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Slam 70-488

ID: 1499516668 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 419 (411)
Sequences: 658 (599.4)
Seq/Len: 1.601
Nf(neff/√len): 29.6

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: 1.601).

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
64_R67_E4.3871.00
86_R105_Q2.9971.00
261_W291_L2.7671.00
367_D399_S2.5341.00
392_L409_N2.5301.00
56_G72_Y2.4941.00
115_P118_L2.3371.00
333_W340_S2.2780.99
306_D326_R2.2190.99
34_R62_D2.2170.99
209_D236_R2.1180.99
144_T171_A2.1100.99
267_A285_L2.1080.99
188_W218_I2.0970.99
309_R352_E2.0830.99
106_F125_Y2.0780.99
110_K123_E2.0500.99
397_T406_Y2.0350.99
302_M328_A1.9800.98
225_K253_F1.9380.98
105_Q108_R1.8900.97
306_D324_G1.8850.97
29_N32_G1.8660.97
94_F128_A1.8640.97
103_A130_R1.8460.97
190_T216_G1.8270.96
394_H409_N1.8220.96
267_A287_I1.8090.96
53_Y84_A1.8010.96
261_W293_F1.7940.96
87_M90_A1.7720.96
73_R93_L1.7690.96
75_L85_V1.7430.95
146_E408_K1.7320.95
174_Y198_G1.7230.95
103_A126_R1.7180.95
351_Y367_D1.7170.95
290_S304_G1.6720.93
225_K255_R1.6710.93
52_L74_E1.6400.93
53_Y88_R1.6290.92
145_R170_T1.6160.92
84_A118_L1.6150.92
55_Q71_H1.6030.91
69_I89_L1.6020.91
71_H74_E1.6010.91
305_L323_Y1.5960.91
86_R108_R1.5810.91
299_Q331_Q1.5700.90
349_R369_E1.5690.90
69_I92_A1.5640.90
84_A88_R1.5580.90
145_R169_G1.5470.89
265_S289_N1.5230.88
59_A67_E1.5040.88
94_F125_Y1.5020.88
380_A388_P1.5000.87
87_M118_L1.4960.87
69_I147_H1.4890.87
146_E410_R1.4840.87
235_R242_A1.4650.86
365_R401_D1.4640.86
385_G388_P1.4590.85
148_N399_S1.4590.85
107_D126_R1.4530.85
56_G71_H1.4370.84
5_I8_E1.4300.84
193_G215_S1.4270.84
148_N367_D1.4240.83
56_G85_V1.4050.82
238_Y243_Y1.3990.82
21_M40_Y1.3960.82
351_Y399_S1.3820.81
229_L251_L1.3570.79
98_Q101_A1.3550.79
320_F349_R1.3540.79
87_M115_P1.3420.78
56_G92_A1.3280.77
378_H381_L1.3210.77
11_L17_L1.3190.76
60_Q95_E1.3180.76
84_A87_M1.3140.76
118_L121_Q1.3030.75
73_R101_A1.2950.75
304_G328_A1.2950.75
141_F289_N1.2930.74
7_G11_L1.2910.74
90_A109_L1.2880.74
346_A368_K1.2870.74
41_L55_Q1.2750.73
135_W180_K1.2700.73
89_L93_L1.2680.72
99_N132_R1.2610.72
87_M91_A1.2590.72
53_Y75_L1.2580.72
116_P119_M1.2510.71
53_Y85_V1.2440.70
59_A71_H1.2430.70
84_A121_Q1.2410.70
24_A27_S1.2370.70
394_H407_E1.2300.69
142_S414_E1.2300.69
171_A201_Y1.2200.68
6_D13_N1.2150.68
295_R301_W1.2090.67
53_Y118_L1.1970.66
53_Y87_M1.1960.66
401_D404_N1.1910.65
137_V178_A1.1910.65
266_S288_S1.1860.65
60_Q92_A1.1780.64
65_V92_A1.1770.64
110_K119_M1.1730.64
229_L413_V1.1700.63
224_R349_R1.1680.63
338_L378_H1.1640.63
87_M122_V1.1580.62
106_F118_L1.1540.62
205_K208_N1.1470.61
5_I9_T1.1470.61
53_Y82_A1.1470.61
146_E169_G1.1450.61
60_Q68_A1.1450.61
106_F122_V1.1360.60
59_A122_V1.1330.60
299_Q329_W1.1280.59
84_A115_P1.1280.59
94_F129_L1.1270.59
24_A36_I1.1270.59
343_R373_S1.1260.59
172_V227_A1.1250.59
369_E397_T1.1230.59
6_D9_T1.1220.59
123_E303_G1.1200.58
49_M75_L1.1200.58
8_E12_K1.1190.58
149_I169_G1.1180.58
76_I86_R1.1170.58
72_Y89_L1.1140.58
5_I12_K1.1140.58
290_S306_D1.1110.57
143_V170_T1.1050.57
76_I115_P1.0990.56
340_S376_L1.0990.56
169_G204_N1.0920.56
380_A385_G1.0900.55
103_A107_D1.0850.55
123_E127_K1.0850.55
325_L346_A1.0840.55
153_P165_K1.0810.54
25_V30_I1.0760.54
151_Q237_T1.0740.54
88_R91_A1.0740.54
354_P364_R1.0710.53
355_G363_E1.0700.53
76_I85_V1.0650.53
91_A95_E1.0640.53
4_Q8_E1.0640.53
31_A34_R1.0630.52
384_K388_P1.0610.52
246_T270_G1.0600.52
94_F99_N1.0580.52
148_N365_R1.0530.51
65_V260_K1.0440.50
87_M121_Q1.0380.50
13_N16_L1.0360.50
88_R274_N1.0360.50
9_T12_K1.0360.50
385_G417_K1.0350.50
53_Y90_A1.0340.49
81_D147_H1.0340.49
171_A248_G1.0290.49
103_A129_L1.0270.49
57_I72_Y1.0250.48
257_Q263_T1.0250.48
169_G388_P1.0220.48
108_R332_E1.0210.48
4_Q12_K1.0180.48
229_L249_A1.0160.48
125_Y128_A1.0150.47
59_A90_A1.0150.47
142_S176_L1.0140.47
132_R141_F1.0140.47
389_R414_E1.0110.47
294_Y300_Y1.0110.47
127_K251_L1.0100.47
30_I33_I1.0100.47
75_L171_A1.0100.47
32_G35_V1.0090.47
133_D183_S1.0070.47
64_R96_N1.0060.46
198_G210_M1.0050.46
307_F321_N1.0050.46
24_A32_G1.0040.46
69_I73_R1.0010.46
351_Y400_N1.0000.46
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  
2xevA30.281699.20.816Contact Map
3gyzA20.298399.10.829Contact Map
4j8fA10.3437990.83Contact Map
4nrhB20.3007990.832Contact Map
3rkvA10.3055990.833Contact Map
3upvA10.2888990.833Contact Map
2dbaA10.3126990.833Contact Map
1ihgA10.3198990.834Contact Map
2fbnA20.3174990.834Contact Map
2if4A10.2625990.835Contact 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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