RL4 - ECOLI - GREMLIN Contacts

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RL4 - 50S ribosomal protein L4

UniProt:	P60723	Sequences: MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA	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

ECOLI - RL4
BACSU - RL4

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_W	78_W	3.696	1.00
45_A	88_R	3.332	1.00
70_S	77_I	3.159	1.00
45_A	51_E	3.064	1.00
134_L	161_A	2.913	1.00
28_V	108_I	2.816	1.00
31_V	96_V	2.308	1.00
51_E	88_R	2.217	1.00
34_A	94_Q	2.210	1.00
159_L	162_R	2.161	1.00
55_S	59_P	2.049	1.00
55_S	73_I	2.033	1.00
46_Q	86_A	2.012	1.00
190_A	194_K	1.958	1.00
48_T	51_E	1.937	1.00
188_M	196_V	1.897	1.00
26_A	30_Q	1.846	1.00
128_A	133_L	1.837	1.00
30_Q	100_M	1.752	1.00
16_E	20_G	1.719	1.00
117_R	185_K	1.711	1.00
10_S	190_A	1.711	1.00
29_H	33_V	1.706	1.00
15_S	197_E	1.703	1.00
194_K	197_E	1.697	1.00
27_L	103_G	1.693	1.00
35_Y	39_A	1.675	1.00
151_G	191_D	1.672	1.00
70_S	75_S	1.671	1.00
129_P	156_N	1.659	1.00
70_S	78_W	1.657	1.00
8_A	11_A	1.653	1.00
60_W	65_T	1.640	1.00
133_L	136_Q	1.624	1.00
119_I	185_K	1.616	1.00
54_G	74_K	1.606	1.00
52_V	82_G	1.605	1.00
125_S	154_D	1.605	1.00
34_A	96_V	1.590	1.00
129_P	160_A	1.581	1.00
97_N	100_M	1.557	1.00
36_A	178_V	1.554	1.00
31_V	104_A	1.534	1.00
44_R	92_H	1.474	1.00
111_E	115_Q	1.471	1.00
135_A	139_K	1.463	1.00
27_L	100_M	1.462	1.00
96_V	100_M	1.457	1.00
136_Q	140_D	1.455	1.00
55_S	72_S	1.446	1.00
45_A	89_P	1.439	1.00
122_E	190_A	1.432	1.00
60_W	67_R	1.431	1.00
44_R	86_A	1.419	1.00
110_S	114_R	1.412	1.00
175_I	196_V	1.382	1.00
28_V	107_S	1.375	1.00
59_P	70_S	1.359	1.00
60_W	70_S	1.338	1.00
135_A	164_L	1.333	1.00
24_N	27_L	1.326	1.00
32_V	181_I	1.310	1.00
56_G	74_K	1.309	1.00
48_T	88_R	1.298	1.00
134_L	137_K	1.293	1.00
161_A	169_V	1.284	1.00
155_E	159_L	1.266	1.00
123_K	191_D	1.262	1.00
156_N	159_L	1.231	1.00
30_Q	94_Q	1.225	0.99
129_P	159_L	1.199	0.99
59_P	78_W	1.196	0.99
54_G	73_I	1.194	0.99
21_R	107_S	1.187	0.99
188_M	193_V	1.186	0.99
35_Y	176_D	1.179	0.99
121_V	124_F	1.166	0.99
21_R	103_G	1.162	0.99
33_V	94_Q	1.149	0.99
113_V	118_L	1.141	0.99
59_P	72_S	1.134	0.99
134_L	148_I	1.127	0.99
31_V	34_A	1.101	0.99
132_K	136_Q	1.097	0.99
35_Y	179_S	1.090	0.99
77_I	84_T	1.085	0.99
49_R	82_G	1.080	0.99
53_T	74_K	1.068	0.99
118_L	188_M	1.061	0.99
20_G	114_R	1.060	0.99
33_V	36_A	1.055	0.98
55_S	74_K	1.055	0.98
145_D	182_A	1.048	0.98
12_L	193_V	1.047	0.98
101_Y	177_P	1.047	0.98
127_E	133_L	1.045	0.98
36_A	39_A	1.042	0.98
191_D	194_K	1.042	0.98
53_T	80_S	1.036	0.98
46_Q	83_V	1.032	0.98
44_R	90_Q	1.030	0.98
28_V	181_I	1.029	0.98
55_S	78_W	1.026	0.98
37_A	94_Q	1.025	0.98
111_E	114_R	1.013	0.98
175_I	180_L	1.008	0.98
57_K	73_I	1.003	0.98
42_G	89_P	0.993	0.98
60_W	68_A	0.989	0.98
56_G	72_S	0.983	0.98
136_Q	139_K	0.979	0.97
19_F	110_S	0.979	0.97
21_R	106_K	0.973	0.97
144_E	185_K	0.972	0.97
26_A	29_H	0.965	0.97
178_V	182_A	0.965	0.97
14_V	19_F	0.964	0.97
145_D	183_F	0.950	0.97
150_T	157_L	0.947	0.97
23_F	107_S	0.946	0.97
23_F	28_V	0.943	0.97
130_K	133_L	0.940	0.97
150_T	154_D	0.936	0.97
168_D	179_S	0.936	0.97
28_V	111_E	0.926	0.96
134_L	157_L	0.925	0.96
50_A	72_S	0.923	0.96
143_L	187_V	0.903	0.96
35_Y	177_P	0.903	0.96
193_V	197_E	0.900	0.96
146_V	187_V	0.897	0.96
34_A	38_G	0.893	0.96
108_I	177_P	0.889	0.96
75_S	78_W	0.889	0.96
134_L	164_L	0.888	0.96
25_E	28_V	0.884	0.95
168_D	183_F	0.879	0.95
120_V	188_M	0.874	0.95
83_V	86_A	0.872	0.95
144_E	184_D	0.869	0.95
146_V	167_V	0.867	0.95
180_L	186_V	0.867	0.95
23_F	110_S	0.863	0.95
148_I	167_V	0.862	0.95
131_T	163_N	0.852	0.94
118_L	186_V	0.842	0.94
34_A	101_Y	0.840	0.94
170_R	174_G	0.840	0.94
164_L	167_V	0.838	0.94
126_V	137_K	0.838	0.94
75_S	84_T	0.837	0.94
141_M	187_V	0.831	0.94
94_Q	97_N	0.831	0.94
73_I	77_I	0.831	0.94
129_P	133_L	0.828	0.94
56_G	59_P	0.828	0.94
138_L	167_V	0.823	0.93
42_G	91_D	0.810	0.93
108_I	180_L	0.806	0.93
130_K	160_A	0.802	0.92
126_V	129_P	0.796	0.92
57_K	67_R	0.790	0.92
158_F	162_R	0.788	0.92
149_I	188_M	0.786	0.92
150_T	171_D	0.782	0.91
170_R	176_D	0.781	0.91
61_R	64_G	0.777	0.91
148_I	187_V	0.775	0.91
151_G	195_Q	0.772	0.91
149_I	175_I	0.769	0.91
25_E	111_E	0.768	0.91
171_D	174_G	0.766	0.91
21_R	110_S	0.765	0.91
23_F	114_R	0.761	0.90
35_Y	174_G	0.761	0.90
42_G	90_Q	0.761	0.90
18_T	106_K	0.757	0.90
76_P	84_T	0.745	0.89
38_G	93_S	0.744	0.89
126_V	157_L	0.744	0.89
112_L	117_R	0.743	0.89
143_L	148_I	0.731	0.88
70_S	73_I	0.731	0.88
137_K	141_M	0.725	0.88
143_L	146_V	0.724	0.88
124_F	137_K	0.723	0.88
195_Q	198_E	0.723	0.88
46_Q	88_R	0.718	0.88
137_K	140_D	0.717	0.87
60_W	77_I	0.711	0.87
35_Y	170_R	0.711	0.87
175_I	200_L	0.709	0.87
194_K	198_E	0.709	0.87
31_V	177_P	0.703	0.86
150_T	189_T	0.692	0.86
149_I	170_R	0.691	0.86
121_V	189_T	0.691	0.86
59_P	73_I	0.689	0.85
40_R	92_H	0.679	0.85
51_E	82_G	0.678	0.84
53_T	73_I	0.674	0.84
12_L	190_A	0.672	0.84
59_P	67_R	0.672	0.84
117_R	184_D	0.671	0.84
73_I	78_W	0.664	0.83
59_P	74_K	0.660	0.83
59_P	65_T	0.658	0.83
72_S	75_S	0.654	0.82
130_K	163_N	0.640	0.81
148_I	161_A	0.638	0.81
70_S	84_T	0.636	0.80
153_L	171_D	0.634	0.80
176_D	179_S	0.633	0.80
100_M	103_G	0.630	0.80
53_T	56_G	0.629	0.80
37_A	92_H	0.627	0.80
14_V	113_V	0.626	0.79
172_A	195_Q	0.626	0.79
120_V	193_V	0.624	0.79
128_A	160_A	0.622	0.79
161_A	164_L	0.621	0.79
73_I	79_R	0.619	0.79
195_Q	199_M	0.616	0.78
126_V	133_L	0.606	0.77
98_K	102_R	0.603	0.77
46_Q	87_A	0.600	0.77
145_D	184_D	0.599	0.76
55_S	60_W	0.598	0.76
30_Q	34_A	0.598	0.76
34_A	104_A	0.598	0.76
67_R	78_W	0.590	0.75
161_A	167_V	0.589	0.75
60_W	72_S	0.589	0.75
154_D	157_L	0.586	0.75
40_R	91_D	0.586	0.75
108_I	111_E	0.584	0.75
24_N	107_S	0.583	0.74
150_T	153_L	0.581	0.74
37_A	93_S	0.580	0.74
146_V	183_F	0.579	0.74
38_G	200_L	0.577	0.74
119_I	187_V	0.576	0.74
83_V	87_A	0.570	0.73
7_D	13_T	0.567	0.72
17_T	106_K	0.566	0.72
173_T	195_Q	0.566	0.72
103_G	106_K	0.562	0.72
76_P	82_G	0.562	0.72
49_R	75_S	0.562	0.72
18_T	193_V	0.561	0.72
50_A	64_G	0.560	0.72
23_F	111_E	0.556	0.71
174_G	200_L	0.554	0.71
168_D	182_A	0.550	0.70
103_G	107_S	0.547	0.70
12_L	118_L	0.547	0.70
49_R	76_P	0.546	0.70
96_V	104_A	0.546	0.70
60_W	75_S	0.545	0.69
18_T	21_R	0.544	0.69
128_A	156_N	0.541	0.69
59_P	75_S	0.541	0.69
53_T	82_G	0.540	0.69
139_K	142_A	0.540	0.69
32_V	178_V	0.540	0.69
138_L	148_I	0.539	0.69
34_A	95_K	0.538	0.68
35_Y	178_V	0.537	0.68
80_S	160_A	0.536	0.68
196_V	199_M	0.536	0.68
74_K	77_I	0.535	0.68
106_K	200_L	0.534	0.68
37_A	40_R	0.533	0.68
133_L	140_D	0.530	0.67
134_L	138_L	0.523	0.66
32_V	177_P	0.522	0.66
146_V	186_V	0.522	0.66
33_V	40_R	0.521	0.66
12_L	120_V	0.518	0.66
44_R	87_A	0.515	0.65
65_T	72_S	0.514	0.65
166_K	183_F	0.511	0.65
27_L	107_S	0.511	0.65
148_I	157_L	0.510	0.64
49_R	72_S	0.509	0.64
10_S	122_E	0.506	0.64
14_V	193_V	0.504	0.64
27_L	30_Q	0.503	0.63
35_Y	96_V	0.501	0.63
108_I	113_V	0.501	0.63
147_L	186_V	0.500	0.63

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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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