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T0852 -force run

ID: 1405101783 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 414 (378)
Sequences: 210 (192.2)
Seq/Len: 0.556
Nf(neff/√len): 9.9

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: 0.556).

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
44_K81_K2.7380.99
31_L111_F2.4650.97
228_F243_Q2.1210.91
54_I82_C1.9450.86
192_A291_V1.9290.85
124_Q129_I1.8800.83
112_F148_Y1.8760.83
35_Q94_D1.8550.82
336_A352_Y1.7760.78
94_D111_F1.7600.77
314_K338_Y1.7490.76
120_V133_K1.7050.74
302_T317_A1.6720.72
138_S233_V1.6630.71
344_D347_K1.6390.70
226_V243_Q1.6130.68
70_V84_V1.6100.68
45_Y128_P1.6030.67
33_R93_E1.5880.66
124_Q240_G1.5750.65
45_Y83_I1.5720.65
192_A240_G1.5490.63
340_E352_Y1.5370.62
39_I180_A1.5360.62
115_V367_D1.5290.62
330_M333_F1.5160.61
164_N196_V1.4920.59
237_K249_F1.4890.59
120_V156_T1.4670.57
56_V87_V1.4320.54
360_N366_G1.4250.54
56_V59_A1.4240.54
41_K45_Y1.4230.53
143_F166_V1.4130.53
41_K71_R1.4120.53
194_A239_Q1.4000.52
301_Y317_A1.3760.50
235_A239_Q1.3700.49
127_Y335_L1.3590.48
19_S36_K1.3540.48
309_D312_S1.3510.48
63_M84_V1.3490.48
190_Y226_V1.3430.47
58_N91_K1.3350.47
35_Q87_V1.3330.46
54_I136_I1.3210.45
124_Q133_K1.3120.45
2_K343_G1.3110.45
19_S159_M1.3100.45
143_F169_P1.3060.44
39_I176_S1.3050.44
41_K128_P1.3000.44
39_I346_K1.2920.43
197_E248_C1.2890.43
370_N374_T1.2790.42
35_Q111_F1.2650.41
244_A314_K1.2590.41
301_Y313_L1.2590.41
159_M188_F1.2510.40
89_E234_N1.2490.40
91_K94_D1.2410.39
321_E335_L1.2410.39
115_V207_Q1.2400.39
176_S302_T1.2360.39
273_E277_N1.2280.38
164_N192_A1.2280.38
148_Y313_L1.2190.38
35_Q58_N1.2190.38
31_L114_F1.2180.37
37_I86_G1.2140.37
94_D129_I1.2140.37
19_S39_I1.2120.37
35_Q118_E1.2050.37
229_K238_L1.2010.36
8_V115_V1.2000.36
134_G159_M1.1980.36
139_E174_E1.1850.35
146_N189_Y1.1850.35
5_L12_V1.1800.35
53_L233_V1.1780.35
107_E292_P1.1760.34
252_Y368_L1.1740.34
28_S118_E1.1720.34
128_P335_L1.1690.34
32_N44_K1.1670.34
134_G195_D1.1650.34
73_Y79_M1.1620.33
20_Q57_L1.1590.33
83_I144_L1.1590.33
222_E336_A1.1570.33
86_G275_L1.1560.33
326_L331_P1.1540.33
116_S156_T1.1520.33
282_I290_K1.1510.33
139_E143_F1.1500.33
40_Y71_R1.1480.32
28_S33_R1.1350.32
85_V123_I1.1350.32
164_N208_F1.1350.32
2_K21_V1.1330.31
360_N365_T1.1310.31
154_K194_A1.1270.31
144_L147_Y1.1260.31
142_G231_S1.1260.31
232_S253_K1.1250.31
146_N167_A1.1220.31
108_S144_L1.1180.30
127_Y279_Y1.1180.30
35_Q114_F1.1160.30
45_Y144_L1.1140.30
220_S323_N1.1140.30
122_Y336_A1.1130.30
132_L249_F1.1120.30
232_S267_L1.1120.30
48_R128_P1.1080.30
56_V86_G1.1050.30
294_L328_T1.0990.29
175_F376_L1.0950.29
326_L335_L1.0930.29
124_Q196_V1.0910.29
208_F305_N1.0880.28
12_V180_A1.0840.28
133_K212_M1.0840.28
113_E155_P1.0830.28
58_N233_V1.0800.28
321_E332_N1.0790.28
58_N118_E1.0770.28
91_K95_V1.0770.28
4_Y10_A1.0740.28
91_K138_S1.0710.27
298_M301_Y1.0670.27
190_Y228_F1.0660.27
208_F264_M1.0640.27
24_E126_K1.0620.27
355_A359_P1.0620.27
96_T143_F1.0600.27
8_V127_Y1.0590.27
164_N316_L1.0590.27
13_T17_A1.0580.27
85_V177_H1.0550.26
191_M204_K1.0500.26
160_I288_V1.0490.26
149_M160_I1.0470.26
88_Y142_G1.0460.26
132_L146_N1.0460.26
10_A16_S1.0450.26
144_L164_N1.0410.25
38_G320_V1.0390.25
132_L159_M1.0360.25
133_K157_F1.0330.25
164_N205_A1.0320.25
106_N168_L1.0320.25
79_M245_L1.0300.25
84_V225_F1.0290.25
57_L81_K1.0280.25
91_K320_V1.0280.25
155_P317_A1.0270.25
317_A334_F1.0260.25
84_V186_R1.0250.25
97_V141_A1.0250.25
107_E129_I1.0250.25
45_Y52_P1.0250.25
45_Y51_Y1.0230.24
55_V242_A1.0220.24
87_V264_M1.0220.24
283_Y294_L1.0220.24
142_G166_V1.0220.24
85_V173_E1.0200.24
160_I221_V1.0200.24
19_S48_R1.0190.24
278_K296_D1.0190.24
12_V125_G1.0150.24
144_L168_L1.0140.24
139_E233_V1.0140.24
119_L325_Y1.0130.24
142_G149_M1.0110.24
28_S35_Q1.0100.24
58_N141_A1.0080.24
334_F337_E1.0080.24
129_I240_G1.0080.24
6_T205_A1.0070.23
97_V169_P1.0070.23
251_I275_L1.0070.23
39_I195_D1.0030.23
132_L330_M1.0030.23
317_A331_P1.0000.23
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: (05Jul14)
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  
3gffA20.70051000.671Contact Map
2gzsA10.553199.90.814Contact Map
3c8dA40.572599.90.816Contact Map
2qm0A20.579799.90.816Contact Map
1jjfA10.545999.90.823Contact Map
4folA40.567699.80.83Contact Map
3ls2A40.5799.70.848Contact Map
4b6gA20.574999.70.855Contact Map
2uz0A40.526699.60.861Contact Map
3fcxA20.577399.60.861Contact 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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