RNM5 - BACSU - GREMLIN Contacts

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RNM5 - Ribonuclease M5

UniProt:	P37547	Sequences: MKIKEIIVVEGRDDTARIKLAVDADTIETNGSAIDDHVIDQIRLAQKTRGVIILTDPDFPGEKIRKTISEAVPGCKHAFLPKHLAKPKNKRGIGVEHASVESIRACLENVHEEMEAQPSDISAEDLIHAGLIGGPAAKCRRERLGDLLKIGYTNGKQLQKRLQMFQIKKSDFMSALDTVMREEQNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	186 (176)
Sequences:	750 (554)
Seq/√Len:	41.7

BACSU - RNM5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_T	28_E	3.842	1.00
17_R	20_L	3.795	1.00
62_E	66_K	3.339	1.00
147_L	178_T	3.164	1.00
5_E	76_K	3.131	1.00
80_L	95_V	3.047	1.00
84_L	102_S	2.838	1.00
15_T	26_T	2.796	1.00
63_K	67_T	2.793	1.00
42_I	51_V	2.621	1.00
54_L	80_L	2.561	1.00
92_G	97_H	2.536	1.00
69_S	77_H	2.521	1.00
129_A	172_F	2.504	1.00
35_D	38_V	2.282	1.00
27_I	42_I	2.255	1.00
25_D	49_R	2.232	1.00
84_L	105_A	2.175	1.00
168_K	171_D	2.132	0.99
125_D	159_Q	2.124	0.99
68_I	72_V	2.041	0.99
44_L	48_T	2.028	0.99
144_L	158_L	1.990	0.99
125_D	169_K	1.987	0.99
81_P	84_L	1.931	0.99
132_I	155_G	1.874	0.99
59_F	63_K	1.802	0.98
18_I	24_A	1.793	0.98
43_R	71_A	1.778	0.98
78_A	107_L	1.765	0.98
34_I	67_T	1.735	0.98
18_I	103_I	1.671	0.97
21_A	100_V	1.669	0.97
39_I	71_A	1.647	0.97
39_I	43_R	1.619	0.96
21_A	104_R	1.576	0.96
18_I	54_L	1.572	0.96
38_V	41_Q	1.555	0.95
111_H	171_D	1.488	0.94
130_G	134_G	1.482	0.94
105_A	108_E	1.468	0.94
134_G	137_A	1.433	0.93
139_C	143_R	1.416	0.92
46_Q	68_I	1.403	0.92
30_N	33_A	1.380	0.91
22_V	107_L	1.355	0.90
34_I	68_I	1.340	0.90
169_K	173_M	1.312	0.89
145_G	150_I	1.294	0.88
119_S	163_Q	1.287	0.88
86_K	93_I	1.283	0.88
69_S	113_E	1.270	0.87
138_K	142_E	1.263	0.87
43_R	47_K	1.231	0.86
137_A	140_R	1.215	0.85
136_A	139_C	1.211	0.85
18_I	21_A	1.189	0.84
53_I	75_C	1.173	0.83
155_G	165_F	1.172	0.83
8_V	42_I	1.159	0.82
46_Q	74_G	1.141	0.81
100_V	104_R	1.140	0.81
80_L	132_I	1.140	0.81
78_A	106_C	1.137	0.81
46_Q	72_V	1.136	0.81
38_V	42_I	1.135	0.81
129_A	140_R	1.133	0.80
80_L	85_A	1.132	0.80
5_E	50_G	1.126	0.80
159_Q	163_Q	1.112	0.79
13_D	16_A	1.109	0.79
51_V	75_C	1.100	0.78
174_S	178_T	1.079	0.77
123_A	159_Q	1.062	0.76
82_K	93_I	1.059	0.76
121_I	162_L	1.059	0.76
6_I	164_M	1.053	0.75
136_A	140_R	1.047	0.75
80_L	102_S	1.042	0.75
83_H	146_D	1.020	0.73
125_D	172_F	1.016	0.73
17_R	100_V	1.011	0.72
82_K	86_K	1.011	0.72
59_F	91_R	0.995	0.71
66_K	70_E	0.994	0.71
126_L	155_G	0.994	0.71
130_G	140_R	0.985	0.70
68_I	75_C	0.981	0.70
87_P	91_R	0.977	0.70
27_I	38_V	0.962	0.68
36_D	40_D	0.961	0.68
143_R	147_L	0.960	0.68
34_I	38_V	0.951	0.68
21_A	24_A	0.949	0.67
53_I	68_I	0.937	0.66
64_I	150_I	0.936	0.66
46_Q	51_V	0.935	0.66
13_D	97_H	0.930	0.66
174_S	177_D	0.929	0.66
87_P	93_I	0.919	0.65
120_D	169_K	0.919	0.65
125_D	129_A	0.917	0.65
107_L	112_E	0.910	0.64
7_I	54_L	0.910	0.64
42_I	72_V	0.910	0.64
133_G	137_A	0.891	0.62
38_V	45_A	0.890	0.62
78_A	110_V	0.887	0.62
101_E	104_R	0.885	0.62
144_L	179_V	0.881	0.62
143_R	179_V	0.878	0.61
153_T	158_L	0.871	0.61
40_D	43_R	0.870	0.61
151_G	161_R	0.850	0.59
3_I	76_K	0.848	0.59
172_F	175_A	0.832	0.57
51_V	72_V	0.831	0.57
34_I	64_I	0.831	0.57
80_L	126_L	0.826	0.57
46_Q	166_Q	0.819	0.56
91_R	97_H	0.807	0.55
16_A	20_L	0.806	0.55
134_G	138_K	0.801	0.54
126_L	156_K	0.801	0.54
13_D	96_E	0.798	0.54
39_I	72_V	0.795	0.54
72_V	75_C	0.789	0.53
36_D	71_A	0.788	0.53
138_K	152_Y	0.782	0.52
34_I	42_I	0.778	0.52
44_L	47_K	0.777	0.52
46_Q	50_G	0.772	0.52
48_T	153_T	0.769	0.51
27_I	45_A	0.761	0.50
105_A	109_N	0.753	0.50
26_T	32_S	0.752	0.50
171_D	174_S	0.751	0.50
5_E	103_I	0.746	0.49
147_L	172_F	0.741	0.49
60_P	75_C	0.739	0.48
21_A	103_I	0.737	0.48
83_H	95_V	0.735	0.48
30_N	41_Q	0.730	0.48
126_L	159_Q	0.729	0.47
124_E	128_H	0.723	0.47
3_I	50_G	0.707	0.45
39_I	82_K	0.705	0.45
60_P	92_G	0.704	0.45
78_A	103_I	0.702	0.45
126_L	132_I	0.700	0.45
169_K	172_F	0.698	0.45
145_G	153_T	0.696	0.44
48_T	171_D	0.694	0.44
20_L	100_V	0.694	0.44
105_A	124_E	0.693	0.44
45_A	50_G	0.693	0.44
82_K	105_A	0.690	0.44
18_I	26_T	0.688	0.44
151_G	154_N	0.686	0.44
81_P	86_K	0.680	0.43
44_L	51_V	0.676	0.43
101_E	139_C	0.674	0.42
103_I	175_A	0.674	0.42
87_P	97_H	0.669	0.42
11_G	14_D	0.668	0.42
10_E	14_D	0.668	0.42
119_S	169_K	0.666	0.42
32_S	67_T	0.665	0.42
25_D	161_R	0.662	0.41
122_S	125_D	0.661	0.41
131_L	148_L	0.659	0.41
74_G	115_E	0.659	0.41
60_P	82_K	0.656	0.41
54_L	134_G	0.651	0.40
18_I	22_V	0.650	0.40
7_I	22_V	0.647	0.40
145_G	151_G	0.645	0.40
3_I	165_F	0.643	0.40
138_K	162_L	0.642	0.40
109_N	135_P	0.642	0.40
127_I	137_A	0.642	0.40
129_A	176_L	0.640	0.39
6_I	45_A	0.636	0.39
136_A	143_R	0.635	0.39
53_I	114_M	0.630	0.38
139_C	142_E	0.627	0.38
84_L	149_K	0.625	0.38
142_E	152_Y	0.619	0.37
127_I	132_I	0.619	0.37
45_A	51_V	0.618	0.37
123_A	126_L	0.614	0.37
53_I	113_E	0.605	0.36
152_Y	157_Q	0.604	0.36
45_A	107_L	0.597	0.36
170_S	174_S	0.597	0.36
34_I	37_H	0.592	0.35
155_G	158_L	0.591	0.35
157_Q	161_R	0.589	0.35
30_N	60_P	0.588	0.35
145_G	158_L	0.586	0.35
62_E	161_R	0.585	0.35
25_D	164_M	0.583	0.34
99_S	102_S	0.583	0.34
121_I	172_F	0.582	0.34
110_V	113_E	0.580	0.34
4_K	125_D	0.579	0.34
108_E	124_E	0.577	0.34
57_P	85_A	0.576	0.34
16_A	90_K	0.572	0.33
27_I	41_Q	0.569	0.33
122_S	163_Q	0.569	0.33
12_R	166_Q	0.567	0.33
145_G	172_F	0.565	0.33
86_K	91_R	0.564	0.33
140_R	155_G	0.564	0.33
17_R	172_F	0.563	0.33
28_E	33_A	0.558	0.32
18_I	28_E	0.555	0.32
154_N	161_R	0.554	0.32
89_N	93_I	0.553	0.32
42_I	53_I	0.553	0.32
82_K	142_E	0.552	0.32
158_L	177_D	0.552	0.32
121_I	163_Q	0.550	0.32
154_N	167_I	0.549	0.32
49_R	161_R	0.549	0.32
5_E	49_R	0.548	0.31
49_R	79_F	0.547	0.31
123_A	134_G	0.546	0.31
20_L	107_L	0.546	0.31
19_K	25_D	0.545	0.31
22_V	104_R	0.544	0.31
135_P	177_D	0.544	0.31
125_D	128_H	0.544	0.31
12_R	167_I	0.542	0.31
13_D	93_I	0.538	0.31
173_M	177_D	0.537	0.31
114_M	177_D	0.536	0.31
84_L	142_E	0.534	0.30
117_Q	174_S	0.534	0.30
86_K	97_H	0.531	0.30
19_K	150_I	0.531	0.30
15_T	18_I	0.530	0.30
145_G	148_L	0.530	0.30
45_A	78_A	0.528	0.30
36_D	80_L	0.528	0.30
9_V	14_D	0.527	0.30
49_R	115_E	0.523	0.29
17_R	24_A	0.522	0.29
4_K	140_R	0.520	0.29
38_V	107_L	0.519	0.29
16_A	63_K	0.518	0.29
32_S	97_H	0.516	0.29
51_V	74_G	0.515	0.29
32_S	63_K	0.512	0.29
53_I	72_V	0.510	0.28
147_L	175_A	0.508	0.28
128_H	135_P	0.506	0.28
39_I	67_T	0.506	0.28
19_K	24_A	0.505	0.28
42_I	45_A	0.504	0.28
104_R	108_E	0.503	0.28
63_K	66_K	0.503	0.28
51_V	164_M	0.500	0.28

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
2fcjA	2	0.6237	100	0.578	Contact Map
1t6t1	2	0.5108	99.5	0.772	Contact Map
2au3A	1	0.8495	99.1	0.814	Contact Map
4edgA	1	0.8656	98.4	0.856	Contact Map
1dd9A	1	0.8602	97.7	0.878	Contact Map
1nuiA	1	0.543	96.1	0.902	Contact Map
1q57A	3	0.9355	94	0.914	Contact Map
2q2eA	2	0.7957	89.9	0.924	Contact Map
1mw9X	1	0.9194	89.6	0.924	Contact Map
1d3yA	2	0.7849	88.3	0.926	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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