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OPENSEQ.org

Slam

ID: 1499168064 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 488 (417)
Sequences: 522 (470.5)
Seq/Len: 1.252
Nf(neff/√len): 23.0

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: 1.252).

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
133_R136_E4.3221.00
375_D395_R2.4591.00
330_W360_L2.3920.99
461_L478_N2.3740.99
402_W409_S2.3200.99
163_F197_A2.3130.99
155_R174_Q2.2520.99
257_W287_I2.1850.99
125_G141_Y2.1140.98
142_R162_L2.0510.98
103_R131_D2.0470.98
184_P187_L2.0380.97
294_K322_F2.0350.97
278_D305_R2.0330.97
371_M397_A2.0310.97
179_K192_E1.9980.97
359_S373_G1.9870.97
98_N101_G1.8500.95
436_D468_S1.8400.95
243_Y267_G1.8070.94
172_A195_R1.7980.94
174_Q177_R1.7890.94
172_A199_R1.7870.94
336_A356_I1.7550.93
294_K324_R1.7460.92
378_R421_E1.7130.92
128_A136_E1.6330.89
213_T240_A1.6210.88
374_L392_Y1.6030.87
124_Q140_H1.5970.87
144_L154_V1.5810.86
175_F194_Y1.5740.86
129_Q164_E1.5450.85
140_H143_E1.5210.83
176_D195_R1.5140.83
76_G80_L1.5140.83
121_L143_E1.5020.82
163_F194_Y1.4920.82
466_T475_Y1.4880.82
110_L124_Q1.4830.81
153_A187_L1.4830.81
336_A354_L1.4540.80
138_I161_A1.4360.78
334_S358_N1.4290.78
214_R239_T1.4240.78
420_Y468_S1.4240.78
247_A318_A1.4210.77
375_D393_G1.4160.77
447_H450_L1.4090.76
192_E196_K1.4090.76
214_R238_G1.3880.75
155_R177_R1.3870.75
236_V277_N1.3870.75
122_Y153_A1.3820.74
463_H478_N1.3820.74
125_G161_A1.3600.73
77_E81_K1.3580.73
72_L81_K1.3310.70
80_L86_L1.3170.69
185_P188_M1.3120.69
68_K73_Q1.3100.69
74_I77_E1.3100.69
359_S375_D1.3090.69
172_A198_L1.3080.69
75_D78_T1.3080.69
204_W249_K1.3070.68
442_S484_F1.3050.68
215_E477_K1.3050.68
304_R311_A1.2980.68
420_Y469_N1.2920.67
298_L320_L1.2900.67
74_I81_K1.2820.66
68_K81_K1.2800.66
259_T285_G1.2730.66
157_R160_A1.2710.65
335_S357_S1.2690.65
78_T81_K1.2690.65
274_K277_N1.2650.65
307_Y312_Y1.2620.65
73_Q81_K1.2590.64
458_R483_E1.2570.64
153_A157_R1.2570.64
330_W362_F1.2570.64
74_I78_T1.2500.63
210_F358_N1.2460.63
122_Y159_A1.2450.63
338_W354_L1.2450.63
240_A270_Y1.2400.63
298_L482_V1.2330.62
179_K188_M1.2310.62
156_M160_A1.2310.62
122_Y157_R1.2280.61
75_D82_N1.2250.61
168_N201_R1.2220.61
68_K71_V1.2200.61
409_S445_L1.2180.60
118_M144_L1.2130.60
389_F418_R1.2110.60
75_D79_L1.1910.58
286_G299_A1.1820.57
262_G284_S1.1800.57
449_A457_P1.1800.57
455_I484_F1.1790.57
238_G276_F1.1790.57
222_P230_W1.1760.56
217_N436_D1.1730.56
217_N468_S1.1720.56
75_D81_K1.1710.56
450_L466_T1.1710.56
211_S245_L1.1620.55
125_G154_V1.1620.55
156_M159_A1.1580.55
319_R335_S1.1570.55
423_P433_R1.1560.55
338_W352_T1.1490.54
368_Q400_Q1.1480.54
407_L447_H1.1470.54
82_N85_L1.1410.53
111_Q394_L1.1370.53
454_G457_P1.1360.53
72_L78_T1.1340.52
72_L79_L1.1280.52
152_P178_L1.1200.51
78_T85_L1.1190.51
93_A96_S1.1130.50
334_S359_S1.1080.50
144_L240_A1.1070.50
139_S445_L1.1060.50
218_I383_A1.1050.50
90_M109_Y1.1030.49
220_Q306_T1.1000.49
285_G350_D1.0980.49
138_I167_Q1.0950.49
73_Q78_T1.0940.48
415_A439_L1.0930.48
141_Y240_A1.0910.48
160_A164_E1.0890.48
463_H476_E1.0880.48
79_L85_L1.0860.48
175_F191_V1.0830.47
454_G486_K1.0790.47
122_Y144_L1.0740.46
162_L270_Y1.0710.46
128_A161_A1.0710.46
170_A370_W1.0710.46
68_K80_L1.0710.46
202_D252_S1.0700.46
134_V329_K1.0690.46
99_I127_L1.0630.45
156_M187_L1.0620.45
373_G397_A1.0590.45
460_T466_T1.0590.45
356_I465_E1.0590.45
76_G79_L1.0580.45
153_A184_P1.0570.45
81_K85_L1.0520.44
305_R420_Y1.0520.44
161_A177_R1.0510.44
97_N125_G1.0500.44
80_L117_K1.0470.44
241_V296_A1.0460.44
415_A463_H1.0450.44
93_A105_I1.0450.44
156_M191_V1.0420.43
212_V239_T1.0410.43
153_A156_M1.0360.43
261_A283_V1.0360.43
280_T441_T1.0340.43
401_E448_R1.0300.42
343_N393_G1.0290.42
206_V441_T1.0290.42
163_F198_L1.0280.42
374_L441_T1.0280.42
93_A101_G1.0270.42
77_E443_L1.0260.42
220_Q238_G1.0260.42
175_F187_L1.0250.42
67_E70_K1.0240.42
119_L397_A1.0200.41
229_K234_K1.0180.41
315_T339_G1.0170.41
253_L287_I1.0130.41
101_G104_V1.0130.41
262_G322_F1.0130.41
154_V158_L1.0110.40
71_V74_I1.0090.40
182_N318_A1.0090.40
129_Q137_A1.0090.40
418_R438_E1.0060.40
145_I155_R1.0060.40
468_S488_F1.0050.40
304_R374_L1.0040.40
153_A190_Q1.0040.40
269_V277_N1.0040.40
100_A445_L1.0010.39
97_N211_S1.0000.39
275_K374_L1.0000.39
99_I102_I1.0000.39
122_Y156_M1.0000.39
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  
2xevA30.2418990.893Contact Map
3upvA10.24898.80.902Contact Map
4cgwA20.235798.80.902Contact Map
3rkvA10.262398.80.903Contact Map
4j8eA20.245998.80.903Contact Map
2kckA10.225498.80.904Contact Map
3fflA40.231698.80.904Contact Map
2lniA10.270598.80.904Contact Map
2dbaA10.297198.70.905Contact Map
1elrA10.24898.70.906Contact 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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