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Cell 1

ID: 1506079143 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 220 (200)
Sequences: 765 (516.8)
Seq/Len: 3.825
Nf(neff/√len): 36.5

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: 3.825).

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
43_S63_L3.5851.00
40_A64_G3.5211.00
188_E191_G2.4471.00
52_S73_D2.3881.00
36_W64_G2.1141.00
85_T126_S2.0631.00
183_W191_G1.8511.00
82_M126_S1.8080.99
176_T183_W1.6940.99
34_A91_V1.6390.99
158_L166_A1.5360.98
62_N69_A1.5290.98
44_F72_A1.4890.97
164_T168_L1.4840.97
131_A151_S1.4640.97
84_Y87_P1.4420.96
27_L54_T1.4310.96
36_W44_F1.3800.95
30_I94_C1.3760.95
202_S205_T1.3740.95
203_N206_R1.3650.95
62_N68_G1.3600.95
118_G174_G1.3380.94
128_G167_L1.3300.94
24_E179_T1.2910.92
48_D69_A1.2900.92
205_T208_D1.2780.92
65_G68_G1.2750.92
82_M130_A1.2740.92
44_F53_Q1.2650.91
183_W188_E1.2610.91
75_L83_A1.2550.91
52_S77_F1.2420.90
87_P176_T1.2420.90
79_F149_L1.2250.89
181_W186_I1.2220.89
27_L31_V1.2200.89
204_R208_D1.2190.89
62_N65_G1.2160.89
205_T209_D1.2110.89
201_A204_R1.2100.89
72_A148_S1.1950.88
199_T205_T1.1910.88
65_G69_A1.1890.87
201_A207_R1.1870.87
82_M85_T1.1830.87
202_S207_R1.1810.87
51_W59_P1.1800.87
14_T17_S1.1710.86
43_S120_L1.1650.86
202_S206_R1.1640.86
199_T207_R1.1610.86
203_N208_D1.1600.86
207_R211_W1.1560.85
208_D211_W1.1480.85
207_R210_T1.1470.85
28_I165_I1.1420.84
200_F205_T1.1410.84
129_L164_T1.1380.84
177_L180_G1.1360.84
51_W73_D1.1270.83
36_W162_G1.1250.83
113_S120_L1.1190.83
87_P130_A1.1180.83
199_T204_R1.1140.82
83_A174_G1.1140.82
202_S208_D1.1060.82
49_P72_A1.1030.82
200_F204_R1.0980.81
201_A205_T1.0890.80
118_G158_L1.0820.80
40_A87_P1.0820.80
97_A101_Q1.0770.79
43_S62_N1.0720.79
203_N207_R1.0670.78
127_C146_I1.0630.78
44_F108_D1.0630.78
116_I124_L1.0620.78
84_Y130_A1.0580.78
161_S175_L1.0580.78
31_V91_V1.0570.78
52_S83_A1.0560.77
199_T203_N1.0540.77
25_A45_N1.0530.77
77_F145_V1.0520.77
199_T202_S1.0490.77
82_M159_H1.0460.77
77_F127_C1.0390.76
21_R24_E1.0380.76
28_I84_Y1.0380.76
206_R211_W1.0350.75
38_M87_P1.0310.75
184_V187_A1.0310.75
103_S190_L1.0280.75
126_S171_W1.0240.74
27_L97_A1.0230.74
44_F50_S1.0140.73
174_G178_F1.0110.73
201_A209_D1.0060.72
88_V151_S1.0050.72
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  
3wdoA10.945521.70.938Contact Map
4ikvA10.918219.10.94Contact Map
1yewC30.440911.20.946Contact Map
4pypA10.818210.60.947Contact Map
4j05A20.82276.90.951Contact Map
4m64A40.88185.40.953Contact Map
2l16A10.23645.30.953Contact Map
2mi2A10.28184.90.954Contact Map
4zw9A104.90.954Contact Map
3l1lA10.89094.70.955Contact 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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