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T0814 -force run

ID: 1404850175 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 424 (412)
Sequences: 232 (210.3)
Seq/Len: 0.563
Nf(neff/√len): 10.4

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: 0.563).

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_E6.3291.00
82_N86_T4.0931.00
160_E410_R3.6191.00
277_D369_Y3.0130.99
402_R409_D2.7180.99
167_A397_I2.6560.98
186_F397_I2.4920.97
134_S160_E2.4660.97
290_D392_Q2.2680.95
345_M356_K2.1290.92
74_Y151_I2.0670.90
327_S344_K1.9480.86
195_I202_L1.9420.86
396_S414_V1.9130.85
157_S411_L1.9080.85
82_N408_Y1.8840.84
66_G74_Y1.8830.83
141_V152_F1.7810.79
211_R214_N1.7770.78
271_N315_H1.7730.78
244_E392_Q1.7040.74
80_H88_S1.6820.73
112_G345_M1.6550.71
329_Y343_S1.6510.71
398_Y411_L1.6490.71
40_V154_A1.6410.70
260_V274_L1.6270.69
340_D343_S1.6270.69
40_V62_I1.6170.68
244_E292_D1.5880.66
40_V60_I1.5680.65
157_S398_Y1.5560.64
203_K402_R1.5530.64
151_I165_I1.5530.64
202_L229_I1.5340.62
88_S198_P1.5170.61
163_V193_F1.5170.61
403_P406_A1.5160.61
245_Y344_K1.5010.60
219_L237_L1.4900.59
134_S184_V1.4760.58
94_E407_R1.4700.58
244_E290_D1.4640.57
297_I326_G1.4590.57
165_I399_V1.4400.55
241_A389_Y1.4130.53
202_L399_V1.4060.53
92_P100_Q1.3720.50
253_N312_Y1.3710.50
62_I154_A1.3560.49
63_N306_D1.3400.47
133_V310_D1.3370.47
207_Y212_R1.3350.47
280_R385_E1.3270.46
176_D181_H1.3200.46
292_D392_Q1.3170.45
276_T317_T1.3070.45
122_L139_I1.2950.44
335_F343_S1.2860.43
11_M51_Y1.2850.43
38_L62_I1.2810.43
153_T236_N1.2670.42
35_I344_K1.2620.41
270_Y389_Y1.2600.41
141_V309_A1.2570.41
171_G178_N1.2470.40
78_V180_S1.2410.40
213_D399_V1.2390.39
82_N409_D1.2370.39
360_L365_Y1.2350.39
79_V140_Q1.2320.39
207_Y398_Y1.2280.39
252_S310_D1.2260.38
93_I287_Y1.2190.38
95_Y158_V1.2170.38
256_N260_V1.2130.37
76_Y126_N1.2080.37
329_Y344_K1.2060.37
171_G251_L1.2050.37
37_T195_I1.1990.36
66_G139_I1.1980.36
206_V347_Y1.1960.36
182_Q393_N1.1920.36
216_V260_V1.1890.36
193_F401_Y1.1870.36
195_I201_D1.1840.35
52_I60_I1.1790.35
204_I301_D1.1770.35
250_F312_Y1.1740.35
166_S360_L1.1730.35
14_F19_G1.1730.35
53_A330_L1.1650.34
351_T355_E1.1650.34
315_H365_Y1.1640.34
94_E309_A1.1630.34
106_D121_R1.1630.34
330_L358_V1.1610.34
23_Q330_L1.1550.33
299_C302_C1.1540.33
28_T31_N1.1520.33
188_I399_V1.1440.32
76_Y98_G1.1420.32
51_Y132_K1.1310.32
247_R364_S1.1290.31
74_Y152_F1.1280.31
318_L384_I1.1200.31
207_Y396_S1.1190.31
131_F284_T1.1160.31
316_F360_L1.1150.30
183_Q238_I1.1140.30
283_G317_T1.1130.30
66_G212_R1.1130.30
97_N130_Q1.1120.30
95_Y345_M1.1090.30
101_G133_V1.1080.30
188_I276_T1.1080.30
162_V241_A1.1060.30
38_L251_L1.1030.30
176_D369_Y1.1030.30
127_D188_I1.0980.29
366_N403_P1.0960.29
12_M373_P1.0930.29
196_T245_Y1.0920.29
28_T251_L1.0910.29
160_E345_M1.0900.29
77_N108_A1.0900.29
165_I415_T1.0870.29
343_S358_V1.0800.28
246_R385_E1.0790.28
328_V358_V1.0780.28
206_V237_L1.0760.28
213_D370_L1.0740.28
215_A401_Y1.0730.28
184_V356_K1.0720.28
55_G166_S1.0720.28
167_A186_F1.0710.28
67_L160_E1.0700.28
251_L364_S1.0690.27
212_R215_A1.0670.27
37_T376_S1.0660.27
188_I413_G1.0660.27
117_Y213_D1.0650.27
84_D190_N1.0650.27
245_Y337_N1.0640.27
138_A206_V1.0610.27
198_P203_K1.0610.27
9_L16_L1.0590.27
119_N341_E1.0590.27
31_N152_F1.0570.27
100_Q152_F1.0560.27
215_A218_D1.0560.27
249_E288_D1.0550.27
107_F203_K1.0540.27
38_L245_Y1.0510.26
124_L131_F1.0490.26
157_S407_R1.0490.26
186_F204_I1.0470.26
245_Y298_R1.0440.26
98_G126_N1.0430.26
90_L260_V1.0420.26
165_I397_I1.0400.26
131_F252_S1.0350.25
21_N345_M1.0320.25
292_D336_N1.0320.25
280_R369_Y1.0320.25
82_N234_N1.0300.25
52_I365_Y1.0280.25
214_N368_Q1.0230.25
40_V249_E1.0220.25
87_Q398_Y1.0150.24
181_H387_N1.0140.24
76_Y287_Y1.0120.24
213_D375_G1.0110.24
252_S255_Y1.0090.24
82_N402_R1.0050.24
403_P410_R1.0040.24
215_A312_Y1.0030.23
86_T346_G1.0020.23
89_Q403_P1.0010.23
197_Y200_T1.0000.23
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  
2qlvB20.202896.90.954Contact Map
4aefA20.280796.20.957Contact Map
4aeeA20.275995.70.959Contact Map
2lu3A10.245395.50.959Contact Map
4cfeB20.224194.60.961Contact Map
1ac0A10.238294.30.962Contact Map
1z0nA30.2052940.962Contact Map
2z0bA60.252488.40.968Contact Map
1m7xA40.294878.80.971Contact Map
4pyhA10.599165.10.974Contact 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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