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C7

ID: 1501519904 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 481 (436)
Sequences: 1760 (1273.5)
Seq/Len: 4.037
Nf(neff/√len): 61.0

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: 4.037).

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
98_N101_A5.0701.00
330_Q333_E4.5631.00
30_D33_E4.4511.00
178_R181_E4.0821.00
321_R337_D4.0611.00
64_R67_E3.8201.00
296_K299_D3.7401.00
258_N261_L3.5931.00
212_C215_K3.3391.00
204_G220_F3.3051.00
89_E105_S3.0921.00
144_D147_K3.0631.00
55_R71_D2.8991.00
305_T321_R2.6111.00
90_G106_F2.5971.00
322_A338_Y2.4441.00
73_Q89_E2.4251.00
308_V318_Y2.3861.00
56_A72_A2.3521.00
89_E93_H2.3311.00
301_I328_T2.3091.00
287_R303_D2.1771.00
325_Y330_Q2.1401.00
380_S383_E2.0691.00
291_N299_D2.0581.00
76_V86_H1.9751.00
203_R219_F1.9681.00
35_Y58_T1.9381.00
335_V354_L1.9241.00
325_Y333_E1.9141.00
325_Y337_D1.8971.00
55_R59_L1.8851.00
263_Y290_V1.8831.00
93_H101_A1.8811.00
59_L67_E1.8091.00
86_H105_S1.8081.00
333_E336_R1.7830.99
250_G266_Y1.7720.99
74_Q77_R1.7620.99
170_A186_A1.7600.99
318_Y337_D1.7580.99
335_V357_A1.7580.99
332_E336_R1.7370.99
306_N309_K1.7070.99
332_E361_L1.6680.99
301_I324_C1.6510.99
39_T55_R1.6420.99
69_L89_E1.5690.98
18_F40_K1.5200.98
262_A266_Y1.5170.98
391_R395_H1.5160.98
338_Y353_L1.5120.98
52_Y74_Q1.5040.98
187_S203_R1.4990.98
93_H98_N1.4910.97
35_Y62_L1.4860.97
339_E358_Q1.4840.97
260_K294_L1.4810.97
113_D116_N1.4660.97
33_E36_N1.4650.97
251_N286_N1.4630.97
340_K344_T1.4590.97
103_C107_Q1.4580.97
35_Y59_L1.4530.97
18_F37_Y1.4490.97
93_H105_S1.4420.97
183_Q210_E1.4300.97
72_A88_R1.4220.96
305_T337_D1.4170.96
106_F122_E1.4020.96
291_N296_K1.3970.96
25_Y33_E1.3950.96
361_L364_S1.3840.96
221_V225_R1.3750.95
90_G109_A1.3730.95
42_I52_Y1.3630.95
173_L178_R1.3580.95
324_C328_T1.3570.95
305_T309_K1.3480.95
340_K343_Q1.3430.95
301_I305_T1.3360.94
35_Y55_R1.3350.94
22_G37_Y1.3340.94
288_G303_D1.3280.94
264_E268_E1.3260.94
307_A310_L1.3260.94
410_E413_K1.3250.94
433_R438_Q1.3210.94
38_Y54_N1.3150.94
298_D328_T1.3150.94
32_N62_L1.3060.93
21_Q25_Y1.3060.93
169_K173_L1.3030.93
103_C127_N1.2920.93
204_G250_G1.2890.93
67_E70_G1.2830.93
298_D302_E1.2800.93
391_R394_M1.2720.92
319_L350_H1.2640.92
422_F426_S1.2570.92
267_T287_R1.2540.92
266_Y286_N1.2470.91
49_A75_S1.2360.91
91_K106_F1.2350.91
412_E416_K1.2350.91
260_K264_E1.2290.90
222_Q225_R1.2270.90
39_T71_D1.2230.90
26_Y31_Y1.2140.90
100_M130_M1.2100.90
173_L181_E1.2050.89
284_Y306_N1.1990.89
284_Y303_D1.1940.89
431_K435_D1.1930.89
190_L200_L1.1920.89
86_H109_A1.1890.88
22_G38_Y1.1840.88
86_H108_R1.1760.88
153_D169_K1.1670.87
361_L365_K1.1600.87
76_V85_G1.1570.87
40_K43_D1.1520.86
432_T436_S1.1470.86
75_S85_G1.1430.86
182_A206_C1.1430.86
216_A220_F1.1400.85
180_P210_E1.1370.85
170_A189_I1.1330.85
223_A233_A1.1320.85
107_Q111_E1.1310.85
299_D302_E1.1250.84
13_R17_T1.1220.84
101_A104_R1.1210.84
253_A258_N1.1190.84
69_L92_C1.1180.84
162_C165_F1.1170.84
208_Y220_F1.1150.84
220_F236_A1.1120.83
304_C320_R1.1110.83
263_Y287_R1.1090.83
289_T320_R1.1060.83
149_V153_D1.1020.83
34_A38_Y1.1000.83
253_A261_L1.0990.82
331_Y357_A1.0970.82
200_L219_F1.0910.82
251_N266_Y1.0900.82
26_Y57_A1.0860.81
273_D276_N1.0860.81
356_N360_E1.0830.81
52_Y71_D1.0810.81
35_Y38_Y1.0800.81
280_N284_Y1.0760.81
25_Y30_D1.0760.81
260_K263_Y1.0760.81
124_K322_A1.0720.80
41_A75_S1.0710.80
270_L280_N1.0700.80
182_A186_A1.0700.80
269_A283_L1.0690.80
443_E446_N1.0640.80
136_A152_M1.0570.79
442_E445_M1.0570.79
247_K251_N1.0560.79
23_N54_N1.0550.79
270_L284_Y1.0540.79
291_N303_D1.0540.79
338_Y342_Y1.0450.78
322_A341_V1.0430.78
440_L443_E1.0430.78
73_Q105_S1.0410.77
370_Y373_L1.0410.77
144_D322_A1.0390.77
42_I71_D1.0390.77
285_C314_Y1.0390.77
54_N57_A1.0380.77
326_M338_Y1.0340.77
14_E18_F1.0320.77
288_G304_C1.0310.77
408_Q412_E1.0260.76
339_E343_Q1.0210.76
204_G223_A1.0210.76
207_L215_K1.0210.76
384_I388_Y1.0210.76
23_N38_Y1.0200.75
296_K302_E1.0130.75
59_L64_R1.0060.74
365_K370_Y1.0040.74
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  
2y4tA30.8691000.386Contact Map
1w3bA20.76721000.532Contact Map
3iegA20.7381000.55Contact Map
4ui9C201000.568Contact Map
3fp2A10.77341000.577Contact Map
2gw1A20.79631000.581Contact Map
4ui9J101000.583Contact Map
4ui9X201000.591Contact Map
4rg9A20.70891000.592Contact Map
4ui9F201000.593Contact 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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