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YjhC

ID: 1517362693 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 372 (360)
Sequences: 11646 (7450.9)
Seq/Len: 32.350
Nf(neff/√len): 392.7

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: 32.350).

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
53_D79_K3.9231.00
101_V341_M3.4441.00
81_A112_V3.3091.00
74_K102_D3.1921.00
130_R134_K3.0911.00
3_N27_K3.0081.00
128_Y131_K2.9681.00
140_E245_T2.9181.00
215_M350_A2.7871.00
78_I106_A2.7861.00
78_I102_D2.7151.00
51_S54_A2.6921.00
5_G55_L2.6711.00
352_L356_Q2.6391.00
74_K99_D2.6291.00
82_K106_A2.6141.00
108_K338_E2.5841.00
121_N179_D2.5471.00
78_I82_K2.4761.00
68_T76_P2.4421.00
86_H113_T2.3311.00
72_L76_P2.3101.00
131_K135_E2.2941.00
75_E79_K2.2871.00
74_K78_I2.2331.00
4_Y63_C2.2071.00
68_T72_L2.2031.00
97_Y348_D2.2011.00
64_V80_A2.1641.00
101_V345_A2.1481.00
128_Y132_L2.1421.00
138_I244_G2.1191.00
105_K109_E2.1171.00
132_L137_V2.0981.00
106_A110_A2.0771.00
96_S99_D2.0721.00
77_V89_C2.0621.00
77_V103_M2.0381.00
101_V105_K2.0361.00
61_V85_K2.0191.00
141_I242_I1.9761.00
38_E42_R1.9661.00
190_E218_E1.9431.00
117_G314_E1.9231.00
129_A249_I1.9231.00
82_K109_E1.9231.00
114_F337_G1.8921.00
52_L79_K1.8771.00
81_A107_C1.8721.00
219_F225_A1.8681.00
5_G61_V1.8651.00
30_C49_M1.8471.00
178_L346_T1.8311.00
187_E221_S1.8291.00
14_A43_E1.7971.00
342_S345_A1.7951.00
130_R183_H1.7821.00
104_V337_G1.7811.00
50_S54_A1.7681.00
190_E220_P1.7601.00
86_H112_V1.7291.00
95_L99_D1.6971.00
74_K103_M1.6841.00
66_V77_V1.6731.00
349_A353_S1.6671.00
3_N62_D1.6651.00
317_F321_I1.6521.00
187_E220_P1.6501.00
82_K110_A1.6431.00
142_L245_T1.6391.00
104_V341_M1.6361.00
320_N324_G1.6011.00
100_C341_M1.5761.00
189_P220_P1.5731.00
63_C318_L1.5631.00
182_Q188_I1.5631.00
79_K82_K1.5351.00
3_N29_T1.5331.00
94_A99_D1.5221.00
52_L76_P1.5171.00
336_N339_A1.5111.00
1_M27_K1.5091.00
145_H241_I1.4991.00
191_T218_E1.4941.00
138_I247_G1.4901.00
100_C344_I1.4861.00
97_Y101_V1.4841.00
9_V31_V1.4801.00
37_G41_A1.4791.00
49_M55_L1.4721.00
30_C55_L1.4701.00
52_L56_V1.4591.00
182_Q219_F1.4471.00
349_A360_V1.4421.00
79_K83_N1.4211.00
23_H316_L1.4161.00
57_S83_N1.4010.99
78_I103_M1.3910.99
69_P72_L1.3900.99
55_L61_V1.3730.99
2_I63_C1.3720.99
56_V80_A1.3700.99
190_E361_K1.3600.99
182_Q342_S1.3510.99
138_I141_I1.3500.99
99_D102_D1.3460.99
192_V359_K1.3360.99
185_L223_K1.3340.99
352_L355_S1.3190.99
39_N43_E1.3160.99
103_M114_F1.3090.99
181_V225_A1.3040.99
94_A103_M1.3030.99
106_A109_E1.2930.99
182_Q339_A1.2920.99
66_V76_P1.2920.99
20_M65_I1.2910.99
59_K85_K1.2850.99
319_H323_C1.2810.99
348_D352_L1.2780.99
138_I249_I1.2730.99
97_Y345_A1.2680.99
356_Q360_V1.2630.99
131_K134_K1.2620.99
132_L135_E1.2600.99
5_G32_Y1.2570.99
81_A87_V1.2540.99
4_Y26_A1.2480.99
25_N323_C1.2460.98
105_K108_K1.2440.98
121_N339_A1.2430.98
37_G48_N1.2420.98
93_I100_C1.2390.98
178_L347_A1.2340.98
32_Y52_L1.2330.98
80_A87_V1.2300.98
81_A106_A1.2260.98
49_M58_S1.2260.98
94_A100_C1.2200.98
241_I250_K1.1960.98
36_N39_N1.1870.98
133_I184_L1.1810.98
144_C242_I1.1700.97
89_C116_A1.1540.97
32_Y55_L1.1540.97
54_A58_S1.1520.97
53_D57_S1.1500.97
144_C181_V1.1500.97
54_A57_S1.1480.97
81_A110_A1.1430.97
104_V108_K1.1390.97
30_C61_V1.1380.97
89_C114_F1.1350.97
98_E102_D1.1340.97
141_I185_L1.1330.97
352_L360_V1.1250.97
144_C185_L1.1240.97
97_Y341_M1.1150.96
102_D105_K1.1110.96
76_P79_K1.1090.96
60_L85_K1.1070.96
145_H228_E1.1060.96
312_R316_L1.1050.96
349_A362_I1.1040.96
84_K110_A1.1010.96
181_V219_F1.0980.96
93_I116_A1.0900.96
34_P38_E1.0810.95
127_Q131_K1.0770.95
58_S61_V1.0770.95
144_C225_A1.0750.95
188_I220_P1.0740.95
47_I58_S1.0640.95
318_L322_L1.0590.95
102_D106_A1.0570.95
113_T325_A1.0550.95
141_I244_G1.0520.95
58_S85_K1.0500.94
349_A352_L1.0400.94
313_K316_L1.0380.94
77_V87_V1.0370.94
3_N61_V1.0260.94
39_N42_R1.0180.93
107_C337_G1.0170.93
113_T324_G1.0150.93
107_C114_F1.0120.93
129_A251_I1.0080.93
188_I342_S1.0010.92
320_N326_K1.0000.92
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  
1h6dA120.90861000.254Contact Map
1zh8A20.84411000.262Contact Map
3dtyA40.92471000.265Contact Map
2nvwA20.89521000.267Contact Map
3v5nA40.8791000.27Contact Map
3euwA40.88171000.28Contact Map
3e18A20.94621000.283Contact Map
3ceaA40.88441000.283Contact Map
3q2iA10.8791000.283Contact Map
3oqbA80.9221000.283Contact 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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