RNZ - SULSO - GREMLIN Contacts

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RNZ - Ribonuclease Z

UniProt:	Q97Z88	Sequences: MIQIFFLGTGAGSPSKKRKLPAFLVRREGVNILLDCGEGTQYTLMNYKLGINSIKIIGISHMHGDHVFGLLGVIASMGLLDRKETLYILGPRKLKDFLYTSFEYSKFNPSFKIEFIDNYNDENITISTFKTCHTIESQGYLIMEKDRVKIDEEKLEKEKIRDWRVIRKLKEGKTVEYNGKLLKPEDYLVIKRGSKVAYTGDTMPCQSVVDSVKGVDILIHDSTFLDEPSAYTYGHSNVTDAAKIALEASVKLLALTHISPRYEDVSEHLKMARRIFPKSILPDDLSYITIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	291 (286)
Sequences:	2364 (1655)
Seq/√Len:	97.9

ECOLI - RBN
BACSU - RNZ YHFI
HALSA - RNZ Q9HPR7
SULSO - RNZ Q981E1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
87_Y	116_I	4.367	1.00
168_K	173_K	3.918	1.00
197_A	215_V	3.453	1.00
95_K	99_Y	3.415	1.00
120_N	145_K	3.282	1.00
96_D	103_E	3.104	1.00
127_S	143_M	3.090	1.00
216_D	251_K	2.688	1.00
214_G	249_S	2.611	1.00
226_D	239_T	2.606	1.00
30_V	55_K	2.575	1.00
132_C	203_M	2.524	1.00
85_T	112_K	2.411	1.00
252_L	280_I	2.395	1.00
87_Y	114_E	2.357	1.00
141_L	195_K	2.329	1.00
195_K	215_V	2.265	1.00
174_T	184_P	2.248	1.00
144_E	194_S	2.232	1.00
239_T	274_R	2.223	1.00
158_E	187_Y	2.217	1.00
224_F	233_Y	2.158	1.00
34_L	142_I	2.099	1.00
39_G	42_Y	2.087	1.00
97_F	101_S	2.073	1.00
125_T	143_M	2.057	1.00
74_I	86_L	2.053	1.00
242_A	275_I	2.005	1.00
143_M	195_K	1.994	1.00
243_K	247_E	1.980	1.00
254_A	282_P	1.968	1.00
182_L	187_Y	1.953	1.00
210_D	213_K	1.930	1.00
24_L	33_L	1.928	1.00
22_A	33_L	1.924	1.00
167_R	171_E	1.904	1.00
269_L	273_R	1.869	1.00
93_K	117_D	1.858	1.00
43_T	46_N	1.852	1.00
4_I	219_I	1.843	1.00
174_T	183_K	1.842	1.00
89_L	116_I	1.836	1.00
283_D	286_S	1.823	1.00
3_Q	26_R	1.809	1.00
58_G	126_I	1.797	1.00
71_L	101_S	1.787	1.00
280_I	286_S	1.784	1.00
254_A	288_I	1.775	1.00
85_T	114_E	1.771	1.00
183_K	186_D	1.770	1.00
220_H	236_S	1.747	1.00
23_F	256_T	1.717	1.00
10_G	15_S	1.707	1.00
154_K	157_K	1.704	1.00
47_Y	285_L	1.702	1.00
203_M	240_D	1.699	1.00
24_L	31_N	1.699	1.00
282_P	286_S	1.671	1.00
177_Y	180_K	1.660	1.00
120_N	125_T	1.647	1.00
56_I	89_L	1.623	1.00
3_Q	287_Y	1.607	1.00
151_D	154_K	1.605	1.00
78_G	110_S	1.591	1.00
197_A	212_V	1.571	1.00
176_E	181_L	1.557	1.00
4_I	25_V	1.551	1.00
213_K	249_S	1.545	1.00
209_V	247_E	1.528	1.00
24_L	49_L	1.525	1.00
222_S	255_L	1.516	1.00
270_K	273_R	1.509	1.00
239_T	275_I	1.502	1.00
3_Q	289_T	1.498	1.00
269_L	281_L	1.492	1.00
22_A	40_T	1.481	1.00
6_F	9_T	1.468	1.00
209_V	244_I	1.457	1.00
54_I	73_V	1.412	1.00
212_V	248_A	1.411	1.00
207_S	210_D	1.405	1.00
19_K	42_Y	1.367	0.99
64_G	68_F	1.364	0.99
129_F	211_S	1.335	0.99
139_G	199_T	1.320	0.99
131_T	139_G	1.313	0.99
25_V	142_I	1.307	0.99
57_I	70_L	1.306	0.99
43_T	285_L	1.297	0.99
172_G	184_P	1.294	0.99
5_F	287_Y	1.293	0.99
184_P	188_L	1.292	0.99
273_R	279_S	1.284	0.99
255_L	272_A	1.269	0.99
32_I	124_I	1.257	0.99
226_D	271_M	1.232	0.99
227_E	271_M	1.228	0.99
150_I	155_L	1.224	0.99
209_V	248_A	1.223	0.99
265_V	281_L	1.221	0.99
95_K	115_F	1.216	0.99
56_I	87_Y	1.213	0.99
238_V	242_A	1.204	0.98
169_L	187_Y	1.202	0.98
21_P	256_T	1.190	0.98
152_E	156_E	1.187	0.98
60_S	140_Y	1.184	0.98
266_S	269_L	1.182	0.98
75_A	107_F	1.176	0.98
280_I	288_I	1.172	0.98
243_K	246_L	1.171	0.98
245_A	253_L	1.169	0.98
88_I	98_L	1.163	0.98
212_V	215_V	1.158	0.98
134_T	234_G	1.157	0.98
34_L	58_G	1.155	0.98
238_V	271_M	1.154	0.98
131_T	199_T	1.153	0.98
225_L	268_H	1.140	0.98
57_I	73_V	1.119	0.97
6_F	282_P	1.115	0.97
237_N	241_A	1.115	0.97
141_L	215_V	1.113	0.97
206_Q	247_E	1.113	0.97
267_E	270_K	1.111	0.97
132_C	234_G	1.107	0.97
160_I	166_I	1.105	0.97
266_S	270_K	1.102	0.97
218_L	250_V	1.090	0.97
176_E	179_G	1.089	0.97
184_P	187_Y	1.061	0.97
228_P	232_T	1.061	0.97
90_G	94_L	1.056	0.96
151_D	189_V	1.047	0.96
95_K	117_D	1.047	0.96
131_T	137_S	1.037	0.96
32_I	142_I	1.037	0.96
141_L	197_A	1.036	0.96
239_T	243_K	1.029	0.96
61_H	66_H	1.022	0.96
252_L	278_K	1.016	0.96
9_T	18_R	1.009	0.95
239_T	271_M	1.007	0.95
19_K	40_T	0.996	0.95
125_T	145_K	0.993	0.95
21_P	198_Y	0.988	0.95
203_M	234_G	0.988	0.95
98_L	115_F	0.977	0.95
231_Y	240_D	0.974	0.94
99_Y	103_E	0.974	0.94
207_S	211_S	0.965	0.94
6_F	23_F	0.962	0.94
41_Q	72_G	0.961	0.94
269_L	279_S	0.956	0.94
88_I	94_L	0.952	0.94
169_L	172_G	0.951	0.94
51_I	54_I	0.948	0.94
204_P	240_D	0.948	0.94
217_I	254_A	0.944	0.93
64_G	223_T	0.942	0.93
146_D	193_G	0.927	0.93
58_G	89_L	0.922	0.93
4_I	217_I	0.917	0.92
199_T	208_V	0.913	0.92
31_N	54_I	0.913	0.92
246_L	275_I	0.906	0.92
204_P	244_I	0.899	0.92
63_H	66_H	0.894	0.91
79_L	82_R	0.890	0.91
130_K	136_E	0.883	0.91
153_E	157_K	0.882	0.91
130_K	138_Q	0.878	0.91
59_I	94_L	0.874	0.91
230_A	237_N	0.872	0.90
168_K	172_G	0.872	0.90
214_G	251_K	0.870	0.90
229_S	233_Y	0.868	0.90
183_K	187_Y	0.867	0.90
208_V	244_I	0.866	0.90
258_I	281_L	0.866	0.90
217_I	252_L	0.865	0.90
174_T	181_L	0.860	0.90
98_L	102_F	0.860	0.90
240_D	243_K	0.857	0.90
215_V	250_V	0.846	0.89
17_K	263_E	0.839	0.89
258_I	265_V	0.838	0.89
61_H	65_D	0.835	0.88
146_D	192_R	0.832	0.88
66_H	201_D	0.832	0.88
270_K	274_R	0.828	0.88
16_K	46_N	0.828	0.88
173_K	184_P	0.822	0.88
10_G	18_R	0.818	0.87
60_S	200_G	0.812	0.87
273_R	278_K	0.808	0.87
106_K	136_E	0.806	0.87
165_V	168_K	0.804	0.86
68_F	75_A	0.803	0.86
70_L	74_I	0.797	0.86
158_E	186_D	0.795	0.86
222_S	238_V	0.795	0.86
226_D	238_V	0.793	0.86
129_F	141_L	0.791	0.86
152_E	166_I	0.787	0.85
154_K	158_E	0.785	0.85
213_K	247_E	0.783	0.85
164_R	168_K	0.782	0.85
118_N	140_Y	0.780	0.85
101_S	105_S	0.776	0.84
25_V	32_I	0.774	0.84
254_A	280_I	0.771	0.84
195_K	216_D	0.771	0.84
55_K	84_E	0.771	0.84
169_L	175_V	0.770	0.84
149_K	189_V	0.766	0.84
154_K	186_D	0.766	0.84
258_I	282_P	0.765	0.84
238_V	272_A	0.764	0.84
51_I	73_V	0.763	0.83
30_V	121_D	0.763	0.83
198_Y	219_I	0.757	0.83
150_I	170_K	0.753	0.83
172_G	175_V	0.751	0.82
165_V	175_V	0.750	0.82
209_V	213_K	0.750	0.82
5_F	47_Y	0.746	0.82
242_A	276_F	0.744	0.82
214_G	250_V	0.737	0.81
33_L	54_I	0.737	0.81
155_L	187_Y	0.736	0.81
67_V	71_L	0.732	0.81
219_I	256_T	0.731	0.81
9_T	282_P	0.731	0.81
222_S	268_H	0.731	0.81
265_V	268_H	0.729	0.81
160_I	169_L	0.727	0.80
283_D	288_I	0.726	0.80
38_E	41_Q	0.725	0.80
33_L	44_L	0.725	0.80
241_A	250_V	0.721	0.80
36_C	40_T	0.721	0.80
200_G	236_S	0.721	0.80
63_H	201_D	0.717	0.79
208_V	212_V	0.715	0.79
44_L	49_L	0.712	0.79
68_F	105_S	0.711	0.79
200_G	220_H	0.710	0.79
44_L	54_I	0.709	0.79
163_W	167_R	0.708	0.79
82_R	111_F	0.708	0.79
99_Y	115_F	0.707	0.79
158_E	182_L	0.705	0.78
19_K	43_T	0.705	0.78
228_P	231_Y	0.705	0.78
68_F	107_F	0.701	0.78
61_H	201_D	0.699	0.78
266_S	283_D	0.698	0.78
97_F	105_S	0.695	0.77
5_F	49_L	0.689	0.77
90_G	93_K	0.689	0.77
177_Y	182_L	0.687	0.77
102_F	107_F	0.687	0.77
92_R	117_D	0.687	0.77
161_R	165_V	0.685	0.76
62_M	94_L	0.684	0.76
25_V	34_L	0.683	0.76
60_S	199_T	0.683	0.76
280_I	283_D	0.682	0.76
10_G	260_P	0.680	0.76
160_I	165_V	0.679	0.76
82_R	86_L	0.678	0.76
153_E	156_E	0.677	0.75
226_D	267_E	0.676	0.75
74_I	111_F	0.676	0.75
129_F	210_D	0.674	0.75
73_V	76_S	0.674	0.75
12_G	20_L	0.673	0.75
174_T	185_E	0.671	0.75
206_Q	209_V	0.666	0.74
133_H	140_Y	0.664	0.74
182_L	186_D	0.663	0.74
276_F	279_S	0.662	0.74
4_I	254_A	0.660	0.74
123_N	145_K	0.659	0.74
11_A	21_P	0.659	0.74
74_I	107_F	0.659	0.74
137_S	140_Y	0.658	0.73
118_N	138_Q	0.656	0.73
137_S	200_G	0.654	0.73
100_T	104_Y	0.649	0.72
229_S	232_T	0.648	0.72
252_L	288_I	0.647	0.72
180_K	186_D	0.645	0.72
67_V	105_S	0.645	0.72
205_C	211_S	0.643	0.72
225_L	238_V	0.642	0.72
59_I	70_L	0.642	0.72
33_L	40_T	0.639	0.71
218_L	244_I	0.637	0.71
30_V	124_I	0.634	0.71
127_S	211_S	0.626	0.70
272_A	276_F	0.626	0.70
176_E	249_S	0.625	0.70
121_D	145_K	0.622	0.69
159_K	163_W	0.622	0.69
36_C	59_I	0.620	0.69
32_I	58_G	0.619	0.69
242_A	245_A	0.619	0.69
106_K	135_I	0.616	0.68
252_L	289_T	0.616	0.68
258_I	284_D	0.615	0.68
26_R	31_N	0.613	0.68
66_H	221_D	0.611	0.68
60_S	198_Y	0.610	0.68
222_S	258_I	0.610	0.68
205_C	212_V	0.608	0.67
77_M	111_F	0.607	0.67
169_L	184_P	0.605	0.67
171_E	192_R	0.605	0.67
172_G	182_L	0.605	0.67
25_V	196_V	0.604	0.67
90_G	117_D	0.604	0.67
59_I	88_I	0.604	0.67
156_E	207_S	0.602	0.67
201_D	257_H	0.601	0.67
256_T	282_P	0.601	0.67
271_M	274_R	0.600	0.66
273_R	280_I	0.599	0.66
12_G	260_P	0.598	0.66
11_A	258_I	0.598	0.66
161_R	166_I	0.597	0.66
174_T	188_L	0.595	0.66
237_N	245_A	0.595	0.66
168_K	175_V	0.592	0.65
17_K	22_A	0.591	0.65
62_M	97_F	0.587	0.65
129_F	139_G	0.586	0.65
242_A	248_A	0.583	0.64
246_L	277_P	0.582	0.64
247_E	275_I	0.581	0.64
128_T	138_Q	0.580	0.64
12_G	223_T	0.579	0.64
26_R	29_G	0.578	0.64
273_R	277_P	0.578	0.64
206_Q	210_D	0.577	0.63
253_L	272_A	0.573	0.63
154_K	187_Y	0.572	0.63
129_F	208_V	0.570	0.63
18_R	284_D	0.570	0.63
139_G	208_V	0.564	0.62
238_V	268_H	0.564	0.62
222_S	282_P	0.564	0.62
35_D	65_D	0.563	0.62
94_L	101_S	0.562	0.61
213_K	248_A	0.562	0.61
66_H	257_H	0.560	0.61
96_D	99_Y	0.558	0.61
204_P	247_E	0.558	0.61
177_Y	181_L	0.558	0.61
11_A	20_L	0.557	0.61
119_Y	124_I	0.556	0.61
264_D	267_E	0.554	0.60
22_A	36_C	0.553	0.60
181_L	231_Y	0.552	0.60
209_V	243_K	0.552	0.60
54_I	57_I	0.552	0.60
91_P	140_Y	0.551	0.60
167_R	175_V	0.551	0.60
200_G	223_T	0.550	0.60
10_G	79_L	0.550	0.60
131_T	208_V	0.549	0.60
204_P	248_A	0.546	0.59
38_E	72_G	0.544	0.59
6_F	254_A	0.544	0.59
208_V	211_S	0.544	0.59
4_I	283_D	0.544	0.59
43_T	47_Y	0.543	0.59
119_Y	164_R	0.542	0.59
202_T	241_A	0.542	0.59
86_L	110_S	0.542	0.59
220_H	244_I	0.541	0.59
143_M	146_D	0.540	0.58
90_G	101_S	0.538	0.58
94_L	98_L	0.537	0.58
131_T	200_G	0.537	0.58
61_H	257_H	0.536	0.58
59_I	62_M	0.536	0.58
9_T	284_D	0.534	0.58
104_Y	107_F	0.534	0.58
70_L	88_I	0.533	0.57
169_L	183_K	0.531	0.57
129_F	140_Y	0.530	0.57
275_I	279_S	0.529	0.57
243_K	275_I	0.529	0.57
121_D	124_I	0.525	0.56
170_K	191_K	0.524	0.56
199_T	220_H	0.524	0.56
259_S	262_Y	0.523	0.56
141_L	212_V	0.523	0.56
197_A	211_S	0.523	0.56
71_L	160_I	0.522	0.56
119_Y	126_I	0.522	0.56
213_K	270_K	0.522	0.56
156_E	161_R	0.521	0.56
227_E	267_E	0.520	0.56
202_T	205_C	0.519	0.55
242_A	272_A	0.517	0.55
123_N	147_R	0.516	0.55
88_I	93_K	0.516	0.55
10_G	16_K	0.515	0.55
222_S	272_A	0.510	0.54
274_R	277_P	0.509	0.54
35_D	61_H	0.508	0.54
158_E	180_K	0.508	0.54
201_D	235_H	0.506	0.54
32_I	56_I	0.504	0.53
203_M	231_Y	0.504	0.53
196_V	215_V	0.504	0.53
44_L	47_Y	0.504	0.53
194_S	272_A	0.503	0.53
245_A	276_F	0.503	0.53
164_R	167_R	0.503	0.53
205_C	208_V	0.502	0.53
212_V	218_L	0.501	0.53
66_H	235_H	0.501	0.53
220_H	241_A	0.501	0.53
205_C	210_D	0.501	0.53
64_G	75_A	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
3zwfA	2	0.7835	100	0.32	Contact Map
2cbnA	2	0.9966	100	0.376	Contact Map
1y44A	2	0.9966	100	0.391	Contact Map
2e7yA	2	0.8729	100	0.537	Contact Map
1zkpA	2	0.8247	100	0.569	Contact Map
3jxpA	2	0.8557	100	0.581	Contact Map
3g1pA	2	0.7766	100	0.595	Contact Map
4ojvA	2	0.8351	100	0.603	Contact Map
3md7A	2	0.7835	100	0.615	Contact Map
3bk2A	2	0.8041	100	0.681	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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