RNPH - BACSU - GREMLIN Contacts

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RNPH - Ribonuclease PH

UniProt:	P28619	Sequences: MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVEDRVPPFLRGGGKGWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDCDVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKEQGILLDLNYEEDSSAEVDMNVIMTGSGRFVELQGTGEEATFSREDLNGLLGLAEKGIQELIDKQKEVLGDSLPELK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	245 (209)
Sequences:	7733 (3604)
Seq/√Len:	249.3

ECOLI - RNPH PNP
BACSU - RNPH PNP
SULSO - RRP41 RRP42

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
194_G	234_K	3.671	1.00
18_L	139_I	3.328	1.00
39_C	132_G	3.213	1.00
15_T	31_T	3.046	1.00
31_T	36_K	2.883	1.00
232_K	235_E	2.742	1.00
41_A	136_A	2.679	1.00
166_I	214_D	2.628	1.00
190_V	222_A	2.574	1.00
157_D	195_S	2.477	1.00
174_L	225_G	2.450	1.00
131_T	229_L	2.405	1.00
157_D	194_G	2.391	1.00
39_C	114_I	2.361	1.00
22_S	34_N	2.359	1.00
211_S	214_D	2.333	1.00
17_D	31_T	2.298	1.00
25_E	68_R	2.194	1.00
225_G	228_E	2.155	1.00
16_F	30_I	2.146	1.00
19_D	139_I	2.145	1.00
134_F	158_F	2.134	1.00
231_D	235_E	2.090	1.00
165_G	176_L	2.018	1.00
177_N	180_E	1.973	1.00
16_F	135_L	1.971	1.00
212_R	216_N	1.961	1.00
194_G	231_D	1.946	1.00
192_M	226_I	1.888	1.00
158_F	234_K	1.854	1.00
172_I	217_G	1.791	1.00
38_I	119_I	1.765	1.00
166_I	185_E	1.742	1.00
37_V	118_V	1.738	1.00
165_G	184_A	1.724	1.00
98_L	133_A	1.707	1.00
21_I	40_N	1.689	1.00
78_S	83_I	1.668	1.00
224_K	228_E	1.664	1.00
69_A	74_T	1.648	1.00
168_K	183_S	1.637	1.00
11_L	174_L	1.610	1.00
57_G	95_G	1.608	1.00
212_R	223_E	1.591	1.00
138_A	237_L	1.547	1.00
160_A	226_I	1.518	1.00
220_G	224_K	1.504	1.00
30_I	128_A	1.501	1.00
16_F	131_T	1.477	1.00
234_K	238_G	1.459	1.00
167_D	173_L	1.458	1.00
106_K	152_T	1.447	1.00
14_I	32_A	1.430	1.00
29_L	36_K	1.422	1.00
172_I	221_L	1.422	1.00
223_E	227_Q	1.413	1.00
228_E	231_D	1.410	1.00
158_F	230_I	1.397	1.00
190_V	219_L	1.384	1.00
166_I	172_I	1.363	1.00
16_F	236_V	1.332	1.00
157_D	193_T	1.300	1.00
97_A	200_E	1.293	1.00
174_L	221_L	1.275	1.00
138_A	155_I	1.272	1.00
227_Q	231_D	1.268	1.00
114_I	133_A	1.249	1.00
16_F	232_K	1.213	1.00
179_E	183_S	1.208	1.00
21_I	24_P	1.206	1.00
214_D	217_G	1.205	1.00
32_A	128_A	1.199	1.00
74_T	77_E	1.186	1.00
98_L	137_M	1.183	1.00
228_E	232_K	1.169	1.00
51_L	56_K	1.165	1.00
122_D	179_E	1.155	1.00
161_A	191_I	1.149	1.00
226_I	230_I	1.144	1.00
28_V	135_L	1.143	1.00
130_I	161_A	1.140	1.00
95_G	99_R	1.136	1.00
213_E	217_G	1.133	1.00
14_I	229_L	1.124	1.00
116_C	129_S	1.119	1.00
74_T	84_S	1.119	1.00
64_S	87_T	1.113	1.00
56_K	105_E	1.112	1.00
230_I	234_K	1.112	1.00
48_P	54_G	1.109	1.00
41_A	114_I	1.102	1.00
25_E	152_T	1.094	1.00
138_A	153_N	1.081	1.00
43_V	110_R	1.074	1.00
216_N	220_G	1.065	1.00
41_A	140_A	1.061	1.00
30_I	132_G	1.041	1.00
163_S	187_D	1.028	1.00
102_V	137_M	1.019	1.00
169_E	185_E	1.008	1.00
172_I	218_L	1.006	1.00
164_V	222_A	0.993	1.00
45_D	110_R	0.985	1.00
71_N	74_T	0.985	1.00
101_V	157_D	0.981	1.00
39_C	133_A	0.980	1.00
84_S	88_M	0.976	1.00
25_E	42_S	0.960	1.00
167_D	183_S	0.958	1.00
167_D	170_Q	0.955	1.00
73_R	76_R	0.951	1.00
192_M	223_E	0.947	1.00
162_I	174_L	0.945	1.00
97_A	191_I	0.945	1.00
18_L	236_V	0.940	1.00
191_I	200_E	0.939	1.00
135_L	236_V	0.926	1.00
134_F	138_A	0.925	1.00
172_I	214_D	0.923	1.00
48_P	53_G	0.919	1.00
127_T	161_A	0.914	1.00
231_D	234_K	0.903	1.00
212_R	220_G	0.900	1.00
64_S	83_I	0.900	1.00
164_V	221_L	0.885	1.00
61_A	94_I	0.883	1.00
24_P	42_S	0.880	1.00
193_T	199_V	0.879	1.00
185_E	208_A	0.874	1.00
44_E	48_P	0.872	1.00
26_G	41_A	0.870	0.99
35_T	123_G	0.869	0.99
134_F	155_I	0.864	0.99
164_V	174_L	0.856	0.99
101_V	193_T	0.855	0.99
77_E	87_T	0.853	0.99
224_K	227_Q	0.853	0.99
232_K	236_V	0.849	0.99
130_I	159_L	0.842	0.99
56_K	104_L	0.839	0.99
33_G	120_Q	0.833	0.99
173_L	180_E	0.832	0.99
84_S	87_T	0.829	0.99
134_F	234_K	0.828	0.99
25_E	43_V	0.828	0.99
67_P	76_R	0.823	0.99
107_L	154_P	0.817	0.99
83_I	88_M	0.814	0.99
63_Y	125_T	0.811	0.99
24_P	40_N	0.805	0.99
18_L	135_L	0.803	0.99
14_I	232_K	0.800	0.99
126_R	163_S	0.799	0.99
135_L	233_Q	0.793	0.99
43_V	106_K	0.789	0.99
101_V	159_L	0.789	0.99
220_G	223_E	0.786	0.99
155_I	158_F	0.783	0.99
14_I	131_T	0.783	0.99
131_T	233_Q	0.782	0.99
12_R	175_D	0.780	0.99
11_L	228_E	0.778	0.99
205_G	208_A	0.774	0.99
26_G	136_A	0.774	0.99
17_D	20_F	0.770	0.99
101_V	134_F	0.770	0.99
10_E	13_P	0.769	0.99
78_S	84_S	0.767	0.99
170_Q	180_E	0.763	0.99
164_V	172_I	0.763	0.99
90_I	124_G	0.762	0.99
164_V	188_M	0.761	0.99
63_Y	129_S	0.760	0.99
77_E	84_S	0.758	0.99
198_F	219_L	0.756	0.99
229_L	233_Q	0.751	0.99
30_I	131_T	0.749	0.98
194_G	230_I	0.747	0.98
103_D	106_K	0.747	0.98
94_I	116_C	0.744	0.98
92_R	99_R	0.743	0.98
37_V	129_S	0.742	0.98
234_K	237_L	0.739	0.98
162_I	225_G	0.736	0.98
20_F	36_K	0.733	0.98
44_E	113_W	0.732	0.98
32_A	127_T	0.731	0.98
131_T	161_A	0.728	0.98
235_E	238_G	0.725	0.98
104_L	107_L	0.717	0.98
19_D	26_G	0.715	0.98
57_G	104_L	0.714	0.98
179_E	182_S	0.711	0.98
164_V	190_V	0.711	0.98
160_A	229_L	0.708	0.98
59_I	102_V	0.706	0.98
186_V	210_F	0.704	0.98
102_V	112_I	0.702	0.98
62_E	115_D	0.702	0.98
221_L	225_G	0.696	0.98
43_V	140_A	0.695	0.98
88_M	91_Q	0.695	0.98
21_I	38_I	0.692	0.97
34_N	122_D	0.689	0.97
126_R	189_N	0.679	0.97
138_A	234_K	0.677	0.97
37_V	128_A	0.677	0.97
181_D	187_D	0.676	0.97
43_V	152_T	0.674	0.97
170_Q	217_G	0.667	0.97
57_G	107_L	0.665	0.97
21_I	28_V	0.655	0.96
131_T	160_A	0.651	0.96
116_C	133_A	0.644	0.96
42_S	113_W	0.642	0.96
29_L	117_D	0.642	0.96
17_D	29_L	0.641	0.96
64_S	115_D	0.638	0.96
28_V	132_G	0.638	0.96
185_E	214_D	0.638	0.96
217_G	220_G	0.637	0.96
92_R	95_G	0.636	0.96
20_F	29_L	0.636	0.96
205_G	209_T	0.634	0.96
32_A	123_G	0.632	0.96
27_S	40_N	0.630	0.96
112_I	137_M	0.630	0.96
31_T	34_N	0.628	0.96
216_N	223_E	0.627	0.96
90_I	126_R	0.626	0.95
75_I	113_W	0.621	0.95
54_G	107_L	0.621	0.95
26_G	139_I	0.621	0.95
46_R	110_R	0.620	0.95
39_C	116_C	0.619	0.95
33_G	123_G	0.616	0.95
193_T	230_I	0.614	0.95
162_I	226_I	0.613	0.95
43_V	108_G	0.611	0.95
86_R	90_I	0.611	0.95
103_D	107_L	0.611	0.95
119_I	125_T	0.611	0.95
114_I	137_M	0.610	0.95
54_G	57_G	0.606	0.95
124_G	181_D	0.602	0.94
188_M	203_G	0.597	0.94
18_L	28_V	0.596	0.94
15_T	29_L	0.596	0.94
186_V	205_G	0.593	0.94
134_F	157_D	0.591	0.94
27_S	38_I	0.590	0.94
34_N	120_Q	0.587	0.94
28_V	139_I	0.587	0.94
210_F	214_D	0.585	0.94
57_G	110_R	0.583	0.93
32_A	131_T	0.583	0.93
53_G	56_K	0.582	0.93
235_E	239_D	0.579	0.93
164_V	218_L	0.579	0.93
45_D	108_G	0.578	0.93
39_C	61_A	0.576	0.93
138_A	158_F	0.574	0.93
24_P	27_S	0.573	0.93
37_V	132_G	0.572	0.93
208_A	214_D	0.567	0.92
163_S	189_N	0.561	0.92
101_V	156_T	0.561	0.92
121_A	178_Y	0.559	0.92
168_K	185_E	0.558	0.92
20_F	40_N	0.558	0.92
70_T	121_A	0.555	0.92
215_L	219_L	0.554	0.92
57_G	112_I	0.552	0.91
127_T	189_N	0.551	0.91
208_A	211_S	0.550	0.91
217_G	221_L	0.549	0.91
44_E	110_R	0.549	0.91
58_W	99_R	0.549	0.91
30_I	37_V	0.548	0.91
35_T	128_A	0.546	0.91
53_G	109_E	0.546	0.91
57_G	92_R	0.545	0.91
118_V	129_S	0.543	0.91
43_V	153_N	0.542	0.91
158_F	194_G	0.537	0.90
32_A	162_I	0.536	0.90
23_H	71_N	0.535	0.90
178_Y	181_D	0.535	0.90
127_T	130_I	0.533	0.90
94_I	130_I	0.531	0.90
175_D	180_E	0.529	0.90
92_R	96_R	0.528	0.90
40_N	117_D	0.525	0.89
227_Q	230_I	0.524	0.89
173_L	177_N	0.524	0.89
177_N	183_S	0.523	0.89
120_Q	123_G	0.521	0.89
23_H	34_N	0.521	0.89
75_I	78_S	0.520	0.89
131_T	135_L	0.519	0.89
44_E	75_I	0.518	0.89
55_G	109_E	0.515	0.88
170_Q	213_E	0.515	0.88
196_G	223_E	0.511	0.88
101_V	155_I	0.511	0.88
124_G	128_A	0.510	0.88
196_G	201_L	0.510	0.88
121_A	125_T	0.509	0.88
74_T	78_S	0.507	0.88
63_Y	87_T	0.505	0.87
119_I	123_G	0.505	0.87
42_S	115_D	0.504	0.87
64_S	74_T	0.503	0.87
64_S	67_P	0.500	0.87

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
1oysA	2	0.8694	100	0.132	Contact Map
1udnA	5	0.9918	100	0.143	Contact Map
3m7nD	1	0.9184	100	0.154	Contact Map
3dd6A	3	0.9878	100	0.156	Contact Map
2je6B	2	0.9061	100	0.16	Contact Map
2wnrB	1	0.8939	100	0.163	Contact Map
1r6lA	3	0.9592	100	0.163	Contact Map
3b4tA	3	0.9714	100	0.165	Contact Map
2nn6B	1	0.9224	100	0.169	Contact Map
2po1A	1	0.9184	100	0.171	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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