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T0814 -force run

ID: 1402513489 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (398)
Sequences: 140 (127.3)
Seq/Len: 0.352
Nf(neff/√len): 6.4

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: 0.352).

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
348_N355_E5.4211.00
82_N86_T2.7680.97
277_D369_Y2.7580.97
186_F397_I2.7080.96
160_E410_R2.4880.93
402_R409_D2.4060.92
167_A397_I2.3350.90
195_I202_L2.2150.86
134_S160_E1.7910.66
141_V152_F1.7790.65
141_V224_I1.7660.64
188_I399_V1.7630.64
280_R385_E1.7340.62
82_N408_Y1.6700.58
40_V62_I1.6510.56
327_S344_K1.6340.55
360_L365_Y1.6180.54
74_Y151_I1.5990.53
244_E290_D1.5910.52
131_F252_S1.5690.51
252_S310_D1.5660.51
157_S411_L1.5640.50
87_Q398_Y1.5060.46
84_D88_S1.4830.45
329_Y343_S1.4720.44
257_G375_G1.4670.44
40_V154_A1.4490.42
92_P100_Q1.4470.42
66_G74_Y1.4260.41
141_V401_Y1.4180.40
38_L251_L1.4080.40
345_M356_K1.4000.39
76_Y98_G1.3950.39
181_H387_N1.3870.38
37_T70_G1.3860.38
78_V86_T1.3800.38
130_Q345_M1.3800.38
167_A186_F1.3760.37
396_S414_V1.3760.37
206_V237_L1.3490.36
290_D392_Q1.3430.35
244_E392_Q1.3410.35
151_I165_I1.3230.34
315_H365_Y1.3190.34
94_E407_R1.3160.34
40_V60_I1.3040.33
62_I154_A1.3020.33
122_L139_I1.2990.33
90_L260_V1.2970.32
141_V411_L1.2950.32
23_Q398_Y1.2920.32
88_S198_P1.2920.32
328_V358_V1.2910.32
28_T251_L1.2890.32
141_V153_T1.2750.31
219_L237_L1.2730.31
207_Y212_R1.2640.30
40_V249_E1.2540.30
66_G212_R1.2520.30
119_N354_Y1.2430.29
97_N130_Q1.2400.29
335_F343_S1.2400.29
330_L358_V1.2400.29
54_L367_Y1.2360.29
211_R214_N1.2360.29
95_Y158_V1.2310.29
171_G251_L1.2300.28
134_S345_M1.2240.28
88_S156_F1.2090.27
287_Y315_H1.2080.27
246_R385_E1.2060.27
280_R369_Y1.2040.27
166_S411_L1.2020.27
36_K74_Y1.2000.27
193_F401_Y1.2000.27
80_H88_S1.1940.26
169_V342_K1.1930.26
94_E343_S1.1930.26
37_T187_N1.1910.26
160_E354_Y1.1790.26
158_V280_R1.1750.25
241_A358_V1.1680.25
195_I201_D1.1670.25
326_G375_G1.1670.25
82_N409_D1.1640.25
208_Q241_A1.1570.24
58_E274_L1.1520.24
55_G166_S1.1510.24
203_K402_R1.1510.24
76_Y126_N1.1500.24
38_L245_Y1.1430.24
249_E370_L1.1410.24
348_N351_T1.1390.24
115_T197_Y1.1360.23
119_N193_F1.1350.23
69_S201_D1.1350.23
157_S407_R1.1330.23
82_N94_E1.1320.23
119_N407_R1.1310.23
124_L191_K1.1280.23
51_Y56_G1.1280.23
133_V310_D1.1280.23
81_C329_Y1.1270.23
365_Y405_G1.1270.23
263_I304_D1.1230.23
112_G345_M1.1210.23
183_Q238_I1.1200.23
157_S212_R1.1170.22
229_I242_G1.1170.22
107_F203_K1.1150.22
318_L384_I1.1110.22
398_Y406_A1.1100.22
206_V378_V1.1080.22
119_N341_E1.1060.22
62_I249_E1.1030.22
143_N149_Q1.1020.22
310_D403_P1.1020.22
35_I344_K1.0950.21
260_V274_L1.0950.21
38_L62_I1.0940.21
98_G126_N1.0920.21
169_V388_Y1.0840.21
31_N310_D1.0820.21
212_R215_A1.0820.21
96_M202_L1.0800.21
285_Y365_Y1.0800.21
215_A401_Y1.0760.21
41_K249_E1.0760.21
119_N160_E1.0750.20
102_T163_V1.0740.20
34_Q359_L1.0720.20
155_C249_E1.0720.20
329_Y358_V1.0720.20
227_N366_N1.0700.20
35_I104_I1.0690.20
143_N257_G1.0670.20
171_G178_N1.0670.20
136_N395_Y1.0610.20
127_D380_Q1.0600.20
100_Q246_R1.0590.20
115_T359_L1.0570.20
132_K409_D1.0560.20
79_V257_G1.0530.19
104_I295_F1.0530.19
104_I118_S1.0520.19
21_N77_N1.0510.19
90_L116_Q1.0510.19
206_V348_N1.0510.19
116_Q204_I1.0480.19
168_S185_S1.0470.19
100_Q131_F1.0450.19
101_G133_V1.0450.19
63_N118_S1.0400.19
80_H113_T1.0400.19
163_V193_F1.0400.19
35_I115_T1.0370.19
121_R387_N1.0370.19
141_V148_D1.0360.19
244_E413_G1.0350.19
213_D375_G1.0300.18
115_T415_T1.0280.18
157_S398_Y1.0280.18
250_F312_Y1.0260.18
78_V314_V1.0250.18
118_S396_S1.0230.18
360_L405_G1.0210.18
82_N97_N1.0170.18
117_Y213_D1.0170.18
403_P410_R1.0150.18
229_I273_E1.0140.18
82_N401_Y1.0140.18
196_T245_Y1.0130.18
118_S339_L1.0110.18
54_L84_D1.0100.18
38_L93_I1.0090.18
78_V230_S1.0080.18
74_Y388_Y1.0070.18
126_N231_Y1.0060.17
52_I340_D1.0040.17
213_D399_V1.0040.17
37_T54_L1.0020.17
198_P260_V1.0020.17
165_I224_I1.0010.17
304_D380_Q1.0010.17
176_D181_H1.0000.17
251_L364_S1.0000.17
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  
4r7fA10.9341000.078Contact Map
4aeeA20.292596.40.959Contact Map
1z0nA30.202895.60.961Contact Map
2qlvB20.200595.40.962Contact Map
2lu3A10.240695.10.963Contact Map
4aefA20.280794.10.965Contact Map
1ac0A10.238292.60.967Contact Map
4cfeB20.219390.80.968Contact Map
2z0bA60.261878.40.973Contact Map
4rkkA20.266563.40.976Contact 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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