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3ZUX_A

ID: 1428208856 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 332 (315)
Sequences: 6079 (3660.8)
Seq/Len: 19.298
Nf(neff/√len): 206.3

Jackhmmer Results: (2015_01_07)
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: 19.298).

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
54_F185_V5.9011.00
129_N258_A5.7671.00
247_F251_W3.0971.00
54_F181_L2.7171.00
163_Q166_G2.7041.00
123_T128_G2.6081.00
66_D70_K2.5781.00
256_Y260_K2.5511.00
255_P258_A2.4351.00
250_K259_Q2.3391.00
107_V233_V2.2711.00
238_N302_S2.2191.00
82_Q115_G2.1991.00
274_A292_G2.1621.00
249_A259_Q2.1061.00
249_A262_L2.0291.00
89_T240_I2.0201.00
112_C151_I1.9361.00
63_S66_D1.9071.00
64_D67_I1.8741.00
109_L278_A1.8731.00
23_W27_F1.8641.00
180_V184_I1.8341.00
80_I84_A1.8241.00
122_M264_I1.8151.00
83_F147_L1.8091.00
22_L26_L1.7781.00
27_F209_V1.7701.00
243_L247_F1.7281.00
86_M241_G1.7241.00
190_G194_E1.7231.00
254_L262_L1.7221.00
76_I80_I1.7111.00
79_V143_T1.7091.00
246_F259_Q1.7041.00
91_W95_K1.6921.00
133_S261_A1.6921.00
143_T147_L1.6831.00
90_A111_G1.6791.00
228_L232_A1.6091.00
123_T261_A1.5961.00
88_A92_C1.5861.00
184_I188_V1.5831.00
25_A29_A1.5811.00
93_L233_V1.5781.00
191_S195_K1.5761.00
94_S104_A1.5711.00
67_I70_K1.5591.00
306_L310_W1.5481.00
235_V298_W1.5461.00
97_L233_V1.5421.00
61_K186_H1.5291.00
189_L192_K1.5101.00
298_W302_S1.5101.00
102_E287_V1.5041.00
123_T133_S1.4821.00
308_T312_A1.4781.00
92_C96_L1.4721.00
165_A169_M1.4481.00
81_A245_G1.4371.00
110_V295_F1.4291.00
186_H194_E1.4281.00
89_T241_G1.4171.00
113_C274_A1.3990.99
309_Y313_K1.3780.99
240_I244_L1.3740.99
14_S18_K1.3670.99
77_I252_T1.3570.99
72_P76_I1.3570.99
208_I212_I1.3520.99
172_V177_L1.3430.99
115_G137_T1.3390.99
271_S296_S1.3200.99
61_K64_D1.3180.99
29_A32_F1.3130.99
35_P38_F1.2990.99
246_F256_Y1.2970.99
34_A37_T1.2870.99
81_A266_V1.2780.99
44_Y47_W1.2730.99
129_N257_D1.2700.99
77_I262_L1.2590.99
259_Q263_T1.2570.99
43_P47_W1.2540.99
305_L309_Y1.2470.99
263_T310_W1.2440.98
185_V189_L1.2380.98
31_A38_F1.2370.98
173_K177_L1.2340.98
126_A307_A1.2320.98
81_A85_I1.2280.98
26_L30_A1.2240.98
254_L258_A1.2230.98
57_G182_G1.2200.98
83_F140_S1.2200.98
120_N265_E1.2180.98
74_V254_L1.2180.98
260_K310_W1.1940.98
151_I155_L1.1890.98
308_T311_A1.1850.98
23_W209_V1.1760.98
105_V156_A1.1750.98
78_G136_V1.1730.98
47_W50_G1.1680.97
183_L187_K1.1680.97
82_Q269_Q1.1530.97
220_K224_M1.1530.97
92_C95_K1.1520.97
249_A254_L1.1460.97
11_K14_S1.1460.97
53_M57_G1.1430.97
75_V139_V1.1430.97
119_S269_Q1.1250.97
112_C152_F1.1250.97
194_E197_T1.1250.97
313_K316_K1.1170.96
147_L151_I1.1140.96
256_Y313_K1.1120.96
313_K317_H1.1060.96
19_T23_W1.1030.96
259_Q310_W1.0960.96
118_A242_Y1.0940.96
74_V132_L1.0840.96
71_H129_N1.0820.96
144_S148_T1.0790.95
135_A138_S1.0750.95
147_L150_A1.0690.95
255_P259_Q1.0640.95
15_F19_T1.0640.95
82_Q137_T1.0620.95
79_V139_V1.0540.95
71_H258_A1.0520.95
103_I230_I1.0480.94
203_V207_A1.0480.94
63_S67_I1.0470.94
98_N101_A1.0420.94
116_G119_S1.0380.94
28_A31_A1.0370.94
100_P104_A1.0360.94
127_R314_A1.0350.94
131_A134_V1.0340.94
191_S194_E1.0320.94
303_G307_A1.0320.94
108_I155_L1.0210.93
36_D40_W1.0180.93
67_I135_A1.0170.93
16_I19_T1.0090.93
89_T92_C1.0090.93
37_T40_W1.0080.93
312_A315_G1.0060.93
108_I112_C1.0010.92
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: (31Jan15)
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  
3zuxA10.92771000.22Contact Map
4n7wA20.92471000.286Contact Map
4bwzA10.927798.10.865Contact Map
4czbA30.927797.60.88Contact Map
4cz8A20.903693.20.916Contact Map
1zcdA20.870585.50.929Contact Map
2cfqA10.614578.40.934Contact Map
4ikvA10.918777.70.934Contact Map
2gfpA20.575371.60.938Contact Map
4q65A10.575367.50.939Contact 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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