278_D362_L1.1100.55
111_S307_A1.1100.55
231_V274_I1.1090.55
110_F121_I1.1050.54
430_R446_F1.1010.54
103_H107_T1.1000.54
178_T184_K1.0990.54
89_S379_L1.0960.54
299_D325_H1.0930.53
126_G244_A1.0870.53
127_C244_A1.0870.53
239_N293_P1.0820.52
408_I419_H1.0810.52
218_I270_L1.0750.51
176_P184_K1.0660.50
308_G376_N1.0580.50
335_F338_T1.0570.50
56_N59_P1.0540.49
462_E469_V1.0520.49
97_M105_F1.0510.49
125_I423_V1.0500.49
297_Y309_A1.0500.49
466_K480_V1.0490.49
296_I306_L1.0450.48
278_D380_D1.0430.48
262_G302_A1.0380.48
215_V219_Q1.0370.47
84_A397_A1.0350.47
109_T118_F1.0340.47
457_L480_V1.0330.47
257_V305_Y1.0290.47
38_A52_R1.0250.46
397_A413_H1.0230.46
143_I227_D1.0230.46
278_D312_H1.0230.46
211_A256_F1.0220.46
88_G135_Y1.0220.46
140_T143_I1.0220.46
332_E370_K1.0190.46
201_Q252_E1.0190.46
118_F419_H1.0180.46
70_L196_S1.0160.45
480_V484_S1.0160.45
389_G394_C1.0160.45
43_T46_L1.0160.45
341_G422_S1.0130.45
398_V469_V1.0060.44
163_I170_I1.0060.44
274_I400_I1.0060.44
424_V456_V1.0050.44
174_A217_W1.0030.44
210_Y214_F1.0020.44
471_D490_W1.0020.44
279_H394_C1.0000.44
51_T57_F1.0000.44
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: (12Jul14)
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  
2nt0A40.95751000.228Contact Map
2wnwA20.88261000.29Contact Map
4ccdA10.7491000.357Contact Map
3clwA60.81171000.362Contact Map
3kl0A40.73081000.424Contact Map
4fmvA10.71261000.441Contact Map
2y24A10.71461000.45Contact Map
4m29A10.74291000.749Contact Map
1w91A80.7531000.775Contact Map
1uhvA40.7531000.782Contact 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.

Page generated in 0.081 seconds.