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T0831_sub -force run

ID: 1407302747 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 197 (196)
Sequences: 121 (91)
Seq/Len: 0.617
Nf(neff/√len): 6.5

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: 0.617).

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
122_F195_V2.1850.94
111_R195_V1.8390.84
184_L195_V1.7950.81
35_W180_E1.7820.81
111_R191_L1.7540.79
105_A112_P1.6850.75
144_E181_Y1.6230.72
117_L195_V1.5770.68
182_K188_W1.5750.68
110_L195_V1.5710.68
65_C72_L1.5670.68
111_R117_L1.5660.68
10_A101_V1.5560.67
111_R122_F1.5360.65
55_V100_N1.5330.65
122_F184_L1.5290.65
111_R184_L1.4940.62
42_A131_E1.4890.62
109_H195_V1.4800.61
110_L182_K1.4740.61
38_V55_V1.4650.60
35_W72_L1.4360.58
112_P117_L1.4140.56
84_K103_E1.4140.56
90_V190_A1.3870.54
34_W144_E1.3760.53
179_K185_H1.3630.52
144_E185_H1.3310.49
126_D139_N1.3240.49
54_R177_W1.3080.47
13_A21_I1.3040.47
109_H122_F1.2910.46
140_I171_M1.2520.43
26_R42_A1.2200.40
39_I72_L1.2180.40
105_A110_L1.2150.40
102_I105_A1.2080.39
111_R179_K1.2060.39
75_Q90_V1.2060.39
132_Y180_E1.2050.39
64_D105_A1.1940.38
137_F141_S1.1900.38
55_V98_S1.1890.38
137_F181_Y1.1820.37
191_L195_V1.1740.37
52_V71_L1.1740.37
26_R57_N1.1700.36
112_P195_V1.1640.36
105_A133_E1.1590.36
59_I183_L1.1550.35
89_A180_E1.1480.35
188_W191_L1.1460.35
16_P20_T1.1350.34
142_E178_K1.1330.34
62_F68_L1.1330.34
67_G153_F1.1310.34
65_C98_S1.1240.33
167_G178_K1.1210.33
77_E152_S1.1200.33
39_I168_S1.1200.33
69_Q167_G1.1200.33
15_Y132_Y1.1140.32
105_A109_H1.1140.32
106_T111_R1.1130.32
165_D168_S1.1120.32
178_K196_S1.1080.32
79_L174_F1.1040.32
14_L89_A1.0970.31
112_P167_G1.0940.31
70_F86_V1.0930.31
70_F150_I1.0890.31
2_K5_T1.0880.30
64_D70_F1.0860.30
186_E192_R1.0840.30
107_V195_V1.0830.30
106_T167_G1.0830.30
109_H119_C1.0770.30
55_V149_A1.0710.29
139_N188_W1.0710.29
109_H117_L1.0690.29
73_T155_K1.0660.29
140_I178_K1.0640.29
110_L117_L1.0610.29
76_M83_Q1.0540.28
66_R77_E1.0540.28
55_V168_S1.0410.27
83_Q180_E1.0380.27
59_I125_A1.0370.27
10_A74_T1.0370.27
55_V195_V1.0360.27
9_E26_R1.0210.26
125_A191_L1.0180.26
7_V16_P1.0170.26
90_V114_R1.0150.26
63_R127_E1.0130.26
137_F144_E1.0080.25
95_G164_V1.0040.25
58_E149_A1.0020.25
34_W185_H1.0000.25
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: (17Jul14)
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  
3ghgC40.482234.30.938Contact Map
3bu8A20.512721.30.944Contact Map
1m1jC20.456917.50.946Contact Map
4aycA10.670113.20.949Contact Map
4m7cA20.502511.50.95Contact Map
2higA20.228411.40.95Contact Map
3ghgA40.446710.50.951Contact Map
1l8dA20.522860.956Contact Map
1deqA40.75635.40.957Contact Map
1m1jA20.45185.40.957Contact 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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