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ID: 1506711032 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 214 (208)
Sequences: 5421 (3164.8)
Seq/Len: 26.062
Nf(neff/√len): 219.4

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: 26.062).

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
113_D172_H4.2111.00
23_K210_E3.0491.00
52_I60_T2.7001.00
35_L64_V2.6381.00
118_D136_K2.5681.00
19_F206_R2.5391.00
169_V173_Q2.5351.00
110_D195_K2.3581.00
120_I164_V2.3521.00
97_K185_E2.3201.00
65_I86_F2.3041.00
183_S195_K2.1471.00
37_A41_S2.1401.00
115_L118_D2.1311.00
38_A70_E2.0941.00
50_K54_D2.0721.00
124_R135_V2.0431.00
23_K206_R2.0121.00
127_A154_T1.9801.00
126_H129_S1.9771.00
71_R76_D1.9631.00
117_V165_R1.9401.00
200_K208_D1.8731.00
109_F198_G1.8661.00
65_I95_A1.8621.00
16_Q209_L1.8611.00
51_D55_A1.8571.00
52_I57_K1.8261.00
127_A151_E1.8231.00
122_G134_H1.7971.00
176_A180_G1.7821.00
48_Q51_D1.7591.00
38_A43_S1.7551.00
161_E165_R1.7391.00
197_D200_K1.6441.00
172_H176_A1.6391.00
131_R148_V1.6311.00
32_G36_R1.5931.00
129_S149_T1.5801.00
97_K182_Y1.5771.00
142_V145_K1.5671.00
61_D92_Q1.5491.00
206_R210_E1.5461.00
200_K204_E1.5121.00
44_E48_Q1.4961.00
113_D169_V1.4921.00
18_Q22_E1.4771.00
113_D165_R1.4721.00
44_E47_K1.4591.00
10_G120_I1.4421.00
90_I94_D1.4401.00
124_R155_T1.4121.00
126_H146_D1.3940.99
141_K147_D1.3880.99
97_K181_Y1.3870.99
146_D149_T1.3810.99
166_K169_V1.3730.99
171_Y175_T1.3610.99
113_D168_L1.3200.99
108_E179_I1.3110.99
38_A67_L1.3020.99
14_G84_D1.2990.99
91_P94_D1.2940.99
134_H137_F1.2890.99
168_L172_H1.2850.99
112_P199_T1.2690.99
129_S146_D1.2650.99
208_D211_K1.2630.99
2_R81_F1.2620.99
180_G183_S1.2620.99
180_G184_K1.2570.99
48_Q66_A1.2530.99
60_T63_L1.2400.98
27_P71_R1.2300.98
19_F203_A1.2140.98
126_H149_T1.2080.98
12_G15_T1.2000.98
16_Q206_R1.2000.98
109_F209_L1.1950.98
201_P204_E1.1940.98
43_S46_G1.1930.98
11_A111_V1.1910.98
71_R74_Q1.1900.98
125_V132_V1.1870.98
38_A41_S1.1810.98
156_R159_D1.1640.97
95_A98_E1.1600.97
19_F22_E1.1560.97
108_E195_K1.1550.97
8_A171_Y1.1470.97
5_L17_A1.1430.97
115_L199_T1.1370.97
37_A71_R1.1010.96
35_L39_V1.0960.96
94_D97_K1.0960.96
122_G135_V1.0880.96
196_V205_V1.0820.96
6_L179_I1.0790.95
39_V53_M1.0730.95
200_K205_V1.0490.94
24_Y210_E1.0340.94
87_P92_Q1.0320.94
8_A116_I1.0310.94
106_V193_Y1.0250.93
144_G147_D1.0210.93
105_Y194_A1.0180.93
111_V198_G1.0130.93
160_Q163_T1.0080.93
34_M38_A1.0040.93
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  
4qbgB10.97661000.274Contact Map
4jzkA211000.28Contact Map
3gmtA20.92521000.28Contact Map
3be4A10.96261000.282Contact Map
4pzlA411000.288Contact Map
3tlxA40.97661000.3Contact Map
2xb4A10.9721000.302Contact Map
1ak2A10.97661000.316Contact Map
1zd8A10.96261000.319Contact Map
1akyA10.97661000.321Contact 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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