RIHA - ECOLI - GREMLIN Contacts

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RIHA - Pyrimidine-specific ribonucleoside hydrolase RihA

UniProt:	P41409	Sequences: MALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLRMLTLLNRTDIPVAGGAVKPLMRELIIADNVHGESGLDGPALPEPTFAPQNCTAVELMAKTLRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTPAAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNPVSTIVAELLDFFLEYHKDEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGKYTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12701
Length:	311 (304)
Sequences:	4007 (2918)
Seq/√Len:	167.3

ECOLI - RIHA RIHB RIHC
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_C	110_K	3.807	1.00
106_E	136_S	3.730	1.00
255_T	293_D	3.315	1.00
175_E	179_Q	3.204	1.00
135_N	176_I	2.971	1.00
4_P	29_D	2.825	1.00
167_I	274_T	2.785	1.00
32_A	107_L	2.571	1.00
67_A	132_L	2.431	1.00
113_R	137_H	2.403	1.00
194_K	293_D	2.399	1.00
175_E	262_G	2.398	1.00
258_E	289_T	2.331	1.00
35_S	46_L	2.315	1.00
134_L	141_H	2.277	1.00
250_K	298_G	2.275	1.00
3_L	146_R	2.231	1.00
22_A	245_I	2.162	1.00
34_T	104_A	2.134	1.00
113_R	143_K	2.123	1.00
122_V	245_I	2.117	1.00
11_P	49_V	2.110	1.00
110_K	114_E	2.105	1.00
7_L	124_T	2.082	1.00
167_I	174_A	2.052	1.00
4_P	31_K	2.047	1.00
192_T	240_H	2.044	1.00
19_I	33_I	2.039	1.00
113_R	139_E	2.027	1.00
256_S	291_M	1.997	1.00
118_P	145_A	1.970	1.00
123_S	130_V	1.967	1.00
109_A	137_H	1.907	1.00
50_L	63_V	1.905	1.00
162_A	273_M	1.896	1.00
295_D	298_G	1.869	1.00
123_S	149_I	1.864	1.00
64_A	107_L	1.832	1.00
20_V	56_L	1.824	1.00
146_R	185_V	1.788	1.00
8_D	129_N	1.777	1.00
6_L	34_T	1.765	1.00
31_K	119_V	1.742	1.00
133_L	137_H	1.737	1.00
112_L	119_V	1.734	1.00
239_L	242_P	1.732	1.00
264_E	270_T	1.663	1.00
47_R	51_R	1.649	1.00
123_S	127_Q	1.631	1.00
9_C	124_T	1.625	1.00
214_T	218_E	1.613	1.00
42_P	65_G	1.612	1.00
23_L	30_V	1.606	1.00
120_T	148_V	1.602	1.00
64_A	100_Q	1.587	1.00
3_L	145_A	1.587	1.00
73_R	271_Q	1.580	1.00
112_L	143_K	1.572	1.00
127_Q	177_V	1.548	1.00
247_W	254_F	1.544	1.00
301_D	305_D	1.532	1.00
109_A	133_L	1.522	1.00
25_S	306_R	1.518	1.00
107_L	111_T	1.518	1.00
187_A	291_M	1.504	1.00
153_A	156_L	1.504	1.00
50_L	98_A	1.499	1.00
253_L	298_G	1.498	1.00
5_I	122_V	1.467	1.00
133_L	140_L	1.458	1.00
149_I	186_M	1.458	1.00
149_I	167_I	1.455	1.00
149_I	178_F	1.453	1.00
43_E	65_G	1.427	1.00
172_E	271_Q	1.427	1.00
108_M	133_L	1.426	1.00
297_Q	301_D	1.424	1.00
111_T	114_E	1.408	1.00
103_T	136_S	1.406	1.00
54_T	97_F	1.404	1.00
42_P	46_L	1.397	1.00
112_L	133_L	1.393	1.00
109_A	140_L	1.376	1.00
137_H	140_L	1.373	1.00
103_T	106_E	1.366	1.00
185_V	289_T	1.349	1.00
111_T	119_V	1.347	1.00
206_R	217_A	1.343	1.00
204_R	301_D	1.309	1.00
130_V	147_I	1.292	1.00
73_R	172_E	1.284	1.00
3_L	120_T	1.280	1.00
4_P	115_S	1.276	1.00
246_A	299_F	1.275	1.00
106_E	110_K	1.270	1.00
9_C	49_V	1.252	1.00
246_A	302_L	1.249	1.00
21_L	302_L	1.240	1.00
167_I	178_F	1.239	1.00
122_V	248_L	1.238	1.00
127_Q	149_I	1.231	1.00
47_R	94_E	1.222	1.00
116_A	143_K	1.219	1.00
120_T	146_R	1.219	1.00
178_F	186_M	1.206	1.00
6_L	32_A	1.202	1.00
112_L	140_L	1.202	1.00
121_I	144_I	1.201	1.00
46_L	65_G	1.196	1.00
147_I	182_I	1.190	1.00
175_E	265_T	1.189	1.00
257_V	292_V	1.189	1.00
115_S	118_P	1.187	1.00
71_L	131_A	1.184	1.00
243_C	254_F	1.172	1.00
151_G	167_I	1.171	1.00
83_G	86_G	1.161	1.00
35_S	49_V	1.159	1.00
270_T	273_M	1.159	1.00
23_L	61_I	1.150	1.00
146_R	183_P	1.148	1.00
85_S	91_A	1.146	1.00
148_V	248_L	1.144	1.00
53_L	61_I	1.142	1.00
256_S	289_T	1.138	1.00
7_L	30_V	1.131	1.00
185_V	247_W	1.127	1.00
25_S	249_L	1.127	1.00
264_E	267_G	1.122	1.00
243_C	294_V	1.121	1.00
54_T	95_P	1.120	1.00
148_V	247_W	1.120	1.00
69_K	135_N	1.118	1.00
7_L	22_A	1.116	1.00
27_E	306_R	1.112	1.00
204_R	304_A	1.111	1.00
40_Q	44_K	1.111	1.00
259_R	290_V	1.109	1.00
55_L	215_I	1.107	1.00
201_D	300_V	1.093	1.00
261_V	288_A	1.083	1.00
196_Q	236_G	1.079	1.00
105_V	133_L	1.075	1.00
203_E	207_A	1.068	1.00
112_L	144_I	1.066	0.99
23_L	58_R	1.066	0.99
144_I	182_I	1.060	0.99
264_E	268_K	1.057	0.99
53_L	63_V	1.054	0.99
7_L	19_I	1.054	0.99
108_M	140_L	1.051	0.99
72_M	172_E	1.047	0.99
41_T	44_K	1.042	0.99
31_K	111_T	1.041	0.99
17_I	303_L	1.040	0.99
85_S	88_D	1.034	0.99
259_R	276_V	1.029	0.99
160_T	163_A	1.028	0.99
185_V	256_S	1.028	0.99
154_M	188_G	1.026	0.99
108_M	130_V	1.021	0.99
84_E	89_G	1.017	0.99
262_G	269_Y	1.016	0.99
112_L	115_S	1.012	0.99
209_G	214_T	1.007	0.99
267_G	270_T	1.007	0.99
122_V	244_T	1.006	0.99
264_E	269_Y	1.002	0.99
33_I	53_L	1.000	0.99
270_T	275_V	0.998	0.99
108_M	112_L	0.993	0.99
30_V	124_T	0.985	0.99
126_P	169_V	0.982	0.99
54_T	96_T	0.980	0.99
139_E	142_S	0.974	0.99
260_W	284_N	0.973	0.99
105_V	136_S	0.972	0.99
123_S	147_I	0.966	0.99
244_T	248_L	0.962	0.99
142_S	145_A	0.959	0.99
132_L	135_N	0.958	0.99
82_H	86_G	0.953	0.99
13_H	223_F	0.941	0.99
11_P	45_T	0.941	0.99
201_D	304_A	0.936	0.99
199_V	203_E	0.934	0.99
198_H	201_D	0.931	0.99
195_A	294_V	0.930	0.99
97_F	100_Q	0.928	0.99
4_P	118_P	0.924	0.99
64_A	102_C	0.923	0.99
150_M	192_T	0.920	0.99
109_A	113_R	0.919	0.98
250_K	302_L	0.916	0.98
21_L	306_R	0.915	0.98
6_L	107_L	0.908	0.98
121_I	130_V	0.905	0.98
16_A	52_M	0.904	0.98
5_I	28_L	0.904	0.98
179_Q	262_G	0.902	0.98
149_I	184_V	0.901	0.98
31_K	115_S	0.900	0.98
40_Q	45_T	0.896	0.98
32_A	111_T	0.893	0.98
206_R	221_D	0.888	0.98
247_W	256_S	0.887	0.98
81_V	226_Y	0.887	0.98
23_L	53_L	0.886	0.98
171_P	271_Q	0.884	0.98
246_A	253_L	0.880	0.98
34_T	129_N	0.878	0.98
46_L	99_P	0.878	0.98
187_A	247_W	0.876	0.98
37_A	169_V	0.875	0.98
252_E	298_G	0.872	0.98
43_E	68_V	0.872	0.98
42_P	45_T	0.867	0.98
186_M	290_V	0.865	0.98
6_L	108_M	0.863	0.98
120_T	145_A	0.862	0.98
163_A	168_Y	0.855	0.98
109_A	136_S	0.855	0.98
147_I	184_V	0.852	0.98
134_L	180_S	0.852	0.98
116_A	119_V	0.851	0.98
67_A	128_T	0.847	0.97
20_V	216_V	0.845	0.97
85_S	89_G	0.845	0.97
65_G	99_P	0.839	0.97
178_F	184_V	0.838	0.97
183_P	289_T	0.837	0.97
263_V	274_T	0.835	0.97
164_E	189_L	0.833	0.97
260_W	287_N	0.831	0.97
34_T	108_M	0.829	0.97
225_E	229_D	0.826	0.97
148_V	244_T	0.824	0.97
54_T	59_T	0.813	0.97
23_L	56_L	0.810	0.97
80_N	159_W	0.810	0.97
78_A	81_V	0.809	0.97
118_P	143_K	0.807	0.97
71_L	173_A	0.807	0.97
71_L	132_L	0.806	0.97
6_L	119_V	0.800	0.96
301_D	304_A	0.798	0.96
254_F	291_M	0.793	0.96
188_G	191_V	0.792	0.96
189_L	240_H	0.791	0.96
76_I	168_Y	0.787	0.96
165_F	169_V	0.786	0.96
35_S	45_T	0.782	0.96
105_V	132_L	0.781	0.96
154_M	186_M	0.776	0.96
21_L	246_A	0.773	0.96
33_I	49_V	0.772	0.96
127_Q	174_A	0.769	0.95
250_K	253_L	0.761	0.95
195_A	299_F	0.759	0.95
17_I	216_V	0.759	0.95
22_A	28_L	0.757	0.95
13_H	88_D	0.752	0.95
39_N	48_N	0.751	0.95
50_L	97_F	0.749	0.95
298_G	302_L	0.748	0.95
71_L	135_N	0.748	0.95
258_E	287_N	0.747	0.95
157_G	163_A	0.747	0.95
56_L	212_V	0.744	0.95
28_L	249_L	0.744	0.95
260_W	286_P	0.743	0.95
245_I	248_L	0.742	0.95
8_D	34_T	0.741	0.94
112_L	141_H	0.740	0.94
72_M	176_I	0.740	0.94
150_M	241_D	0.739	0.94
47_R	95_P	0.739	0.94
187_A	244_T	0.737	0.94
160_T	168_Y	0.737	0.94
46_L	50_L	0.732	0.94
178_F	274_T	0.731	0.94
244_T	247_W	0.729	0.94
18_A	245_I	0.727	0.94
58_R	61_I	0.724	0.94
156_L	193_H	0.723	0.94
44_K	47_R	0.720	0.94
52_M	215_I	0.720	0.94
67_A	103_T	0.716	0.93
211_P	214_T	0.714	0.93
19_I	22_A	0.713	0.93
115_S	119_V	0.713	0.93
134_L	144_I	0.711	0.93
115_S	143_K	0.711	0.93
172_E	265_T	0.710	0.93
112_L	137_H	0.708	0.93
6_L	111_T	0.706	0.93
261_V	274_T	0.706	0.93
35_S	129_N	0.704	0.93
15_D	241_D	0.702	0.93
186_M	274_T	0.702	0.93
20_V	52_M	0.700	0.93
5_I	22_A	0.696	0.92
209_G	213_S	0.696	0.92
22_A	122_V	0.694	0.92
112_L	116_A	0.694	0.92
215_I	219_L	0.691	0.92
71_L	176_I	0.688	0.92
121_I	147_I	0.687	0.92
12_G	16_A	0.684	0.92
53_L	58_R	0.683	0.92
124_T	244_T	0.682	0.92
154_M	292_V	0.677	0.91
296_R	300_V	0.676	0.91
127_Q	167_I	0.674	0.91
117_E	143_K	0.671	0.91
114_E	117_E	0.671	0.91
117_E	145_A	0.670	0.91
36_S	125_G	0.668	0.91
14_D	241_D	0.667	0.91
34_T	107_L	0.664	0.91
253_L	302_L	0.660	0.90
206_R	214_T	0.658	0.90
120_T	248_L	0.652	0.90
41_T	77_I	0.651	0.90
247_W	291_M	0.648	0.90
302_L	306_R	0.646	0.89
243_C	299_F	0.642	0.89
146_R	251_P	0.641	0.89
105_V	109_A	0.640	0.89
146_R	289_T	0.637	0.89
32_A	64_A	0.634	0.89
141_H	181_G	0.633	0.88
69_K	74_E	0.632	0.88
155_G	190_D	0.629	0.88
210_N	213_S	0.629	0.88
191_V	294_V	0.626	0.88
158_N	189_L	0.625	0.88
302_L	305_D	0.625	0.88
153_A	157_G	0.625	0.88
19_I	23_L	0.623	0.88
134_L	182_I	0.621	0.87
4_P	117_E	0.620	0.87
140_L	143_K	0.619	0.87
107_L	110_K	0.616	0.87
196_Q	238_P	0.615	0.87
153_A	190_D	0.614	0.87
17_I	220_L	0.613	0.87
37_A	165_F	0.609	0.86
216_V	219_L	0.609	0.86
255_T	292_V	0.607	0.86
85_S	90_P	0.607	0.86
148_V	187_A	0.606	0.86
30_V	33_I	0.605	0.86
146_R	247_W	0.604	0.86
111_T	115_S	0.604	0.86
36_S	129_N	0.603	0.86
141_H	144_I	0.602	0.86
141_H	182_I	0.599	0.86
208_I	213_S	0.599	0.86
176_I	179_Q	0.595	0.85
201_D	204_R	0.593	0.85
35_S	65_G	0.592	0.85
50_L	99_P	0.592	0.85
42_P	68_V	0.590	0.85
227_H	237_A	0.589	0.85
187_A	256_S	0.589	0.85
137_H	143_K	0.589	0.85
172_E	266_Q	0.584	0.84
105_V	112_L	0.583	0.84
127_Q	130_V	0.583	0.84
133_L	136_S	0.581	0.84
174_A	177_V	0.581	0.84
257_V	278_Y	0.579	0.84
49_V	53_L	0.578	0.83
150_M	240_H	0.575	0.83
204_R	207_A	0.574	0.83
200_E	203_E	0.570	0.83
128_T	170_D	0.569	0.83
51_R	55_L	0.568	0.82
38_G	126_P	0.566	0.82
259_R	292_V	0.566	0.82
98_A	101_N	0.564	0.82
28_L	248_L	0.564	0.82
159_W	168_Y	0.561	0.82
71_L	128_T	0.561	0.82
197_I	237_A	0.560	0.82
53_L	59_T	0.559	0.81
217_A	221_D	0.559	0.81
56_L	216_V	0.558	0.81
267_G	271_Q	0.558	0.81
151_G	174_A	0.557	0.81
104_A	129_N	0.557	0.81
154_M	276_V	0.556	0.81
202_T	221_D	0.555	0.81
72_M	175_E	0.554	0.81
256_S	292_V	0.554	0.81
81_V	89_G	0.553	0.81
106_E	109_A	0.551	0.81
142_S	146_R	0.551	0.81
186_M	288_A	0.551	0.81
102_C	106_E	0.549	0.80
75_L	169_V	0.549	0.80
148_V	185_V	0.549	0.80
228_K	235_V	0.549	0.80
77_I	80_N	0.548	0.80
124_T	149_I	0.547	0.80
12_G	240_H	0.546	0.80
24_A	306_R	0.546	0.80
201_D	205_F	0.544	0.80
224_L	237_A	0.541	0.79
140_L	144_I	0.540	0.79
269_Y	275_V	0.540	0.79
206_R	218_E	0.539	0.79
197_I	220_L	0.537	0.79
201_D	296_R	0.536	0.79
154_M	190_D	0.535	0.79
205_F	213_S	0.534	0.78
90_P	218_E	0.534	0.78
134_L	176_I	0.534	0.78
191_V	194_K	0.533	0.78
51_R	85_S	0.532	0.78
72_M	135_N	0.529	0.78
132_L	136_S	0.528	0.78
59_T	97_F	0.528	0.78
70_P	73_R	0.526	0.77
47_R	50_L	0.525	0.77
28_L	122_V	0.525	0.77
25_S	302_L	0.523	0.77
158_N	163_A	0.522	0.77
221_D	225_E	0.521	0.77
21_L	245_I	0.520	0.77
65_G	68_V	0.518	0.76
86_G	89_G	0.518	0.76
59_T	62_P	0.516	0.76
153_A	164_E	0.515	0.76
11_P	48_N	0.515	0.76
102_C	114_E	0.514	0.76
108_M	121_I	0.514	0.76
134_L	140_L	0.514	0.76
38_G	48_N	0.514	0.76
260_W	282_T	0.513	0.76
216_V	307_L	0.513	0.76
51_R	95_P	0.511	0.75
150_M	158_N	0.510	0.75
80_N	89_G	0.510	0.75
193_H	276_V	0.508	0.75
104_A	108_M	0.507	0.75
18_A	124_T	0.505	0.75
261_V	290_V	0.505	0.75
10_D	14_D	0.505	0.75
154_M	261_V	0.505	0.75
195_A	243_C	0.503	0.74
265_T	271_Q	0.501	0.74
173_A	177_V	0.501	0.74
158_N	164_E	0.500	0.74
109_A	112_L	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
4wr2A	4	0.9678	100	0.044	Contact Map
2masA	3	0.9936	100	0.061	Contact Map
1q8fA	4	0.9904	100	0.062	Contact Map
4kpoA	2	0.9904	100	0.07	Contact Map
4kpnA	2	0.9904	100	0.071	Contact Map
3t8jA	3	0.9839	100	0.084	Contact Map
3t8iA	3	0.9775	100	0.098	Contact Map
3fz0A	3	0.9743	100	0.103	Contact Map
4i71A	2	0.955	100	0.135	Contact Map
3epwA	2	0.9711	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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