GREMLIN Database
RL4 - 50S ribosomal protein L4
UniProt: P42921 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 207 (202)
Sequences: 3152 (1763)
Seq/√Len: 124.1

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
65_W83_W3.6731.00
50_K93_T3.2981.00
75_Q82_Q3.1791.00
50_K56_E3.0721.00
139_M167_A2.9221.00
33_V113_V2.8711.00
5_A13_T2.8051.00
8_N12_S2.6741.00
36_A101_L2.3201.00
56_E93_T2.1971.00
165_L168_R2.1851.00
39_M99_Y2.1671.00
60_G64_P2.0831.00
60_G78_I2.0261.00
51_V91_G2.0131.00
196_K200_E1.9911.00
53_N56_E1.9231.00
194_I202_V1.9191.00
31_S35_D1.7971.00
35_D105_V1.7541.00
200_E203_E1.7511.00
134_A162_A1.7461.00
133_T138_E1.7311.00
34_F38_L1.7291.00
40_Q44_L1.7221.00
21_A25_G1.7171.00
122_N191_K1.6991.00
75_Q80_S1.6931.00
32_V108_L1.6791.00
157_A197_A1.6781.00
65_W70_T1.6621.00
20_N203_E1.6521.00
130_T160_N1.6441.00
75_Q83_W1.6441.00
138_E141_A1.6401.00
13_T16_D1.6271.00
59_G79_R1.6031.00
57_V87_G1.5961.00
124_I191_K1.5751.00
41_R184_L1.5651.00
134_A166_S1.5531.00
39_M101_L1.5491.00
36_A109_A1.5391.00
102_P105_V1.5301.00
101_L105_V1.4941.00
116_S120_D1.4771.00
115_S119_I1.4581.00
32_V105_V1.4511.00
60_G77_S1.4481.00
49_H97_Y1.4461.00
50_K94_P1.4461.00
65_W72_R1.4311.00
181_I202_V1.4301.00
140_A144_K1.4211.00
49_H91_G1.4151.00
141_A145_G1.3941.00
127_E196_K1.3791.00
64_P75_Q1.3601.00
33_V112_S1.3591.00
61_G79_R1.3381.00
65_W75_Q1.3241.00
37_I187_V1.3151.00
53_N93_T1.3121.00
128_D197_A1.2891.00
29_N32_V1.2801.00
140_A170_I1.2781.00
139_M142_I1.2781.00
5_A16_D1.2561.00
64_P83_W1.2451.00
35_D99_Y1.2300.99
162_A165_L1.2260.99
167_A175_V1.2230.99
59_G78_I1.1870.99
26_I112_S1.1840.99
194_I199_V1.1780.99
40_Q182_N1.1720.99
64_P77_S1.1610.99
118_V123_I1.1580.99
26_I108_L1.1540.99
15_G196_K1.1480.99
38_L99_Y1.1470.99
137_K141_A1.1460.99
134_A165_L1.1440.99
161_E165_L1.1430.99
126_L129_L1.1270.99
36_A39_M1.1200.99
82_Q89_V1.1150.99
58_R79_R1.1140.99
139_M154_I1.1030.99
151_K188_N1.0910.99
25_G119_I1.0820.99
38_L41_R1.0800.99
40_Q185_D1.0770.99
60_G79_R1.0700.98
141_A144_K1.0690.98
8_N14_A1.0660.98
58_R85_G1.0590.98
106_R183_V1.0580.98
197_A200_E1.0540.98
54_R87_G1.0490.98
24_F115_S1.0380.98
49_H95_R1.0380.98
33_V187_V1.0370.98
42_A99_Y1.0360.98
132_D138_E1.0350.98
51_V88_V1.0250.98
123_I194_I1.0210.98
41_R44_L1.0200.98
181_I186_V1.0140.98
60_G83_W1.0140.98
199_V203_E1.0140.98
28_P33_V1.0060.98
62_R78_I0.9940.98
61_G77_S0.9900.97
17_I199_V0.9810.97
116_S119_I0.9790.97
19_L24_F0.9700.97
31_S34_F0.9670.97
55_S77_S0.9540.97
184_L188_N0.9430.97
26_I111_K0.9400.97
8_N127_E0.9260.96
156_T163_V0.9260.96
7_Y13_T0.9230.96
174_T185_D0.9190.96
40_Q183_V0.9180.96
151_K189_H0.9180.96
47_G94_P0.9120.96
65_W73_A0.9110.96
28_P112_S0.9000.96
156_T160_N0.8870.95
139_M163_V0.8860.95
113_V183_V0.8830.95
33_V116_S0.8780.95
152_A173_V0.8780.95
148_V193_L0.8720.95
80_S83_W0.8710.95
186_V192_L0.8710.95
144_K149_E0.8710.95
131_L134_A0.8690.95
39_M43_S0.8670.95
176_V180_G0.8640.94
123_I192_L0.8610.94
152_A193_L0.8600.94
155_V181_I0.8570.94
30_E33_V0.8560.94
39_M106_R0.8550.94
125_V194_I0.8520.94
61_G64_P0.8490.94
28_P115_S0.8480.94
4_V19_L0.8440.94
80_S89_V0.8380.94
174_T189_H0.8380.94
135_K166_S0.8380.94
170_I173_V0.8360.93
99_Y102_P0.8340.93
156_T177_E0.8300.93
139_M170_I0.8290.93
88_V91_G0.8210.93
135_K138_E0.8210.93
146_L193_L0.8200.93
131_L142_I0.8200.93
66_R69_G0.8070.92
113_V186_V0.8060.92
11_G146_L0.8060.92
176_V182_N0.8040.92
78_I82_Q0.7960.92
143_L173_V0.7950.92
154_I173_V0.7940.92
149_E191_K0.7940.92
154_I193_L0.7930.92
155_V194_I0.7900.91
134_A138_E0.7890.91
164_A168_R0.7860.91
136_T169_N0.7840.91
40_Q180_G0.7810.91
47_G96_S0.7770.91
157_A201_K0.7750.91
117_K122_N0.7650.90
28_P119_I0.7560.90
23_V111_K0.7510.89
47_G95_R0.7510.89
81_P89_V0.7500.89
62_R72_R0.7440.89
177_E180_G0.7420.89
30_E116_S0.7390.88
75_Q78_I0.7300.88
6_L17_I0.7230.87
40_Q176_V0.7180.87
201_K204_E0.7150.87
4_V125_V0.7140.87
36_A183_V0.7110.86
131_L163_V0.7090.86
148_V152_A0.7090.86
26_I115_S0.7080.86
129_L142_I0.7040.86
78_I83_W0.7030.86
126_L195_T0.7010.86
64_P78_I0.6990.86
58_R78_I0.6890.85
64_P79_R0.6880.85
154_I167_A0.6860.84
64_P72_R0.6830.84
142_I146_L0.6830.84
200_E204_E0.6770.84
56_E87_G0.6760.84
45_R97_Y0.6760.84
65_W82_Q0.6740.83
131_L138_E0.6740.83
155_V176_V0.6740.83
10_N14_A0.6740.83
77_S80_S0.6730.83
182_N185_D0.6670.83
142_I145_G0.6650.83
43_S98_S0.6590.82
51_V93_T0.6580.82
122_N190_E0.6560.82
105_V108_L0.6560.82
159_A177_E0.6530.81
64_P70_T0.6450.81
75_Q89_V0.6420.80
6_L14_A0.6400.80
133_T166_S0.6400.80
156_T195_T0.6390.80
103_K107_R0.6370.80
58_R61_G0.6230.78
201_K205_V0.6210.78
7_Y11_G0.6160.78
42_A97_Y0.6130.77
148_V154_I0.6120.77
151_K190_E0.6110.77
4_V17_I0.6100.77
178_A201_K0.6090.77
125_V199_V0.6080.77
167_A170_I0.6070.77
19_L118_V0.6060.76
54_R80_S0.6050.76
39_M109_A0.6000.76
51_V92_P0.5980.75
135_K169_N0.5940.75
17_I196_K0.5930.75
65_W77_S0.5910.75
55_S69_G0.5900.74
78_I84_R0.5890.74
48_T94_P0.5880.74
42_A98_S0.5870.74
29_N112_S0.5870.74
160_N163_V0.5850.74
72_R83_W0.5840.74
35_D39_M0.5840.74
45_R96_S0.5840.74
17_I123_I0.5800.73
22_S111_K0.5800.73
113_V116_S0.5790.73
132_D166_S0.5780.73
60_G65_W0.5750.73
9_Q142_I0.5740.72
167_A173_V0.5690.72
179_N201_K0.5680.72
111_K206_L0.5670.72
10_N141_A0.5670.72
144_K147_S0.5660.71
108_L111_K0.5640.71
181_I206_L0.5610.71
108_L112_S0.5570.70
81_P87_G0.5560.70
88_V92_P0.5560.70
37_I184_L0.5520.70
10_N13_T0.5480.69
172_G189_H0.5460.69
65_W80_S0.5460.69
113_V118_V0.5460.69
85_G166_S0.5440.68
64_P80_S0.5430.68
58_R87_G0.5420.68
174_T188_N0.5400.68
38_L45_R0.5320.67
23_V199_V0.5320.67
70_T77_S0.5320.67
54_R81_P0.5320.67
79_R82_Q0.5320.67
136_T170_I0.5260.66
28_P116_S0.5250.66
49_H92_P0.5250.66
124_I193_L0.5220.65
40_Q184_L0.5220.65
152_A189_H0.5210.65
156_T159_A0.5210.65
54_R77_S0.5190.65
164_A193_L0.5170.65
202_V205_V0.5170.65
41_R188_N0.5160.64
180_G206_L0.5150.64
61_G65_W0.5130.64
4_V7_Y0.5130.64
153_L192_L0.5120.64
101_L109_A0.5100.64
32_V112_S0.5070.63
37_I183_V0.5060.63
32_V35_D0.5050.63
6_L12_S0.5050.63
35_D38_L0.5020.62
39_M100_K0.5000.62
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
3j3wE 1 0.9952 100 0.07 Contact Map
1dmgA 1 0.7391 100 0.076 Contact Map
3j7yF 1 1 100 0.094 Contact Map
4ce4F 1 0.9275 100 0.098 Contact Map
3bboG 1 0.9903 100 0.101 Contact Map
4tp9E 1 0.971 100 0.105 Contact Map
4rb6F 1 0.9662 100 0.108 Contact Map
2zjrC 1 0.942 100 0.115 Contact Map
1vw3D 1 1 100 0.127 Contact Map
3j39C 1 0.9952 100 0.197 Contact Map

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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