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T0830

ID: 1403641988 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 575 (526)
Sequences: 1662 (1415.1)
Seq/Len: 3.160
Nf(neff/√len): 61.7

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: 3.160).

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
126_A355_I3.6531.00
308_R311_V3.3511.00
126_A135_A3.3301.00
199_A207_G3.0751.00
327_W352_A2.9601.00
121_V167_C2.9141.00
193_W236_G2.5451.00
134_A358_G2.4621.00
117_L163_G2.3731.00
96_G106_Q2.3701.00
207_G211_P2.2611.00
142_L148_W2.2321.00
123_M139_G2.1981.00
71_D254_R2.1931.00
85_K203_K2.1871.00
62_I82_Y2.1441.00
61_E64_R2.1411.00
200_I240_M2.1011.00
88_F202_T2.0481.00
131_G134_A2.0471.00
197_G243_I2.0131.00
85_K345_Y2.0121.00
226_G229_R1.9951.00
144_A296_W1.9771.00
203_K345_Y1.9671.00
96_G100_F1.8610.99
96_G110_A1.8540.99
171_F195_A1.8360.99
271_Y338_S1.8190.99
53_G489_T1.7940.99
167_C195_A1.7780.99
271_Y334_F1.7540.99
138_T358_G1.7230.99
158_D203_K1.7200.99
58_R348_P1.7180.99
43_F116_L1.6980.99
126_A138_T1.6730.98
164_V202_T1.6580.98
141_A358_G1.6080.98
55_D342_L1.6050.98
85_K270_R1.5940.98
53_G340_S1.5810.97
82_Y157_L1.5800.97
104_E493_Y1.5620.97
114_S163_G1.5620.97
67_F98_E1.5560.97
284_Y341_K1.5450.97
90_M157_L1.5450.97
67_F94_V1.5400.97
88_F198_V1.5390.97
103_G106_Q1.5330.97
141_A357_A1.5310.97
61_E65_E1.5230.96
59_Y82_Y1.5210.96
286_L332_F1.5050.96
114_S160_T1.4920.96
55_D344_G1.4850.96
82_Y266_E1.4850.96
171_F188_W1.4840.96
97_Y107_A1.4830.96
86_P203_K1.4780.96
105_W109_L1.4710.95
326_I330_A1.4690.95
46_L112_A1.4610.95
113_L117_L1.4510.95
119_I142_L1.4420.95
228_W231_L1.4240.94
85_K158_D1.4160.94
92_V160_T1.4130.94
246_P250_L1.4110.94
248_F262_F1.4050.94
176_Q218_Y1.3970.94
379_V383_G1.3790.93
152_A159_M1.3770.93
158_D345_Y1.3750.93
115_G152_A1.3740.93
336_S341_K1.3730.93
168_V196_M1.3700.93
303_L308_R1.3640.92
84_E266_E1.3640.92
387_S390_V1.3620.92
195_A198_V1.3620.92
127_R132_A1.3610.92
464_A468_P1.3610.92
74_T83_F1.3540.92
251_V255_N1.3460.92
175_G189_M1.3400.92
351_P354_G1.3280.91
161_L206_V1.3270.91
95_V99_L1.3230.91
285_F341_K1.3210.91
65_E76_R1.3150.91
128_R174_M1.3150.91
34_F38_A1.3100.90
82_Y488_H1.3070.90
89_H160_T1.3010.90
205_L267_H1.2930.90
283_F341_K1.2930.90
518_V521_D1.2830.89
281_S341_K1.2810.89
135_A138_T1.2760.89
278_R281_S1.2730.89
119_I139_G1.2720.89
63_S97_Y1.2680.88
267_H271_Y1.2680.88
388_P391_A1.2630.88
82_Y261_F1.2630.88
125_A173_L1.2630.88
42_W112_A1.2610.88
209_A213_L1.2590.88
190_V235_L1.2510.87
118_G166_S1.2470.87
74_T255_N1.2460.87
414_F418_L1.2380.87
75_I156_T1.2380.87
147_M292_G1.2370.87
75_I90_M1.2320.86
118_G148_W1.2300.86
240_M244_T1.2270.86
203_K270_R1.2240.86
63_S93_T1.2210.86
108_R201_L1.2200.86
283_F287_P1.2180.85
249_Y253_V1.2160.85
69_S76_R1.2130.85
158_D341_K1.2130.85
118_G163_G1.2120.85
122_S142_L1.2120.85
169_L323_M1.2110.85
204_G348_P1.2080.85
96_G109_L1.2070.85
111_V155_N1.2060.85
59_Y84_E1.2040.85
59_Y157_L1.2010.84
34_F123_M1.1980.84
85_K91_W1.1980.84
425_R429_R1.1880.84
49_R52_V1.1870.83
280_G284_Y1.1850.83
56_E108_R1.1830.83
58_R267_H1.1830.83
49_R53_G1.1800.83
238_V242_V1.1800.83
303_L307_M1.1780.83
270_R345_Y1.1770.83
323_M327_W1.1760.83
121_V163_G1.1760.83
305_T309_A1.1660.82
97_Y102_L1.1640.82
59_Y90_M1.1630.82
129_W173_L1.1630.82
226_G230_R1.1620.82
201_L247_W1.1570.81
257_E260_N1.1530.81
525_F528_L1.1510.81
172_M189_M1.1500.81
207_G296_W1.1500.81
215_L219_T1.1470.80
65_E79_A1.1460.80
516_Q521_D1.1450.80
380_A387_S1.1410.80
262_F267_H1.1400.80
51_L493_Y1.1350.79
300_F357_A1.1320.79
47_D112_A1.1310.79
450_A454_H1.1300.79
332_F349_V1.1300.79
135_A139_G1.1300.79
55_D59_Y1.1300.79
245_V249_Y1.1300.79
42_W153_H1.1290.79
58_R65_E1.1220.78
509_F513_V1.1200.78
383_G390_V1.1180.78
420_G424_A1.1170.78
221_V322_L1.1160.78
86_P345_Y1.1160.78
126_A129_W1.1130.78
157_L344_G1.1130.78
258_F262_F1.1120.78
278_R341_K1.1090.77
89_H93_T1.1080.77
304_W308_R1.1070.77
157_L161_L1.1050.77
127_R135_A1.1040.77
171_F191_A1.1010.77
379_V386_A1.1010.77
156_T344_G1.0990.76
303_L311_V1.0990.76
412_V416_V1.0950.76
427_L440_A1.0920.76
71_D76_R1.0900.76
259_P262_F1.0870.75
75_I107_A1.0860.75
89_H111_V1.0850.75
247_W348_P1.0840.75
340_S344_G1.0830.75
194_A243_I1.0820.75
172_M215_L1.0810.75
264_I267_H1.0740.74
468_P471_A1.0740.74
276_H340_S1.0730.74
46_L116_L1.0710.74
251_V256_P1.0710.74
379_V391_A1.0700.74
281_S336_S1.0660.73
415_V419_L1.0650.73
90_M342_L1.0640.73
123_M135_A1.0620.73
510_G515_P1.0620.73
64_R68_A1.0620.73
58_R77_Y1.0610.73
518_V529_W1.0600.73
164_V167_C1.0590.73
55_D157_L1.0570.72
192_C196_M1.0560.72
510_G513_V1.0510.72
58_R340_S1.0500.72
251_V258_F1.0480.71
283_F336_S1.0480.71
102_L492_F1.0460.71
156_T342_L1.0460.71
527_K531_N1.0450.71
262_F266_E1.0420.71
223_R226_G1.0420.71
217_V326_I1.0410.71
133_R362_D1.0400.71
416_V420_G1.0400.71
123_M136_A1.0380.70
328_A349_V1.0380.70
523_D527_K1.0330.70
55_D82_Y1.0330.70
82_Y340_S1.0300.70
60_A63_S1.0280.69
421_I425_R1.0280.69
439_Y442_G1.0260.69
307_M311_V1.0250.69
59_Y344_G1.0250.69
124_M128_R1.0240.69
340_S488_H1.0230.69
189_M193_W1.0230.69
90_M246_P1.0220.69
151_A156_T1.0220.69
413_A417_M1.0220.69
389_V393_L1.0210.69
151_A344_G1.0210.69
508_T512_T1.0210.69
73_V251_V1.0200.68
288_L292_G1.0190.68
58_R82_Y1.0180.68
321_A359_V1.0120.68
34_F119_I1.0120.68
303_L306_A1.0110.67
71_D74_T1.0100.67
82_Y267_H1.0100.67
83_F255_N1.0100.67
536_M541_P1.0100.67
242_V246_P1.0070.67
521_D524_S1.0050.67
521_D525_F1.0040.67
159_M489_T1.0030.67
418_L421_I1.0020.66
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: (21Jun14)
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  
3wajA10.841000.763Contact Map
3rceA10.81911000.783Contact Map
4p02A10.43352.80.97Contact Map
2xr1A20.205221.20.975Contact Map
3cnlA10.093914.50.977Contact Map
3af5A10.1965140.977Contact Map
2ycbA20.203513.40.977Contact Map
1pujA10.100912.40.978Contact Map
2igrA10.041710.80.978Contact Map
2mmpA10.089.10.979Contact 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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