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T0830 1-400

ID: 1405373951 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 400 (371)
Sequences: 4959 (4272.6)
Seq/Len: 13.367
Nf(neff/√len): 221.8

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: 13.367).

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
121_V167_C3.9681.00
117_L163_G3.6501.00
126_A355_I3.5381.00
126_A135_A3.5121.00
167_C195_A3.1741.00
134_A358_G2.9751.00
114_S163_G2.9251.00
327_W352_A2.7751.00
118_G166_S2.6771.00
125_A173_L2.5771.00
128_R174_M2.5521.00
128_R177_H2.5171.00
171_F195_A2.4821.00
96_G106_Q2.4001.00
119_I139_G2.3981.00
142_L148_W2.3641.00
115_G152_A2.3341.00
126_A138_T2.3171.00
175_G189_M2.3051.00
38_A119_I2.2831.00
113_L117_L2.2571.00
226_G229_R2.2571.00
158_D203_K2.2281.00
171_F188_W2.1921.00
56_E108_R2.1801.00
171_F191_A2.1601.00
123_M139_G2.1271.00
193_W197_G2.1091.00
114_S160_T2.0081.00
96_G110_A2.0041.00
88_F202_T1.9981.00
118_G163_G1.9501.00
124_M170_A1.9461.00
122_S142_L1.8921.00
67_F94_V1.8441.00
103_G106_Q1.8351.00
197_G243_I1.8021.00
43_F116_L1.7981.00
164_V202_T1.7851.00
127_R135_A1.7481.00
130_F359_V1.7381.00
97_Y107_A1.7361.00
135_A139_G1.7301.00
123_M135_A1.7271.00
193_W236_G1.7041.00
246_P250_L1.6991.00
121_V163_G1.6971.00
95_V99_L1.6811.00
138_T358_G1.6731.00
305_T309_A1.6701.00
131_G134_A1.6501.00
227_L230_R1.6271.00
97_Y102_L1.5941.00
244_T248_F1.5901.00
61_E64_R1.5891.00
199_A207_G1.5441.00
67_F98_E1.5421.00
170_A174_M1.5271.00
164_V198_V1.5101.00
120_G124_M1.4921.00
243_I246_P1.4881.00
119_I142_L1.4671.00
141_A354_G1.4631.00
96_G100_F1.4461.00
125_A166_S1.4401.00
133_R362_D1.4381.00
39_L43_F1.4291.00
239_V243_I1.4281.00
141_A358_G1.4060.99
122_S138_T1.3990.99
63_S94_V1.3660.99
86_P203_K1.3630.99
119_I143_L1.3590.99
105_W109_L1.3570.99
39_L116_L1.3530.99
209_A213_L1.3480.99
59_Y157_L1.3440.99
64_R68_A1.3370.99
242_V246_P1.3300.99
243_I247_W1.3170.99
200_I240_M1.3150.99
43_F112_A1.3130.99
326_I330_A1.3110.99
238_V242_V1.3030.99
127_R132_A1.3020.99
35_V116_L1.2960.99
95_V98_E1.2830.99
308_R312_E1.2810.99
46_L112_A1.2620.99
35_V120_G1.2560.99
85_K90_M1.2450.98
121_V166_S1.2360.98
141_A357_A1.2340.98
129_W173_L1.2330.98
118_G148_W1.2250.98
89_H157_L1.2220.98
62_I82_Y1.2210.98
284_Y341_K1.2170.98
135_A138_T1.2170.98
124_M128_R1.2130.98
331_I334_F1.2100.98
308_R311_V1.2080.98
240_M244_T1.2070.98
85_K91_W1.2050.98
188_W191_A1.2040.98
243_I248_F1.2010.98
379_V386_A1.1980.98
88_F198_V1.1970.98
123_M127_R1.1960.98
164_V195_A1.1880.98
281_S284_Y1.1790.98
185_R188_W1.1770.98
174_M188_W1.1760.98
269_Q272_T1.1740.98
304_W308_R1.1730.98
331_I335_F1.1730.98
199_A206_V1.1720.98
85_K157_L1.1710.98
93_T155_N1.1640.97
195_A198_V1.1630.97
283_F287_P1.1630.97
163_G167_C1.1590.97
339_R342_L1.1520.97
168_V196_M1.1480.97
293_F297_A1.1440.97
40_V44_V1.1420.97
45_S153_H1.1340.97
354_G358_G1.1300.97
111_V160_T1.1180.96
118_G122_S1.1120.96
292_G297_A1.1040.96
115_G148_W1.1030.96
172_M192_C1.1030.96
115_G119_I1.1020.96
198_V202_T1.0990.96
89_H160_T1.0940.96
211_P214_V1.0930.96
38_A42_W1.0850.96
125_A170_A1.0850.96
247_W250_L1.0820.96
302_K306_A1.0790.95
42_W115_G1.0790.95
59_Y345_Y1.0780.95
85_K203_K1.0770.95
152_A159_M1.0750.95
216_V220_L1.0710.95
63_S93_T1.0680.95
330_A333_V1.0680.95
226_G230_R1.0670.95
385_L388_P1.0670.95
184_A187_G1.0660.95
358_G362_D1.0620.95
94_V98_E1.0610.95
126_A130_F1.0600.95
385_L389_V1.0560.95
160_T202_T1.0510.94
106_Q109_L1.0500.94
215_L219_T1.0460.94
124_M127_R1.0460.94
63_S90_M1.0390.94
130_F134_A1.0390.94
126_A129_W1.0390.94
96_G109_L1.0370.94
92_V160_T1.0070.93
249_Y253_V1.0040.93
89_H93_T1.0040.93
63_S97_Y1.0000.92
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: (12Jul14)
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  
3wajA10.8551000.59Contact Map
3rceA10.872599.90.631Contact Map
3dh4A40.1214.70.958Contact Map
2xq2A10.1459.10.962Contact Map
4p02A10.276.10.965Contact Map
4p02B10.292540.968Contact Map
3fymA10.023.60.969Contact Map
1wazA10.1153.10.97Contact Map
2m8rA10.1252.80.97Contact Map
3l1lA10.5552.50.971Contact 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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