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T0826 1-220

ID: 1403943265 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 220 (213)
Sequences: 485 (384.5)
Seq/Len: 2.277
Nf(neff/√len): 26.3

Jackhmmer Results: (2014_04_16)
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: 2.277).

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
131_G135_A3.0571.00
62_N162_S3.0161.00
82_L138_Y2.7041.00
52_T177_Y2.3711.00
87_A127_I2.3461.00
79_P139_I2.2441.00
173_Q177_Y2.1371.00
23_S65_F2.0810.99
79_P138_Y2.0720.99
15_L138_Y2.0210.99
79_P135_A2.0190.99
91_Q118_L1.9780.99
59_F165_C1.9200.99
22_Y27_L1.8450.98
49_F177_Y1.8370.98
104_L203_K1.7750.98
92_E99_F1.7670.98
151_E155_R1.7360.97
91_Q99_F1.7360.97
71_P75_K1.6880.97
108_L203_K1.6530.96
152_L160_A1.5650.95
24_S58_F1.5450.94
19_L78_I1.5450.94
94_F138_Y1.5170.93
62_N158_L1.4490.91
188_T198_G1.4440.91
31_F35_V1.4160.90
63_F159_A1.4140.90
31_F185_K1.4040.89
20_S27_L1.3640.87
165_C168_G1.3440.86
95_F153_L1.3410.86
161_V164_L1.3110.84
75_K79_P1.3070.84
15_L78_I1.2980.84
145_Y151_E1.2910.83
92_E95_F1.2880.83
99_F214_Y1.2880.83
137_A217_L1.2860.83
30_A93_I1.2700.82
68_I77_L1.2660.81
23_S172_L1.2600.81
103_M106_N1.2590.81
100_N103_M1.2590.81
31_F57_L1.2480.80
31_F192_V1.2460.80
192_V198_G1.2390.79
75_K81_I1.2170.78
63_F163_F1.2110.77
31_F198_G1.2090.77
140_A144_K1.2060.77
10_L18_F1.2020.77
31_F92_E1.1990.76
129_C136_L1.1970.76
49_F173_Q1.1930.76
99_F118_L1.1830.75
63_F166_A1.1830.75
127_I132_V1.1710.74
23_S81_I1.1660.73
163_F167_L1.1600.73
136_L140_A1.1520.72
204_Y208_K1.1510.72
156_L160_A1.1390.71
43_G46_A1.1380.71
175_Q183_N1.1180.69
174_Y178_A1.1180.69
52_T57_L1.1160.69
170_A183_N1.1000.67
190_L195_N1.0990.67
94_F122_G1.0930.66
125_L152_L1.0900.66
24_S27_L1.0850.66
179_S183_N1.0810.65
59_F169_I1.0780.65
71_P190_L1.0720.64
86_A161_V1.0680.64
11_G84_I1.0660.64
63_F155_R1.0660.64
21_L58_F1.0560.62
91_Q214_Y1.0540.62
128_V132_V1.0430.61
10_L14_A1.0380.60
132_V164_L1.0350.60
33_A120_T1.0350.60
126_W130_L1.0340.60
185_K194_S1.0320.60
95_F100_N1.0300.60
111_T188_T1.0230.59
86_A131_G1.0220.59
63_F216_Q1.0210.59
92_E217_L1.0120.58
29_Y85_S1.0050.57
20_S61_S1.0030.57
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: (21Jun14)
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  
1fmeA10.10453.90.969Contact Map
2ww9C10.09552.80.971Contact Map
2wwbC10.15912.60.971Contact Map
2hi2A10.32.40.972Contact Map
4lz6A10.84552.20.972Contact Map
2a65A10.5520.973Contact Map
4humA10.84551.80.973Contact Map
4httA20.27271.80.974Contact Map
4m48A10.64551.60.974Contact Map
3cx5G20.19551.60.974Contact 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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