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T0830 340-575

ID: 1405378591 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 236 (229)
Sequences: 465 (412.3)
Seq/Len: 2.031
Nf(neff/√len): 27.2

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: 2.031).

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
81_G85_A2.7001.00
30_W34_L2.2141.00
34_L38_A1.8640.98
124_G127_I1.7990.98
127_I131_I1.7060.96
19_G199_V1.6920.96
33_Q41_A1.6790.96
66_A69_V1.6740.96
19_G158_P1.6700.96
191_K194_Q1.6250.95
19_G23_D1.5760.94
48_S51_V1.5720.94
41_A45_L1.5580.93
190_W194_Q1.4980.91
186_F189_L1.4930.91
64_Y68_A1.4870.91
82_I85_A1.4830.91
46_L89_L1.4780.91
96_S100_Y1.4750.90
51_V55_N1.4690.90
170_F174_V1.4520.89
189_L194_Q1.4490.89
100_Y104_M1.4080.87
81_G88_L1.4050.87
34_L41_A1.3930.87
190_W196_A1.3880.86
5_G172_A1.3720.86
5_G149_H1.3610.85
111_A114_G1.3290.83
30_W33_Q1.3100.82
123_S154_Y1.3060.81
187_T190_W1.3040.81
45_L52_A1.2980.81
187_T194_Q1.2870.80
166_D170_F1.2870.80
220_D223_R1.2850.80
197_M202_P1.2750.79
166_D174_V1.2670.79
121_P124_G1.2530.78
7_I14_L1.2520.78
128_A131_I1.2470.77
75_F78_M1.2430.77
7_I11_I1.2360.76
186_F190_W1.2190.75
161_M171_G1.2170.75
78_M82_I1.2090.74
80_L83_A1.2080.74
8_V132_A1.2020.73
22_L150_T1.2010.73
216_V219_R1.1910.72
141_L159_L1.1890.72
35_I46_L1.1880.72
38_A41_A1.1830.72
2_K7_I1.1810.72
182_D185_S1.1790.71
215_Y228_N1.1790.71
15_G106_L1.1630.70
95_P100_Y1.1620.70
8_V19_G1.1590.69
69_V72_A1.1570.69
82_I186_F1.1570.69
166_D171_G1.1550.69
78_M86_R1.1490.69
187_T191_K1.1490.69
192_N196_A1.1480.68
75_F85_A1.1410.68
8_V98_A1.1380.67
135_L157_H1.1320.67
78_M85_A1.1320.67
135_L155_L1.1320.67
16_I151_L1.1200.66
73_V77_V1.1180.65
103_G114_G1.1090.65
5_G120_R1.1090.65
211_T214_M1.1060.64
220_D224_V1.1050.64
191_K196_A1.1030.64
54_L60_P1.0930.63
77_V81_G1.0920.63
219_R224_V1.0910.63
149_H161_M1.0910.63
63_F68_A1.0900.63
65_R68_A1.0890.62
47_A52_A1.0890.62
32_K41_A1.0830.62
12_P15_G1.0830.62
82_I89_L1.0810.62
95_P103_G1.0790.61
19_G117_T1.0780.61
214_M226_V1.0770.61
45_L73_V1.0700.60
189_L192_N1.0690.60
10_V13_A1.0680.60
114_G118_V1.0650.60
2_K167_E1.0650.60
41_A44_G1.0640.60
2_K5_G1.0630.60
69_V73_V1.0600.59
67_Y70_W1.0580.59
15_G19_G1.0570.59
14_L167_E1.0470.58
3_L167_E1.0470.58
110_V113_L1.0450.58
107_G112_L1.0440.58
125_A154_Y1.0400.57
13_A174_V1.0350.57
186_F191_K1.0340.57
78_M81_G1.0330.56
146_M149_H1.0320.56
143_G146_M1.0290.56
219_R223_R1.0270.56
167_E171_G1.0260.56
46_L87_L1.0240.55
141_L196_A1.0240.55
199_V219_R1.0210.55
218_A223_R1.0180.55
66_A70_W1.0110.54
30_W40_V1.0100.54
80_L84_V1.0100.54
30_W38_A1.0100.54
12_P19_G1.0080.54
35_I41_A1.0080.54
39_I42_A1.0060.53
95_P114_G1.0050.53
168_L177_Q1.0030.53
13_A153_F1.0030.53
114_G123_S1.0020.53
95_P102_M1.0020.53
107_G115_H1.0020.53
59_I63_F1.0010.53
100_Y103_G1.0010.53
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  
4gx0A40.864427.60.937Contact Map
4i0uA100.33926.60.938Contact Map
1lnqA80.745825.80.938Contact Map
4ev6A50.347525.70.938Contact Map
3hsaA50.419512.30.947Contact Map
2mgyA10.512711.90.947Contact Map
3hxiA10.37717.40.952Contact Map
4p02A10.90255.30.955Contact Map
1wazA10.13565.20.955Contact Map
4k0jA60.48314.90.956Contact 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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