RNH2 - BACSU - GREMLIN Contacts

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RNH2 - Ribonuclease HII

UniProt:	O31744	Sequences: MNTLTVKDIKDRLQEVKDAQDPFIAQCENDPRKSVQTLVEQWLKKQAKEKALKEQWVNMTSYERLARNKGFRLIAGVDEVGRGPLAGPVVASAVILPEECEILGLTDSKKLSEKKREEYYELIMKEALAVGIGIVEATVIDEINIYEASKMAMVKAIQDLSDTPDYLLVDAMTLPLDTAQASIIKGDAKSVSIAAGACIAKVTRDRMMSAYAETYPMYGFEKNKGYGTKEHLEALAAYGPTELHRKTFAPVQSFR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	255 (197)
Sequences:	2023 (1389)
Seq/√Len:	99.0

ECOLI - RNH2
BACSU - RNH2 RNH3
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
212_A	221_E	5.782	1.00
217_M	238_Y	3.910	1.00
211_Y	243_L	3.288	1.00
130_V	199_I	3.148	1.00
124_M	130_V	2.594	1.00
90_V	134_I	2.572	1.00
166_Y	181_A	2.537	1.00
91_A	152_A	2.455	1.00
120_Y	124_M	2.418	1.00
219_G	230_E	2.416	1.00
168_L	193_I	2.351	1.00
117_E	206_R	2.338	1.00
146_Y	172_M	2.216	1.00
106_T	110_K	2.114	1.00
113_E	209_S	2.059	1.00
115_K	118_E	2.038	1.00
139_V	151_M	2.036	1.00
131_G	159_D	1.956	1.00
233_E	237_A	1.903	1.00
71_F	165_D	1.857	1.00
235_L	240_P	1.855	1.00
135_V	155_K	1.767	1.00
124_M	199_I	1.758	1.00
143_I	151_M	1.739	1.00
141_D	247_T	1.721	1.00
105_L	198_C	1.718	1.00
122_L	126_E	1.709	1.00
222_K	230_E	1.704	1.00
62_Y	189_K	1.667	1.00
120_Y	206_R	1.657	1.00
60_T	191_V	1.654	1.00
67_R	98_E	1.652	1.00
66_A	166_Y	1.625	1.00
121_E	206_R	1.617	1.00
73_L	165_D	1.615	1.00
120_Y	203_T	1.584	1.00
86_A	220_F	1.584	1.00
212_A	217_M	1.574	1.00
120_Y	202_V	1.563	1.00
139_V	155_K	1.556	1.00
229_K	233_E	1.545	1.00
219_G	234_A	1.543	1.00
93_A	160_L	1.534	1.00
75_A	93_A	1.519	1.00
106_T	188_A	1.499	1.00
136_E	139_V	1.490	1.00
129_A	161_S	1.485	1.00
217_M	234_A	1.460	1.00
123_I	127_A	1.438	1.00
140_I	145_I	1.434	1.00
134_I	203_T	1.414	1.00
85_L	232_L	1.409	1.00
147_E	150_K	1.398	1.00
138_T	246_K	1.362	0.99
210_A	213_E	1.349	0.99
71_F	166_Y	1.338	0.99
186_G	193_I	1.338	0.99
219_G	223_N	1.334	0.99
77_V	167_L	1.315	0.99
134_I	207_M	1.289	0.99
207_M	211_Y	1.287	0.99
219_G	222_K	1.270	0.99
77_V	149_S	1.266	0.99
75_A	95_I	1.261	0.99
80_V	223_N	1.249	0.99
86_A	208_M	1.245	0.99
59_M	194_A	1.243	0.99
89_V	145_I	1.214	0.99
113_E	117_E	1.210	0.99
220_F	223_N	1.205	0.99
249_A	252_Q	1.196	0.98
139_V	143_I	1.192	0.98
111_L	198_C	1.190	0.98
160_L	164_P	1.188	0.98
172_M	182_S	1.186	0.98
183_I	189_K	1.170	0.98
185_K	188_A	1.144	0.98
132_I	203_T	1.141	0.98
110_K	188_A	1.128	0.98
223_N	234_A	1.127	0.98
105_L	191_V	1.126	0.98
235_L	251_V	1.122	0.98
72_R	165_D	1.102	0.97
151_M	155_K	1.093	0.97
117_E	202_V	1.093	0.97
233_E	236_A	1.087	0.97
232_L	236_A	1.086	0.97
154_V	176_L	1.074	0.97
154_V	158_Q	1.074	0.97
128_L	162_D	1.063	0.97
80_V	199_I	1.054	0.97
240_P	246_K	1.042	0.96
90_V	203_T	1.042	0.96
92_S	132_I	1.042	0.96
144_N	149_S	1.034	0.96
135_V	151_M	1.033	0.96
209_S	224_K	1.026	0.96
93_A	156_A	1.025	0.96
166_Y	179_A	1.024	0.96
185_K	189_K	1.011	0.96
91_A	149_S	1.009	0.96
105_L	194_A	1.006	0.95
67_R	74_I	0.999	0.95
105_L	195_A	0.997	0.95
102_I	105_L	0.975	0.95
144_N	147_E	0.974	0.95
167_L	178_T	0.965	0.94
100_C	126_E	0.960	0.94
61_S	65_L	0.958	0.94
139_V	142_E	0.957	0.94
104_G	115_K	0.941	0.94
137_A	243_L	0.939	0.93
227_G	232_L	0.926	0.93
119_Y	198_C	0.923	0.93
183_I	193_I	0.918	0.93
80_V	120_Y	0.918	0.93
66_A	181_A	0.917	0.93
62_Y	183_I	0.914	0.93
72_R	98_E	0.907	0.92
133_G	152_A	0.903	0.92
97_P	100_C	0.899	0.92
60_T	64_R	0.895	0.92
114_K	118_E	0.885	0.91
80_V	224_K	0.878	0.91
135_V	152_A	0.876	0.91
75_A	164_P	0.876	0.91
112_S	115_K	0.874	0.91
215_Y	242_E	0.873	0.91
220_F	243_L	0.872	0.91
121_E	124_M	0.870	0.91
65_L	181_A	0.868	0.90
135_V	139_V	0.864	0.90
203_T	207_M	0.864	0.90
150_K	175_P	0.863	0.90
171_A	182_S	0.861	0.90
167_L	180_Q	0.861	0.90
129_A	162_D	0.860	0.90
91_A	135_V	0.858	0.90
157_I	167_L	0.838	0.89
113_E	224_K	0.833	0.89
150_K	172_M	0.833	0.89
232_L	250_P	0.827	0.88
118_E	122_L	0.820	0.88
56_W	59_M	0.818	0.88
96_L	105_L	0.818	0.88
138_T	142_E	0.817	0.88
77_V	153_M	0.815	0.87
111_L	119_Y	0.815	0.87
77_V	169_V	0.815	0.87
223_N	228_T	0.815	0.87
56_W	191_V	0.807	0.87
167_L	176_L	0.806	0.87
57_V	64_R	0.803	0.87
85_L	227_G	0.802	0.87
174_L	180_Q	0.797	0.86
95_I	160_L	0.797	0.86
91_A	131_G	0.792	0.86
173_T	180_Q	0.791	0.86
91_A	133_G	0.789	0.86
215_Y	243_L	0.787	0.86
86_A	243_L	0.783	0.85
137_A	141_D	0.778	0.85
86_A	244_H	0.771	0.84
210_A	214_T	0.767	0.84
202_V	206_R	0.766	0.84
75_A	160_L	0.760	0.84
94_V	123_I	0.758	0.83
132_I	199_I	0.758	0.83
143_I	147_E	0.757	0.83
146_Y	173_T	0.757	0.83
212_A	224_K	0.755	0.83
133_G	156_A	0.751	0.83
119_Y	123_I	0.747	0.83
80_V	202_V	0.745	0.82
222_K	228_T	0.743	0.82
235_L	241_T	0.741	0.82
89_V	144_N	0.739	0.82
146_Y	171_A	0.734	0.81
150_K	171_A	0.732	0.81
157_I	176_L	0.725	0.81
94_V	130_V	0.725	0.81
151_M	154_V	0.725	0.81
120_Y	130_V	0.715	0.80
89_V	149_S	0.715	0.80
183_I	186_G	0.714	0.80
111_L	115_K	0.709	0.79
64_R	67_R	0.706	0.79
220_F	241_T	0.699	0.78
223_N	230_E	0.698	0.78
209_S	213_E	0.698	0.78
80_V	134_I	0.697	0.78
75_A	157_I	0.696	0.78
121_E	125_K	0.695	0.78
208_M	220_F	0.694	0.78
80_V	203_T	0.694	0.78
63_E	70_G	0.687	0.77
190_S	194_A	0.682	0.76
102_I	119_Y	0.682	0.76
203_T	206_R	0.680	0.76
230_E	234_A	0.679	0.76
95_I	164_P	0.677	0.76
58_N	61_S	0.675	0.76
92_S	130_V	0.672	0.75
171_A	184_I	0.672	0.75
131_G	160_L	0.666	0.75
184_I	193_I	0.660	0.74
56_W	60_T	0.659	0.74
229_K	232_L	0.659	0.74
146_Y	149_S	0.658	0.74
138_T	242_E	0.658	0.74
215_Y	241_T	0.657	0.74
94_V	127_A	0.656	0.74
214_T	243_L	0.646	0.72
124_M	203_T	0.644	0.72
65_L	69_K	0.644	0.72
150_K	174_L	0.643	0.72
89_V	146_Y	0.639	0.72
96_L	127_A	0.636	0.71
217_M	241_T	0.634	0.71
198_C	243_L	0.631	0.71
117_E	120_Y	0.631	0.71
80_V	234_A	0.627	0.70
168_L	186_G	0.624	0.70
169_V	182_S	0.623	0.70
65_L	68_N	0.619	0.69
137_A	241_T	0.618	0.69
94_V	199_I	0.614	0.69
122_L	125_K	0.609	0.68
223_N	241_T	0.604	0.67
84_P	140_I	0.602	0.67
133_G	155_K	0.599	0.67
73_L	162_D	0.594	0.66
71_F	74_I	0.593	0.66
110_K	185_K	0.590	0.66
95_I	129_A	0.589	0.65
93_A	153_M	0.588	0.65
169_V	181_A	0.582	0.65
80_V	92_S	0.581	0.64
101_E	191_V	0.580	0.64
223_N	235_L	0.578	0.64
155_K	159_D	0.578	0.64
247_T	250_P	0.576	0.64
85_L	250_P	0.575	0.64
155_K	158_Q	0.567	0.63
230_E	233_E	0.567	0.63
136_E	142_E	0.566	0.62
102_I	122_L	0.565	0.62
135_V	143_I	0.565	0.62
224_K	241_T	0.564	0.62
102_I	126_E	0.562	0.62
169_V	180_Q	0.561	0.62
97_P	128_L	0.561	0.62
221_E	224_K	0.561	0.62
131_G	156_A	0.559	0.61
212_A	238_Y	0.557	0.61
235_L	250_P	0.556	0.61
127_A	130_V	0.556	0.61
89_V	156_A	0.554	0.61
214_T	242_E	0.553	0.61
229_K	236_A	0.552	0.60
146_Y	150_K	0.552	0.60
89_V	133_G	0.552	0.60
136_E	243_L	0.550	0.60
96_L	195_A	0.550	0.60
85_L	145_I	0.548	0.60
63_E	190_S	0.548	0.60
154_V	169_V	0.546	0.60
158_Q	177_D	0.545	0.60
154_V	174_L	0.543	0.59
95_I	128_L	0.541	0.59
123_I	199_I	0.540	0.59
227_G	244_H	0.540	0.59
152_A	156_A	0.537	0.58
171_A	183_I	0.533	0.58
73_L	163_T	0.533	0.58
84_P	146_Y	0.531	0.58
106_T	119_Y	0.529	0.57
84_P	144_N	0.524	0.57
231_H	244_H	0.518	0.56
174_L	182_S	0.518	0.56
214_T	217_M	0.516	0.55
115_K	119_Y	0.509	0.54
137_A	223_N	0.508	0.54
146_Y	248_F	0.507	0.54
59_M	110_K	0.507	0.54
56_W	103_L	0.506	0.54
167_L	174_L	0.506	0.54
97_P	101_E	0.505	0.54
246_K	251_V	0.505	0.54
85_L	140_I	0.504	0.54
124_M	206_R	0.503	0.54
163_T	178_T	0.501	0.53
60_T	105_L	0.501	0.53
217_M	221_E	0.501	0.53
205_D	226_Y	0.501	0.53
223_N	244_H	0.500	0.53

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
2etjA	1	0.7137	100	0.248	Contact Map
1uaxA	1	0.7059	100	0.329	Contact Map
1i39A	1	0.6902	100	0.332	Contact Map
1io2A	1	0.7059	100	0.334	Contact Map
1ekeA	2	0.702	100	0.34	Contact Map
3kioA	1	0.8118	100	0.347	Contact Map
2d0bA	1	0.9647	100	0.373	Contact Map
3vn5A	1	0.9294	100	0.393	Contact Map
4py5A	1	0.9333	100	0.395	Contact Map
3gocA	2	0.7176	51.2	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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