RIHB - ECOLI - GREMLIN Contacts

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RIHB - Pyrimidine-specific ribonucleoside hydrolase RihB

UniProt:	P33022	Sequences: MEKRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLNVCQKLEINVPVYAGMPQPIMRQQIVADNIHGETGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAYGTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIARMERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEECVRGYIKTH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12030
Length:	313 (302)
Sequences:	4007 (2889)
Seq/√Len:	166.2

ECOLI - RIHB RIHC RIHA
SULSO - Q97WH6 Q97ZS5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
102_T	110_D	3.908	1.00
106_K	136_M	3.709	1.00
175_R	179_T	3.277	1.00
254_K	292_T	2.993	1.00
135_R	176_V	2.983	1.00
5_K	30_D	2.914	1.00
167_I	273_T	2.619	1.00
67_M	132_V	2.582	1.00
33_G	107_Y	2.578	1.00
113_M	137_Q	2.488	1.00
194_Q	292_T	2.454	1.00
257_E	288_K	2.348	1.00
175_R	261_E	2.309	1.00
36_I	47_L	2.278	1.00
249_N	297_W	2.240	1.00
110_D	114_A	2.221	1.00
134_M	141_L	2.219	1.00
122_V	244_I	2.179	1.00
113_M	143_K	2.176	1.00
8_L	124_V	2.141	1.00
4_R	146_E	2.125	1.00
20_I	34_I	2.118	1.00
113_M	139_A	2.115	1.00
23_A	244_I	2.092	1.00
35_T	104_A	2.073	1.00
5_K	32_L	2.029	1.00
118_D	145_R	2.007	1.00
167_I	174_A	1.984	1.00
109_I	137_Q	1.945	1.00
12_P	50_G	1.944	1.00
51_L	63_V	1.943	1.00
162_S	272_R	1.941	1.00
123_P	130_I	1.939	1.00
255_T	290_G	1.923	1.00
192_T	239_H	1.849	1.00
294_D	297_W	1.828	1.00
123_P	149_L	1.805	1.00
112_L	119_I	1.786	1.00
64_Y	100_E	1.743	1.00
32_L	119_I	1.742	1.00
64_Y	107_Y	1.728	1.00
21_M	57_L	1.700	1.00
73_R	270_Y	1.674	1.00
48_I	52_N	1.670	1.00
7_I	35_T	1.665	1.00
146_E	185_V	1.659	1.00
133_A	137_Q	1.649	1.00
24_A	31_L	1.640	1.00
43_L	65_A	1.634	1.00
238_V	241_A	1.624	1.00
6_I	122_V	1.618	1.00
263_D	269_C	1.611	1.00
9_D	129_N	1.608	1.00
107_Y	111_T	1.608	1.00
109_I	140_I	1.591	1.00
206_E	217_S	1.587	1.00
4_R	145_R	1.562	1.00
26_H	305_C	1.554	1.00
10_C	124_V	1.536	1.00
109_I	133_A	1.533	1.00
120_T	148_V	1.531	1.00
127_L	177_V	1.516	1.00
103_H	106_K	1.513	1.00
123_P	127_L	1.509	1.00
300_G	304_E	1.494	1.00
51_L	98_Q	1.493	1.00
149_L	186_M	1.482	1.00
187_M	290_G	1.475	1.00
149_L	167_I	1.470	1.00
214_E	218_D	1.465	1.00
246_Y	253_I	1.451	1.00
149_L	178_F	1.448	1.00
133_A	140_I	1.441	1.00
137_Q	140_I	1.427	1.00
111_T	114_A	1.423	1.00
252_G	297_W	1.402	1.00
296_D	300_G	1.376	1.00
112_L	143_K	1.367	1.00
44_D	65_A	1.361	1.00
172_E	270_Y	1.356	1.00
112_L	133_A	1.355	1.00
185_V	288_K	1.353	1.00
130_I	147_I	1.346	1.00
43_L	47_L	1.336	1.00
103_H	136_M	1.331	1.00
167_I	178_F	1.325	1.00
5_K	115_S	1.324	1.00
204_R	300_G	1.323	1.00
120_T	146_E	1.316	1.00
22_M	301_L	1.298	1.00
83_G	86_G	1.295	1.00
106_K	110_D	1.283	1.00
8_L	31_L	1.280	1.00
4_R	120_T	1.265	1.00
108_I	133_A	1.263	1.00
263_D	267_G	1.261	1.00
47_L	65_A	1.257	1.00
266_S	269_C	1.251	1.00
48_I	94_P	1.250	1.00
115_S	118_D	1.249	1.00
54_C	61_V	1.242	1.00
245_G	298_F	1.238	1.00
245_G	301_L	1.236	1.00
255_T	288_K	1.234	1.00
127_L	149_L	1.234	1.00
263_D	266_S	1.228	1.00
111_T	119_I	1.224	1.00
204_R	303_E	1.209	1.00
10_C	50_G	1.200	1.00
24_A	61_V	1.195	1.00
73_R	172_E	1.191	1.00
256_Q	291_I	1.189	1.00
178_F	186_M	1.187	1.00
122_V	247_L	1.183	1.00
26_H	248_I	1.178	1.00
55_Q	97_R	1.171	1.00
242_T	253_I	1.168	1.00
242_T	293_I	1.167	1.00
116_D	143_K	1.166	1.00
121_L	144_I	1.165	1.00
185_V	255_T	1.140	1.00
8_L	23_A	1.137	1.00
112_L	144_I	1.135	1.00
105_V	136_M	1.133	1.00
56_K	215_L	1.133	1.00
36_I	50_G	1.132	1.00
201_V	299_W	1.127	1.00
28_A	305_C	1.121	1.00
71_I	131_A	1.121	1.00
7_I	33_G	1.119	1.00
175_R	264_V	1.108	1.00
31_L	124_V	1.098	1.00
69_Q	135_R	1.097	1.00
105_V	133_A	1.094	1.00
258_M	289_V	1.082	1.00
258_M	275_C	1.082	1.00
112_L	140_I	1.079	1.00
196_V	235_G	1.076	1.00
260_V	287_T	1.075	1.00
108_I	112_L	1.071	0.99
185_V	246_Y	1.061	0.99
54_C	58_E	1.059	0.99
108_I	140_I	1.058	0.99
263_D	268_P	1.056	0.99
160_T	163_A	1.053	0.99
148_V	246_Y	1.046	0.99
54_C	63_V	1.045	0.99
209_G	214_E	1.044	0.99
142_P	145_R	1.042	0.99
269_C	274_V	1.034	0.99
42_T	45_K	1.032	0.99
203_A	207_R	1.031	0.99
22_M	305_C	1.029	0.99
32_L	111_T	1.027	0.99
84_E	89_G	1.024	0.99
85_T	88_D	1.023	0.99
195_T	293_I	1.021	0.99
151_G	167_I	1.019	0.99
147_I	182_V	1.019	0.99
72_M	172_E	1.019	0.99
41_Q	45_K	1.018	0.99
82_H	86_G	1.017	0.99
148_V	247_L	1.003	0.99
225_K	229_E	0.995	0.99
8_L	20_I	0.995	0.99
199_P	203_A	0.984	0.99
123_P	147_I	0.981	0.99
24_A	58_E	0.979	0.99
85_T	91_V	0.978	0.99
121_L	130_I	0.977	0.99
122_V	243_C	0.976	0.99
109_I	113_M	0.975	0.99
7_I	108_I	0.968	0.99
154_Y	188_G	0.967	0.99
261_E	268_P	0.966	0.99
178_F	184_L	0.964	0.99
34_I	54_C	0.962	0.99
132_V	135_R	0.961	0.99
24_A	54_C	0.957	0.99
81_I	226_T	0.957	0.99
147_I	184_L	0.956	0.99
146_E	183_P	0.955	0.99
144_I	182_V	0.946	0.99
108_I	130_I	0.946	0.99
58_E	61_V	0.945	0.99
269_C	272_R	0.944	0.99
251_D	297_W	0.942	0.99
18_I	302_V	0.940	0.99
139_A	142_P	0.939	0.99
134_M	180_S	0.939	0.99
47_L	99_A	0.936	0.99
210_G	213_G	0.934	0.99
55_Q	95_L	0.933	0.99
201_V	303_E	0.931	0.99
249_N	301_L	0.923	0.99
246_Y	255_T	0.923	0.99
187_M	246_Y	0.922	0.98
14_H	223_T	0.918	0.98
38_A	169_A	0.913	0.98
198_T	201_V	0.913	0.98
112_L	115_S	0.911	0.98
163_A	168_F	0.909	0.98
17_A	53_V	0.905	0.98
109_I	136_M	0.903	0.98
23_A	122_V	0.899	0.98
179_T	261_E	0.897	0.98
6_I	29_I	0.897	0.98
150_M	192_T	0.893	0.98
35_T	108_I	0.893	0.98
23_A	29_I	0.889	0.98
55_Q	96_T	0.885	0.98
67_M	128_S	0.884	0.98
259_Y	283_K	0.884	0.98
7_I	107_Y	0.883	0.98
126_P	169_A	0.883	0.98
80_N	159_F	0.882	0.98
206_E	221_N	0.882	0.98
5_K	118_D	0.882	0.98
64_Y	102_T	0.882	0.98
243_C	247_L	0.880	0.98
71_I	132_V	0.873	0.98
208_A	213_G	0.873	0.98
44_D	68_P	0.872	0.98
35_T	129_N	0.871	0.98
300_G	303_E	0.860	0.98
149_L	184_L	0.857	0.98
171_P	270_Y	0.855	0.98
183_P	288_K	0.855	0.98
7_I	119_I	0.854	0.98
33_G	111_T	0.854	0.98
262_V	273_T	0.850	0.97
41_Q	46_T	0.847	0.97
195_T	298_F	0.840	0.97
120_T	145_R	0.840	0.97
118_D	143_K	0.838	0.97
165_F	169_A	0.831	0.97
12_P	46_T	0.830	0.97
55_Q	59_I	0.829	0.97
154_Y	186_M	0.818	0.97
259_Y	286_N	0.816	0.97
257_E	286_N	0.812	0.97
245_G	252_G	0.811	0.97
65_A	99_A	0.808	0.97
160_T	168_F	0.806	0.96
297_W	301_L	0.802	0.96
186_M	289_V	0.799	0.96
18_I	216_F	0.794	0.96
209_G	213_G	0.792	0.96
72_M	176_V	0.789	0.96
127_L	174_A	0.788	0.96
228_F	234_A	0.788	0.96
67_M	103_H	0.788	0.96
43_L	46_T	0.788	0.96
260_V	273_T	0.788	0.96
36_I	46_T	0.785	0.96
116_D	119_I	0.782	0.96
244_I	247_L	0.779	0.96
24_A	57_L	0.778	0.96
32_L	115_S	0.777	0.96
189_L	239_H	0.768	0.95
76_I	168_F	0.767	0.95
105_V	132_V	0.766	0.95
78_A	81_I	0.766	0.95
34_I	50_G	0.765	0.95
172_E	264_V	0.762	0.95
178_F	273_T	0.755	0.95
243_C	246_Y	0.755	0.95
148_V	243_C	0.754	0.95
13_G	17_A	0.753	0.95
134_M	144_I	0.750	0.95
164_E	189_L	0.750	0.95
29_I	248_I	0.747	0.95
21_M	216_F	0.746	0.95
150_M	240_D	0.745	0.95
115_S	119_I	0.742	0.94
85_T	89_G	0.742	0.94
112_L	137_Q	0.742	0.94
157_G	163_A	0.739	0.94
14_H	88_D	0.739	0.94
22_M	245_G	0.736	0.94
196_V	237_P	0.736	0.94
47_L	51_L	0.734	0.94
71_I	173_A	0.733	0.94
45_K	48_I	0.731	0.94
172_E	266_S	0.731	0.94
121_L	147_I	0.728	0.94
253_I	290_G	0.726	0.94
127_L	167_I	0.726	0.94
188_G	191_L	0.722	0.94
7_I	111_T	0.721	0.94
97_R	100_E	0.715	0.93
9_D	35_T	0.714	0.93
249_N	252_G	0.711	0.93
57_L	212_A	0.710	0.93
40_N	49_N	0.708	0.93
105_V	109_I	0.700	0.93
187_M	243_C	0.699	0.92
77_V	169_A	0.697	0.92
112_L	141_L	0.696	0.92
295_T	299_W	0.694	0.92
146_E	246_Y	0.689	0.92
51_L	99_A	0.685	0.92
20_I	23_A	0.684	0.92
82_H	88_D	0.679	0.91
16_D	240_D	0.678	0.91
211_P	214_E	0.678	0.91
21_M	53_V	0.675	0.91
146_E	288_K	0.674	0.91
215_L	219_I	0.673	0.91
186_M	273_T	0.673	0.91
31_L	34_I	0.670	0.91
301_L	305_C	0.669	0.91
51_L	97_R	0.668	0.91
35_T	107_Y	0.666	0.91
117_G	145_R	0.664	0.90
71_I	176_V	0.663	0.90
71_I	135_R	0.662	0.90
242_T	298_F	0.662	0.90
191_L	293_I	0.662	0.90
158_N	189_L	0.660	0.90
259_Y	285_A	0.657	0.90
36_I	129_N	0.655	0.90
252_G	301_L	0.654	0.90
37_V	125_G	0.651	0.90
54_C	59_I	0.649	0.89
153_A	190_D	0.648	0.89
153_A	156_T	0.647	0.89
19_A	244_I	0.646	0.89
53_V	215_L	0.645	0.89
154_Y	291_I	0.644	0.89
15_D	240_D	0.639	0.89
148_V	187_M	0.637	0.89
114_A	117_G	0.635	0.88
120_T	247_L	0.633	0.88
106_K	109_I	0.632	0.88
107_Y	110_D	0.622	0.87
141_L	144_I	0.622	0.87
83_G	88_D	0.619	0.87
254_K	294_D	0.619	0.87
134_M	182_V	0.618	0.87
146_E	250_P	0.617	0.87
43_L	68_P	0.617	0.87
140_I	143_K	0.615	0.87
25_K	305_C	0.614	0.87
112_L	116_D	0.613	0.87
187_M	255_T	0.613	0.87
104_A	129_N	0.610	0.86
117_G	143_K	0.609	0.86
301_L	304_E	0.609	0.86
174_A	177_V	0.607	0.86
158_N	164_E	0.606	0.86
85_T	90_P	0.605	0.86
102_T	106_K	0.605	0.86
69_Q	74_Q	0.602	0.86
115_S	143_K	0.602	0.86
52_N	56_K	0.601	0.86
140_I	144_I	0.600	0.85
246_Y	290_G	0.600	0.85
268_P	274_V	0.599	0.85
216_F	219_I	0.598	0.85
258_M	291_I	0.597	0.85
113_M	140_I	0.592	0.85
65_A	68_P	0.590	0.84
176_V	179_T	0.590	0.84
111_T	115_S	0.588	0.84
83_G	89_G	0.588	0.84
124_V	149_L	0.586	0.84
217_S	221_N	0.585	0.84
91_V	94_P	0.584	0.84
159_F	168_F	0.584	0.84
13_G	239_H	0.581	0.84
6_I	23_A	0.579	0.83
200_D	203_A	0.576	0.83
201_V	204_R	0.576	0.83
57_L	216_F	0.575	0.83
150_M	239_H	0.575	0.83
49_N	83_G	0.574	0.83
5_K	117_G	0.574	0.83
141_L	181_G	0.573	0.83
33_G	64_Y	0.572	0.83
206_E	214_E	0.569	0.82
276_D	279_G	0.565	0.82
256_Q	277_E	0.565	0.82
155_G	190_D	0.564	0.82
20_I	24_A	0.563	0.82
226_T	230_N	0.561	0.81
189_L	192_T	0.561	0.81
137_Q	143_K	0.559	0.81
78_A	82_H	0.557	0.81
282_G	285_A	0.555	0.81
42_T	77_V	0.554	0.81
86_G	89_G	0.554	0.81
141_L	182_V	0.553	0.81
38_A	165_F	0.553	0.81
109_I	112_L	0.552	0.80
259_Y	281_L	0.551	0.80
124_V	243_C	0.551	0.80
133_A	136_M	0.551	0.80
72_M	135_R	0.550	0.80
37_V	129_N	0.550	0.80
154_Y	275_C	0.548	0.80
202_I	221_N	0.546	0.80
151_G	174_A	0.545	0.80
130_I	144_I	0.544	0.79
11_D	15_D	0.542	0.79
71_I	128_S	0.542	0.79
102_T	114_A	0.539	0.79
260_V	289_V	0.538	0.79
201_V	205_M	0.538	0.79
26_H	301_L	0.538	0.79
29_I	247_L	0.538	0.79
22_M	244_I	0.537	0.79
18_I	220_M	0.537	0.79
36_I	65_A	0.534	0.78
195_T	242_T	0.533	0.78
49_N	86_G	0.532	0.78
206_E	218_D	0.532	0.78
127_L	130_I	0.531	0.78
75_Q	169_A	0.531	0.78
204_R	207_R	0.530	0.78
154_Y	260_V	0.529	0.78
221_N	225_K	0.529	0.78
205_M	213_G	0.528	0.77
154_Y	190_D	0.527	0.77
103_H	132_V	0.527	0.77
17_A	49_N	0.527	0.77
4_R	28_A	0.525	0.77
134_M	140_I	0.524	0.77
174_A	262_V	0.523	0.77
173_A	177_V	0.522	0.77
80_N	89_G	0.522	0.77
264_V	270_Y	0.519	0.76
128_S	170_D	0.519	0.76
186_M	287_T	0.519	0.76
131_A	176_V	0.517	0.76
148_V	185_V	0.517	0.76
40_N	82_H	0.516	0.76
52_N	95_L	0.515	0.76
297_W	300_G	0.515	0.76
92_F	95_L	0.514	0.76
105_V	112_L	0.512	0.75
8_L	12_P	0.511	0.75
257_E	284_P	0.511	0.75
39_G	49_N	0.510	0.75
216_F	306_V	0.510	0.75
9_D	123_P	0.510	0.75
72_M	175_R	0.506	0.74
102_T	107_Y	0.506	0.74
150_M	158_N	0.503	0.74
193_N	239_H	0.503	0.74
266_S	270_Y	0.502	0.74
161_P	281_L	0.502	0.74
255_T	291_I	0.500	0.74

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
1q8fA	4	0.984	100	0.041	Contact Map
4wr2A	4	0.9585	100	0.049	Contact Map
2masA	3	0.9904	100	0.063	Contact Map
4kpoA	2	0.9808	100	0.068	Contact Map
4kpnA	2	0.9808	100	0.069	Contact Map
3t8jA	3	0.9776	100	0.076	Contact Map
3fz0A	3	0.9681	100	0.092	Contact Map
3t8iA	3	0.9681	100	0.095	Contact Map
4i71A	2	0.9489	100	0.137	Contact Map
3epwA	2	0.9617	100	0.14	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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