RNH3 - BACSU - GREMLIN Contacts

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RNH3 - Ribonuclease HIII

UniProt:	P94541	Sequences: MSHSVIKVSLSAIDQMKMTYSGSLTASVPQGAVFQAKPPGCTITAYQSGKVLFQGKNAAAESARWGTAEPQEKKKTAKKPADPRYAPPADIAGMSVIGSDEVGTGDYFGPMTVVCAYVDKTMLPLMKELGVKDSKDLKDPQIIEIARNLIKTIPYSLLVLKNEKYNSMQEKGMSQGKMKALLHNQAITHLLRKLDGVKPEAILIDQFAEPGVYFNHLKGRDIVKERTYFSTKAEGIHLAVAAASIIARYSFLMEMDKLSRAAGMTLPKGAGPHVDEAAAKLILKKGASALRTFTKLHFANTQKAQRLADKKRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	313 (265)
Sequences:	633 (517)
Seq/√Len:	31.8

ECOLI - RNH2
BACSU - RNH3 RNH2
HALSA - RNH2
SULSO - RNH2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
259_S	267_P	4.256	1.00
258_L	293_F	3.866	1.00
107_Y	301_T	3.680	1.00
102_V	269_G	3.489	1.00
132_K	136_D	3.417	1.00
141_Q	144_E	3.407	1.00
116_A	243_A	3.069	1.00
156_S	193_K	2.846	1.00
233_A	240_V	2.800	1.00
230_S	236_I	2.584	1.00
263_G	285_K	2.563	1.00
104_T	111_M	2.524	1.00
119_D	122_M	2.459	0.99
263_G	280_K	2.324	0.99
157_L	250_S	2.305	0.99
150_I	246_I	2.279	0.99
156_S	189_H	2.247	0.99
230_S	237_H	2.216	0.99
113_V	182_L	2.189	0.99
106_D	268_K	2.143	0.98
145_I	245_I	2.119	0.98
208_A	212_V	2.088	0.98
265_T	276_E	2.062	0.98
299_A	303_K	2.019	0.98
281_L	293_F	2.006	0.98
31_G	47_Q	1.999	0.98
281_L	289_A	1.978	0.97
262_A	281_L	1.973	0.97
99_S	202_I	1.931	0.97
171_K	207_F	1.928	0.97
299_A	302_Q	1.894	0.97
212_V	215_N	1.892	0.97
146_A	245_I	1.887	0.96
36_A	40_G	1.881	0.96
58_A	62_S	1.847	0.96
150_I	155_Y	1.844	0.96
55_G	58_A	1.828	0.96
45_A	51_V	1.818	0.96
46_Y	50_K	1.794	0.95
29_P	32_A	1.767	0.95
118_V	239_A	1.753	0.95
107_Y	294_T	1.747	0.95
158_L	182_L	1.730	0.94
216_H	233_A	1.708	0.94
278_A	304_A	1.705	0.94
53_F	58_A	1.663	0.93
261_A	292_T	1.662	0.93
254_E	257_K	1.650	0.93
207_F	229_F	1.649	0.93
114_V	247_A	1.594	0.91
163_E	292_T	1.589	0.91
61_E	65_W	1.588	0.91
114_V	157_L	1.567	0.91
215_N	218_K	1.558	0.90
262_A	266_L	1.557	0.90
125_L	152_T	1.538	0.90
104_T	176_G	1.527	0.89
132_K	141_Q	1.517	0.89
155_Y	246_I	1.515	0.89
262_A	293_F	1.504	0.89
141_Q	155_Y	1.500	0.89
169_Q	178_M	1.499	0.89
201_A	228_Y	1.460	0.87
264_M	277_A	1.457	0.87
174_S	216_H	1.442	0.87
106_D	274_V	1.440	0.86
273_H	276_E	1.429	0.86
104_T	179_K	1.415	0.85
46_Y	49_G	1.384	0.84
143_I	249_Y	1.353	0.83
142_I	249_Y	1.336	0.82
206_Q	231_T	1.299	0.80
267_P	277_A	1.295	0.80
185_Q	189_H	1.294	0.80
160_L	168_M	1.288	0.80
79_K	145_I	1.284	0.79
32_A	44_T	1.283	0.79
51_V	62_S	1.282	0.79
105_G	135_K	1.259	0.78
33_V	36_A	1.257	0.78
143_I	253_M	1.255	0.78
139_D	256_D	1.235	0.77
140_P	144_E	1.229	0.76
164_K	167_S	1.224	0.76
135_K	205_D	1.213	0.75
107_Y	296_L	1.208	0.75
150_I	253_M	1.204	0.75
85_Y	92_A	1.201	0.74
121_T	124_P	1.190	0.74
100_D	135_K	1.187	0.74
104_T	175_Q	1.181	0.73
100_D	105_G	1.179	0.73
88_P	91_I	1.179	0.73
179_K	183_H	1.175	0.73
96_V	203_L	1.175	0.73
258_L	266_L	1.173	0.73
150_I	249_Y	1.173	0.73
160_L	185_Q	1.171	0.73
43_I	51_V	1.159	0.72
262_A	289_A	1.153	0.71
248_R	295_K	1.147	0.71
37_K	42_T	1.146	0.71
149_L	238_L	1.145	0.71
180_A	207_F	1.140	0.71
112_T	250_S	1.140	0.71
117_Y	218_K	1.136	0.70
279_A	304_A	1.133	0.70
249_Y	253_M	1.130	0.70
105_G	205_D	1.129	0.70
177_K	180_A	1.113	0.69
46_Y	54_Q	1.106	0.68
112_T	157_L	1.098	0.68
209_E	212_V	1.083	0.67
106_D	251_F	1.083	0.67
285_K	289_A	1.082	0.66
43_I	114_V	1.081	0.66
100_D	205_D	1.074	0.66
90_D	94_M	1.060	0.65
296_L	301_T	1.059	0.65
40_G	57_N	1.059	0.65
139_D	270_A	1.055	0.64
50_K	54_Q	1.045	0.64
105_G	134_S	1.007	0.61
281_L	291_R	0.999	0.60
233_A	289_A	0.996	0.60
190_L	215_N	0.991	0.60
165_Y	297_H	0.985	0.59
143_I	147_R	0.985	0.59
137_L	141_Q	0.981	0.59
153_I	238_L	0.965	0.57
37_K	40_G	0.959	0.57
48_S	52_L	0.958	0.57
96_V	237_H	0.958	0.57
175_Q	212_V	0.952	0.56
203_L	237_H	0.950	0.56
173_M	237_H	0.946	0.56
209_E	215_N	0.944	0.56
135_K	244_S	0.942	0.56
264_M	280_K	0.939	0.55
100_D	134_S	0.936	0.55
105_G	244_S	0.934	0.55
142_I	145_I	0.933	0.55
273_H	277_A	0.932	0.55
87_P	91_I	0.928	0.54
210_P	227_T	0.926	0.54
203_L	240_V	0.924	0.54
126_M	149_L	0.921	0.54
100_D	244_S	0.920	0.54
255_M	268_K	0.912	0.53
123_L	129_L	0.910	0.53
87_P	90_D	0.909	0.53
212_V	216_H	0.905	0.53
183_H	207_F	0.902	0.52
32_A	35_Q	0.898	0.52
160_L	182_L	0.897	0.52
169_Q	173_M	0.895	0.52
96_V	230_S	0.894	0.52
38_P	41_C	0.888	0.51
164_K	168_M	0.884	0.51
181_L	184_N	0.881	0.51
111_M	162_N	0.880	0.51
31_G	190_L	0.878	0.50
111_M	179_K	0.878	0.50
147_R	253_M	0.878	0.50
55_G	61_E	0.877	0.50
202_I	227_T	0.877	0.50
80_P	83_P	0.876	0.50
215_N	289_A	0.870	0.50
46_Y	162_N	0.865	0.49
143_I	252_L	0.859	0.49
158_L	186_A	0.859	0.49
89_A	120_K	0.854	0.48
130_G	304_A	0.850	0.48
134_S	205_D	0.850	0.48
97_I	238_L	0.848	0.48
281_L	284_K	0.848	0.48
50_K	53_F	0.845	0.48
57_N	61_E	0.843	0.48
158_L	164_K	0.843	0.48
46_Y	52_L	0.843	0.48
183_H	234_E	0.839	0.47
33_V	47_Q	0.838	0.47
205_D	244_S	0.835	0.47
57_N	265_T	0.833	0.47
97_I	187_I	0.833	0.47
125_L	145_I	0.832	0.47
40_G	43_I	0.831	0.47
203_L	230_S	0.830	0.46
271_G	277_A	0.827	0.46
167_S	284_K	0.819	0.46
158_L	185_Q	0.817	0.45
211_G	215_N	0.815	0.45
141_Q	148_N	0.813	0.45
56_K	70_P	0.813	0.45
125_L	128_E	0.812	0.45
99_S	129_L	0.812	0.45
128_E	145_I	0.808	0.45
281_L	301_T	0.801	0.44
79_K	82_D	0.800	0.44
256_D	259_S	0.795	0.44
38_P	149_L	0.792	0.43
156_S	190_L	0.791	0.43
116_A	153_I	0.787	0.43
42_T	54_Q	0.785	0.43
185_Q	188_T	0.784	0.43
102_V	173_M	0.784	0.43
244_S	247_A	0.781	0.43
190_L	249_Y	0.779	0.42
153_I	157_L	0.779	0.42
96_V	201_A	0.778	0.42
40_G	60_A	0.777	0.42
164_K	185_Q	0.777	0.42
162_N	268_K	0.773	0.42
45_A	48_S	0.772	0.42
137_L	149_L	0.770	0.42
78_K	82_D	0.765	0.41
148_N	151_K	0.761	0.41
122_M	152_T	0.761	0.41
159_V	250_S	0.758	0.41
301_T	304_A	0.758	0.41
167_S	260_R	0.757	0.41
88_P	203_L	0.754	0.40
261_A	293_F	0.752	0.40
234_E	271_G	0.748	0.40
95_S	200_E	0.744	0.40
269_G	290_L	0.744	0.40
91_I	96_V	0.744	0.40
30_Q	189_H	0.744	0.40
102_V	184_N	0.742	0.39
248_R	252_L	0.742	0.39
207_F	270_A	0.740	0.39
165_Y	295_K	0.739	0.39
63_A	66_G	0.739	0.39
33_V	57_N	0.738	0.39
302_Q	305_Q	0.738	0.39
289_A	293_F	0.733	0.39
71_Q	260_R	0.726	0.38
63_A	67_T	0.724	0.38
104_T	251_F	0.720	0.38
43_I	48_S	0.718	0.38
121_T	265_T	0.717	0.38
146_A	246_I	0.717	0.38
61_E	64_R	0.713	0.37
115_C	186_A	0.708	0.37
82_D	86_A	0.707	0.37
268_K	274_V	0.706	0.37
112_T	215_N	0.705	0.37
106_D	248_R	0.704	0.37
113_V	251_F	0.704	0.37
121_T	266_L	0.702	0.36
281_L	290_L	0.699	0.36
99_S	115_C	0.698	0.36
258_L	262_A	0.697	0.36
204_I	228_Y	0.695	0.36
138_K	147_R	0.694	0.36
278_A	300_N	0.693	0.36
78_K	81_A	0.690	0.35
256_D	260_R	0.689	0.35
86_A	92_A	0.689	0.35
248_R	251_F	0.685	0.35
252_L	295_K	0.683	0.35
97_I	115_C	0.683	0.35
264_M	289_A	0.683	0.35
102_V	271_G	0.681	0.35
131_V	174_S	0.681	0.35
234_E	295_K	0.678	0.35
206_Q	229_F	0.678	0.35
174_S	209_E	0.677	0.34
134_S	244_S	0.672	0.34
70_P	74_K	0.671	0.34
173_M	176_G	0.671	0.34
85_Y	210_P	0.671	0.34
53_F	64_R	0.670	0.34
148_N	152_T	0.669	0.34
93_G	201_A	0.665	0.34
256_D	270_A	0.661	0.33
53_F	61_E	0.660	0.33
106_D	255_M	0.659	0.33
151_K	189_H	0.658	0.33
111_M	267_P	0.658	0.33
111_M	233_A	0.655	0.33
85_Y	88_P	0.653	0.33
234_E	248_R	0.649	0.32
40_G	45_A	0.648	0.32
106_D	180_A	0.648	0.32
31_G	52_L	0.647	0.32
251_F	295_K	0.647	0.32
37_K	44_T	0.645	0.32
62_S	72_E	0.642	0.32
135_K	247_A	0.642	0.32
233_A	237_H	0.639	0.32
181_L	189_H	0.637	0.32
71_Q	74_K	0.637	0.32
156_S	250_S	0.637	0.32
166_N	183_H	0.636	0.32
44_T	52_L	0.636	0.32
102_V	214_F	0.634	0.31
105_G	247_A	0.633	0.31
213_Y	220_R	0.632	0.31
88_P	228_Y	0.631	0.31
165_Y	248_R	0.629	0.31
108_F	183_H	0.629	0.31
145_I	148_N	0.628	0.31
178_M	183_H	0.627	0.31
146_A	253_M	0.624	0.31
32_A	45_A	0.622	0.31
59_A	62_S	0.621	0.30
278_A	294_T	0.620	0.30
41_C	138_K	0.616	0.30
183_H	206_Q	0.616	0.30
106_D	173_M	0.616	0.30
40_G	48_S	0.615	0.30
118_V	126_M	0.614	0.30
182_L	251_F	0.612	0.30
38_P	63_A	0.611	0.30
169_Q	206_Q	0.610	0.30
56_K	60_A	0.607	0.30
250_S	254_E	0.607	0.30
81_A	85_Y	0.605	0.29
212_V	273_H	0.604	0.29
32_A	36_A	0.596	0.29
55_G	59_A	0.594	0.29
100_D	247_A	0.594	0.29
205_D	247_A	0.594	0.29
148_N	161_K	0.593	0.29
291_R	294_T	0.593	0.29
275_D	300_N	0.592	0.29
96_V	138_K	0.590	0.28
106_D	295_K	0.590	0.28
102_V	250_S	0.589	0.28
202_I	225_E	0.586	0.28
161_K	254_E	0.582	0.28
45_A	49_G	0.581	0.28
32_A	150_I	0.580	0.28
50_K	267_P	0.579	0.28
179_K	300_N	0.578	0.28
111_M	169_Q	0.577	0.28
102_V	246_I	0.575	0.27
213_Y	217_L	0.575	0.27
180_A	270_A	0.572	0.27
204_I	300_N	0.570	0.27
106_D	162_N	0.570	0.27
203_L	236_I	0.569	0.27
164_K	181_L	0.569	0.27
147_R	252_L	0.567	0.27
250_S	253_M	0.567	0.27
69_E	185_Q	0.566	0.27
31_G	175_Q	0.566	0.27
35_Q	187_I	0.565	0.27
30_Q	264_M	0.564	0.27
124_P	215_N	0.561	0.26
299_A	304_A	0.561	0.26
179_K	206_Q	0.560	0.26
171_K	215_N	0.560	0.26
140_P	260_R	0.560	0.26
204_I	299_A	0.557	0.26
275_D	279_A	0.556	0.26
45_A	69_E	0.554	0.26
156_S	182_L	0.554	0.26
261_A	284_K	0.552	0.26
160_L	268_K	0.551	0.26
82_D	238_L	0.551	0.26
116_A	157_L	0.550	0.26
83_P	86_A	0.549	0.26
176_G	222_I	0.549	0.26
233_A	276_E	0.549	0.26
163_E	291_R	0.549	0.26
142_I	295_K	0.549	0.26
113_V	246_I	0.548	0.26
44_T	132_K	0.547	0.26
91_I	94_M	0.539	0.25
55_G	290_L	0.538	0.25
57_N	272_P	0.536	0.25
166_N	295_K	0.535	0.25
265_T	280_K	0.535	0.25
92_A	299_A	0.534	0.25
186_A	298_F	0.531	0.25
227_T	239_A	0.530	0.25
142_I	252_L	0.528	0.24
65_W	149_L	0.525	0.24
110_P	242_A	0.525	0.24
122_M	125_L	0.522	0.24
97_I	117_Y	0.521	0.24
234_E	251_F	0.521	0.24
37_K	43_I	0.520	0.24
166_N	248_R	0.520	0.24
106_D	289_A	0.513	0.24
237_H	255_M	0.511	0.23
142_I	248_R	0.510	0.23
44_T	65_W	0.510	0.23
67_T	153_I	0.510	0.23
47_Q	73_K	0.507	0.23
190_L	199_P	0.505	0.23
49_G	54_Q	0.504	0.23
262_A	285_K	0.504	0.23
241_A	298_F	0.502	0.23
159_V	254_E	0.501	0.23
102_V	237_H	0.500	0.23

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
2d0bA	1	0.9808	100	0.205	Contact Map
4py5A	1	0.8403	100	0.281	Contact Map
3vn5A	1	0.8115	100	0.329	Contact Map
1ekeA	2	0.6741	100	0.405	Contact Map
1io2A	1	0.6677	100	0.405	Contact Map
1uaxA	1	0.655	100	0.414	Contact Map
1i39A	1	0.6326	100	0.431	Contact Map
3kioA	1	0.7668	100	0.448	Contact Map
2etjA	1	0.6038	100	0.461	Contact Map
3eikA	2	0.2428	54.7	0.959	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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