GREMLIN Database
RL4 - 50S ribosomal protein L4
UniProt: P60723 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10867
Length: 201 (194)
Sequences: 3132 (1767)
Seq/√Len: 126.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
60_W78_W3.6961.00
45_A88_R3.3321.00
70_S77_I3.1591.00
45_A51_E3.0641.00
134_L161_A2.9131.00
28_V108_I2.8161.00
31_V96_V2.3081.00
51_E88_R2.2171.00
34_A94_Q2.2101.00
159_L162_R2.1611.00
55_S59_P2.0491.00
55_S73_I2.0331.00
46_Q86_A2.0121.00
190_A194_K1.9581.00
48_T51_E1.9371.00
188_M196_V1.8971.00
26_A30_Q1.8461.00
128_A133_L1.8371.00
30_Q100_M1.7521.00
16_E20_G1.7191.00
117_R185_K1.7111.00
10_S190_A1.7111.00
29_H33_V1.7061.00
15_S197_E1.7031.00
194_K197_E1.6971.00
27_L103_G1.6931.00
35_Y39_A1.6751.00
151_G191_D1.6721.00
70_S75_S1.6711.00
129_P156_N1.6591.00
70_S78_W1.6571.00
8_A11_A1.6531.00
60_W65_T1.6401.00
133_L136_Q1.6241.00
119_I185_K1.6161.00
54_G74_K1.6061.00
52_V82_G1.6051.00
125_S154_D1.6051.00
34_A96_V1.5901.00
129_P160_A1.5811.00
97_N100_M1.5571.00
36_A178_V1.5541.00
31_V104_A1.5341.00
44_R92_H1.4741.00
111_E115_Q1.4711.00
135_A139_K1.4631.00
27_L100_M1.4621.00
96_V100_M1.4571.00
136_Q140_D1.4551.00
55_S72_S1.4461.00
45_A89_P1.4391.00
122_E190_A1.4321.00
60_W67_R1.4311.00
44_R86_A1.4191.00
110_S114_R1.4121.00
175_I196_V1.3821.00
28_V107_S1.3751.00
59_P70_S1.3591.00
60_W70_S1.3381.00
135_A164_L1.3331.00
24_N27_L1.3261.00
32_V181_I1.3101.00
56_G74_K1.3091.00
48_T88_R1.2981.00
134_L137_K1.2931.00
161_A169_V1.2841.00
155_E159_L1.2661.00
123_K191_D1.2621.00
156_N159_L1.2311.00
30_Q94_Q1.2250.99
129_P159_L1.1990.99
59_P78_W1.1960.99
54_G73_I1.1940.99
21_R107_S1.1870.99
188_M193_V1.1860.99
35_Y176_D1.1790.99
121_V124_F1.1660.99
21_R103_G1.1620.99
33_V94_Q1.1490.99
113_V118_L1.1410.99
59_P72_S1.1340.99
134_L148_I1.1270.99
31_V34_A1.1010.99
132_K136_Q1.0970.99
35_Y179_S1.0900.99
77_I84_T1.0850.99
49_R82_G1.0800.99
53_T74_K1.0680.99
118_L188_M1.0610.99
20_G114_R1.0600.99
33_V36_A1.0550.98
55_S74_K1.0550.98
145_D182_A1.0480.98
12_L193_V1.0470.98
101_Y177_P1.0470.98
127_E133_L1.0450.98
36_A39_A1.0420.98
191_D194_K1.0420.98
53_T80_S1.0360.98
46_Q83_V1.0320.98
44_R90_Q1.0300.98
28_V181_I1.0290.98
55_S78_W1.0260.98
37_A94_Q1.0250.98
111_E114_R1.0130.98
175_I180_L1.0080.98
57_K73_I1.0030.98
42_G89_P0.9930.98
60_W68_A0.9890.98
56_G72_S0.9830.98
136_Q139_K0.9790.97
19_F110_S0.9790.97
21_R106_K0.9730.97
144_E185_K0.9720.97
26_A29_H0.9650.97
178_V182_A0.9650.97
14_V19_F0.9640.97
145_D183_F0.9500.97
150_T157_L0.9470.97
23_F107_S0.9460.97
23_F28_V0.9430.97
130_K133_L0.9400.97
150_T154_D0.9360.97
168_D179_S0.9360.97
28_V111_E0.9260.96
134_L157_L0.9250.96
50_A72_S0.9230.96
143_L187_V0.9030.96
35_Y177_P0.9030.96
193_V197_E0.9000.96
146_V187_V0.8970.96
34_A38_G0.8930.96
108_I177_P0.8890.96
75_S78_W0.8890.96
134_L164_L0.8880.96
25_E28_V0.8840.95
168_D183_F0.8790.95
120_V188_M0.8740.95
83_V86_A0.8720.95
144_E184_D0.8690.95
146_V167_V0.8670.95
180_L186_V0.8670.95
23_F110_S0.8630.95
148_I167_V0.8620.95
131_T163_N0.8520.94
118_L186_V0.8420.94
34_A101_Y0.8400.94
170_R174_G0.8400.94
164_L167_V0.8380.94
126_V137_K0.8380.94
75_S84_T0.8370.94
141_M187_V0.8310.94
94_Q97_N0.8310.94
73_I77_I0.8310.94
129_P133_L0.8280.94
56_G59_P0.8280.94
138_L167_V0.8230.93
42_G91_D0.8100.93
108_I180_L0.8060.93
130_K160_A0.8020.92
126_V129_P0.7960.92
57_K67_R0.7900.92
158_F162_R0.7880.92
149_I188_M0.7860.92
150_T171_D0.7820.91
170_R176_D0.7810.91
61_R64_G0.7770.91
148_I187_V0.7750.91
151_G195_Q0.7720.91
149_I175_I0.7690.91
25_E111_E0.7680.91
171_D174_G0.7660.91
21_R110_S0.7650.91
23_F114_R0.7610.90
35_Y174_G0.7610.90
42_G90_Q0.7610.90
18_T106_K0.7570.90
76_P84_T0.7450.89
38_G93_S0.7440.89
126_V157_L0.7440.89
112_L117_R0.7430.89
143_L148_I0.7310.88
70_S73_I0.7310.88
137_K141_M0.7250.88
143_L146_V0.7240.88
124_F137_K0.7230.88
195_Q198_E0.7230.88
46_Q88_R0.7180.88
137_K140_D0.7170.87
60_W77_I0.7110.87
35_Y170_R0.7110.87
175_I200_L0.7090.87
194_K198_E0.7090.87
31_V177_P0.7030.86
150_T189_T0.6920.86
149_I170_R0.6910.86
121_V189_T0.6910.86
59_P73_I0.6890.85
40_R92_H0.6790.85
51_E82_G0.6780.84
53_T73_I0.6740.84
12_L190_A0.6720.84
59_P67_R0.6720.84
117_R184_D0.6710.84
73_I78_W0.6640.83
59_P74_K0.6600.83
59_P65_T0.6580.83
72_S75_S0.6540.82
130_K163_N0.6400.81
148_I161_A0.6380.81
70_S84_T0.6360.80
153_L171_D0.6340.80
176_D179_S0.6330.80
100_M103_G0.6300.80
53_T56_G0.6290.80
37_A92_H0.6270.80
14_V113_V0.6260.79
172_A195_Q0.6260.79
120_V193_V0.6240.79
128_A160_A0.6220.79
161_A164_L0.6210.79
73_I79_R0.6190.79
195_Q199_M0.6160.78
126_V133_L0.6060.77
98_K102_R0.6030.77
46_Q87_A0.6000.77
145_D184_D0.5990.76
55_S60_W0.5980.76
30_Q34_A0.5980.76
34_A104_A0.5980.76
67_R78_W0.5900.75
161_A167_V0.5890.75
60_W72_S0.5890.75
154_D157_L0.5860.75
40_R91_D0.5860.75
108_I111_E0.5840.75
24_N107_S0.5830.74
150_T153_L0.5810.74
37_A93_S0.5800.74
146_V183_F0.5790.74
38_G200_L0.5770.74
119_I187_V0.5760.74
83_V87_A0.5700.73
7_D13_T0.5670.72
17_T106_K0.5660.72
173_T195_Q0.5660.72
103_G106_K0.5620.72
76_P82_G0.5620.72
49_R75_S0.5620.72
18_T193_V0.5610.72
50_A64_G0.5600.72
23_F111_E0.5560.71
174_G200_L0.5540.71
168_D182_A0.5500.70
103_G107_S0.5470.70
12_L118_L0.5470.70
49_R76_P0.5460.70
96_V104_A0.5460.70
60_W75_S0.5450.69
18_T21_R0.5440.69
128_A156_N0.5410.69
59_P75_S0.5410.69
53_T82_G0.5400.69
139_K142_A0.5400.69
32_V178_V0.5400.69
138_L148_I0.5390.69
34_A95_K0.5380.68
35_Y178_V0.5370.68
80_S160_A0.5360.68
196_V199_M0.5360.68
74_K77_I0.5350.68
106_K200_L0.5340.68
37_A40_R0.5330.68
133_L140_D0.5300.67
134_L138_L0.5230.66
32_V177_P0.5220.66
146_V186_V0.5220.66
33_V40_R0.5210.66
12_L120_V0.5180.66
44_R87_A0.5150.65
65_T72_S0.5140.65
166_K183_F0.5110.65
27_L107_S0.5110.65
148_I157_L0.5100.64
49_R72_S0.5090.64
10_S122_E0.5060.64
14_V193_V0.5040.64
27_L30_Q0.5030.63
35_Y96_V0.5010.63
108_I113_V0.5010.63
147_L186_V0.5000.63
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  
1dmgA 1 0.7313 100 0.093 Contact Map
3j3wE 1 1 100 0.094 Contact Map
4tp9E 1 0.99 100 0.096 Contact Map
3j7yF 1 0.995 100 0.104 Contact Map
4ce4F 1 0.9502 100 0.105 Contact Map
1vw3D 1 1 100 0.124 Contact Map
3bboG 1 0.9851 100 0.125 Contact Map
4rb6F 1 0.9602 100 0.131 Contact Map
2zjrC 1 0.9403 100 0.139 Contact Map
3j39C 1 0.99 100 0.214 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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