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dcp2_jackhammer

ID: 1502385276 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 300 (269)
Sequences: 372 (242.5)
Seq/Len: 1.383
Nf(neff/√len): 14.8

Jackhmmer Results: (2016_04)
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: 1.383).

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
110_Q181_L3.1441.00
101_A144_V2.4061.00
124_G127_K2.3991.00
99_R136_D2.3880.99
105_D109_Q2.3690.99
101_A152_C2.2770.99
48_F190_R2.0830.98
163_D172_R1.9840.97
115_K194_S1.8760.96
155_R179_I1.8690.96
32_E89_F1.8450.96
13_D71_H1.8050.95
103_M112_V1.7930.95
136_D187_S1.6900.92
26_E54_D1.6350.90
56_L232_W1.6260.90
105_D110_Q1.6150.90
105_D181_L1.6050.89
40_Q99_R1.5890.89
199_H219_F1.5790.88
150_F155_R1.5580.87
106_M166_I1.5020.85
104_L175_I1.4850.84
175_I236_R1.4500.82
69_F75_L1.4270.80
51_A191_K1.4250.80
27_E96_I1.4180.80
117_W191_K1.4170.80
161_F172_R1.4170.80
168_G206_T1.3760.77
16_S68_L1.3590.76
98_V127_K1.3490.75
157_N186_E1.3480.75
132_K199_H1.3480.75
99_R187_S1.3170.72
30_S89_F1.3160.72
201_L233_I1.3030.71
189_T224_P1.2970.71
262_S265_K1.2890.70
21_L174_Y1.2870.70
39_E44_F1.2850.70
17_A40_Q1.2850.70
91_R150_F1.2810.69
39_E93_K1.2280.64
127_K136_D1.2250.64
99_R130_I1.2240.64
17_A99_R1.2220.64
113_L199_H1.2040.62
18_R36_F1.2010.62
161_F174_Y1.1990.62
89_F115_K1.1990.62
14_D18_R1.1970.62
43_W47_D1.1960.61
14_D44_F1.1900.61
96_I131_D1.1890.61
62_R157_N1.1870.61
50_R61_L1.1850.60
25_A234_K1.1850.60
62_R105_D1.1840.60
21_L68_L1.1830.60
259_Q262_S1.1810.60
32_E98_V1.1760.60
157_N163_D1.1720.59
174_Y217_N1.1710.59
106_M178_G1.1490.57
203_D220_Y1.1470.57
160_E175_I1.1450.56
263_L266_S1.1420.56
26_E141_I1.1410.56
102_I173_L1.1330.55
268_T272_D1.1320.55
15_L39_E1.1260.55
79_S201_L1.1190.54
93_K185_F1.1160.54
156_I170_N1.1140.53
61_L86_F1.1110.53
115_K199_H1.1090.53
59_L91_R1.1040.52
264_L268_T1.1040.52
21_L161_F1.1020.52
150_F185_F1.0990.52
15_L44_F1.0990.52
33_R39_E1.0960.52
169_Q232_W1.0910.51
264_L267_S1.0900.51
260_L263_L1.0870.51
27_E131_D1.0850.50
254_A258_S1.0840.50
253_D256_A1.0820.50
267_S272_D1.0740.49
35_C85_A1.0730.49
266_S272_D1.0730.49
38_I71_H1.0690.49
205_P219_F1.0640.48
68_L167_R1.0630.48
114_V193_I1.0620.48
37_Q219_F1.0610.48
269_A272_D1.0580.48
107_S232_W1.0570.48
205_P229_L1.0530.47
32_E115_K1.0510.47
23_L37_Q1.0480.47
265_K272_D1.0470.47
117_W194_S1.0460.46
81_V84_E1.0450.46
105_D135_S1.0410.46
86_F117_W1.0400.46
112_V202_M1.0390.46
267_S271_S1.0360.45
270_P273_L1.0350.45
46_E115_K1.0320.45
261_L269_A1.0290.45
156_I176_I1.0280.45
45_Y149_G1.0280.45
267_S270_P1.0260.44
258_S262_S1.0250.44
46_E118_K1.0240.44
135_S233_I1.0230.44
37_Q96_I1.0230.44
257_S260_L1.0220.44
203_D230_K1.0210.44
6_A174_Y1.0200.44
46_E191_K1.0190.44
138_D153_S1.0180.44
12_L176_I1.0170.44
250_V254_A1.0150.43
264_L271_S1.0120.43
27_E33_R1.0110.43
265_K268_T1.0090.43
28_Q40_Q1.0080.43
102_I204_L1.0070.43
22_N33_R1.0060.42
163_D170_N1.0050.42
137_V179_I1.0050.42
95_R98_V1.0050.42
260_L268_T1.0030.42
247_N251_D1.0020.42
21_L172_R1.0010.42
263_L273_L1.0000.42
86_F118_K1.0000.42
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  
2a6tA20.76671000.526Contact Map
2qklB10.31000.68Contact Map
4kg3A30.483399.90.794Contact Map
3o8sA10.4499.80.84Contact Map
3q1pA20.646799.70.848Contact Map
4hfqA20.656799.70.848Contact Map
1f3yA10.476799.60.855Contact Map
4ickA20.4599.60.856Contact Map
3fcmA20.536799.60.859Contact Map
1vk6A10.703399.60.86Contact 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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