RNH2 - HALSA - GREMLIN Contacts

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RNH2 - Ribonuclease HII

UniProt:	Q9HNR3	Sequences: MARFGVDEAGKGPVLGSMFAAAVAGDPAAVPDGVADSKRLSADRRAELDDRVRASMRVGVAEVPVDRIDDPETDMNTLTVAAQADALGRVVADGMAGYVDAGDVNEQRFGRRVANRVAADVAVTAEHGADDEYDLVAAASIVAKVARDAHVDALAAAFDADIGSGYPSDSTTREFLAAYVREHGELPECARASWQTSRDALGAAEQSALDEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	212 (178)
Sequences:	4948 (3344)
Seq/√Len:	250.7

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
155_A	161_D	4.732	1.00
160_A	179_Y	3.287	1.00
96_A	124_T	2.836	1.00
35_A	131_D	2.710	1.00
49_D	53_R	2.634	1.00
154_L	189_C	2.466	1.00
58_V	142_V	2.448	1.00
69_D	193_S	2.396	1.00
59_G	89_R	2.359	1.00
19_F	62_E	2.348	1.00
35_A	39_R	2.321	1.00
174_E	178_A	2.311	1.00
46_A	149_A	2.222	1.00
44_R	47_E	2.118	1.00
129_A	136_V	2.065	1.00
53_R	58_V	2.024	1.00
20_A	82_A	2.006	1.00
195_Q	199_D	1.915	1.00
42_A	152_D	1.784	1.00
162_I	170_S	1.766	1.00
62_E	150_H	1.765	1.00
49_D	149_A	1.760	1.00
126_E	132_E	1.734	1.00
49_D	145_V	1.729	1.00
22_A	86_A	1.652	1.00
49_D	146_A	1.651	1.00
128_G	131_D	1.613	1.00
39_R	131_D	1.597	1.00
42_A	164_S	1.588	1.00
67_R	81_A	1.575	1.00
170_S	175_F	1.575	1.00
76_N	102_G	1.560	1.00
71_P	81_A	1.542	1.00
63_V	85_D	1.540	1.00
77_T	80_V	1.495	1.00
26_D	29_A	1.457	1.00
60_V	146_A	1.421	1.00
98_Y	136_V	1.413	1.00
96_A	122_A	1.411	1.00
67_R	85_D	1.400	1.00
81_A	85_D	1.394	1.00
76_N	103_D	1.374	1.00
62_E	146_A	1.371	1.00
42_A	46_A	1.366	1.00
169_D	174_E	1.349	1.00
4_F	24_A	1.333	1.00
155_A	160_A	1.331	1.00
84_A	88_G	1.321	1.00
34_V	137_A	1.311	1.00
104_V	123_V	1.310	1.00
153_A	156_A	1.282	1.00
17_S	62_E	1.275	1.00
46_A	145_V	1.274	1.00
64_P	67_R	1.267	1.00
4_F	22_A	1.266	1.00
19_F	146_A	1.255	1.00
163_G	175_F	1.254	1.00
20_A	79_T	1.238	1.00
68_I	75_M	1.235	1.00
104_V	125_A	1.224	1.00
61_A	86_A	1.221	1.00
17_S	150_H	1.219	1.00
174_E	177_A	1.215	1.00
14_V	167_P	1.198	1.00
150_H	154_L	1.194	1.00
57_R	91_V	1.193	1.00
67_R	71_P	1.191	1.00
63_V	82_A	1.170	1.00
67_R	70_D	1.166	1.00
186_L	192_A	1.160	1.00
34_V	141_I	1.160	1.00
176_L	186_L	1.149	1.00
47_E	51_R	1.135	1.00
97_G	121_V	1.130	1.00
33_G	44_R	1.129	1.00
41_S	44_R	1.124	1.00
87_L	97_G	1.118	1.00
40_L	141_I	1.114	1.00
6_V	79_T	1.110	1.00
157_A	189_C	1.101	1.00
6_V	87_L	1.097	1.00
152_D	156_A	1.089	1.00
15_L	151_V	1.079	1.00
84_A	116_R	1.065	1.00
50_D	53_R	1.059	1.00
40_L	44_R	1.058	1.00
163_G	168_S	1.056	1.00
102_G	125_A	1.037	1.00
150_H	153_A	1.037	1.00
6_V	97_G	1.031	1.00
152_D	164_S	1.027	1.00
98_Y	133_Y	1.026	1.00
15_L	189_C	1.025	1.00
158_F	189_C	1.013	1.00
133_Y	137_A	1.012	1.00
126_E	133_Y	1.000	1.00
9_A	145_V	0.995	1.00
21_A	60_V	0.990	1.00
50_D	149_A	0.984	1.00
40_L	48_L	0.979	1.00
195_Q	198_R	0.969	1.00
34_V	138_A	0.967	1.00
11_K	79_T	0.967	1.00
74_D	77_T	0.957	1.00
90_V	94_G	0.949	1.00
80_V	102_G	0.943	1.00
160_A	175_F	0.937	1.00
61_A	82_A	0.936	1.00
46_A	152_D	0.932	1.00
53_R	146_A	0.932	1.00
53_R	142_V	0.931	1.00
186_L	200_A	0.930	1.00
126_E	136_V	0.930	1.00
128_G	132_E	0.925	1.00
51_R	54_A	0.924	1.00
19_F	150_H	0.923	1.00
22_A	90_V	0.920	1.00
63_V	81_A	0.919	1.00
4_F	94_G	0.913	1.00
50_D	54_A	0.912	1.00
146_A	150_H	0.912	1.00
63_V	67_R	0.901	1.00
4_F	87_L	0.896	1.00
18_M	75_M	0.893	1.00
71_P	77_T	0.887	1.00
146_A	149_A	0.887	1.00
65_V	69_D	0.887	1.00
80_V	103_D	0.881	1.00
52_V	55_S	0.874	1.00
4_F	97_G	0.868	0.99
34_V	134_D	0.865	0.99
74_D	79_T	0.843	0.99
66_D	70_D	0.839	0.99
177_A	199_D	0.830	0.99
145_V	149_A	0.823	0.99
101_A	127_H	0.817	0.99
163_G	170_S	0.814	0.99
61_A	85_D	0.806	0.99
24_A	57_R	0.802	0.99
6_V	99_V	0.797	0.99
76_N	80_V	0.796	0.99
197_S	200_A	0.792	0.99
14_V	197_S	0.791	0.99
164_S	168_S	0.790	0.99
20_A	61_A	0.788	0.99
126_E	129_A	0.784	0.99
162_I	168_S	0.783	0.99
60_V	142_V	0.781	0.99
81_A	84_A	0.778	0.99
9_A	49_D	0.775	0.99
9_A	164_S	0.772	0.99
25_G	34_V	0.770	0.99
17_S	64_P	0.767	0.99
6_V	83_Q	0.767	0.99
170_S	174_E	0.760	0.99
66_D	188_E	0.760	0.99
59_G	86_A	0.759	0.99
134_D	137_A	0.758	0.99
44_R	48_L	0.758	0.99
176_L	197_S	0.743	0.98
65_V	189_C	0.742	0.98
186_L	196_T	0.740	0.98
23_V	138_A	0.740	0.98
56_M	92_A	0.722	0.98
15_L	190_A	0.716	0.98
177_A	200_A	0.715	0.98
80_V	105_N	0.709	0.98
149_A	153_A	0.707	0.98
69_D	192_A	0.706	0.98
4_F	90_V	0.705	0.98
185_E	188_E	0.704	0.98
48_L	141_I	0.704	0.98
79_T	83_Q	0.699	0.98
76_N	79_T	0.695	0.98
47_E	50_D	0.693	0.98
24_A	90_V	0.691	0.97
9_A	20_A	0.690	0.97
14_V	196_T	0.688	0.97
25_G	134_D	0.687	0.97
161_D	171_T	0.687	0.97
84_A	104_V	0.685	0.97
103_D	123_V	0.685	0.97
57_R	92_A	0.681	0.97
33_G	48_L	0.678	0.97
43_D	47_E	0.677	0.97
15_L	187_P	0.677	0.97
61_A	89_R	0.677	0.97
66_D	192_A	0.673	0.97
26_D	30_V	0.671	0.97
176_L	196_T	0.671	0.97
24_A	94_G	0.670	0.97
101_A	125_A	0.670	0.97
130_D	137_A	0.664	0.97
48_L	51_R	0.664	0.97
163_G	167_P	0.661	0.97
17_S	65_V	0.660	0.97
80_V	84_A	0.658	0.97
9_A	142_V	0.655	0.97
105_N	123_V	0.648	0.96
4_F	95_M	0.646	0.96
97_G	123_V	0.641	0.96
48_L	52_V	0.639	0.96
186_L	197_S	0.635	0.96
74_D	78_L	0.635	0.96
49_D	142_V	0.632	0.96
59_G	90_V	0.631	0.96
163_G	189_C	0.630	0.96
98_Y	135_L	0.630	0.96
18_M	79_T	0.628	0.96
117_V	121_V	0.626	0.96
23_V	52_V	0.626	0.96
168_S	194_W	0.625	0.96
187_P	190_A	0.620	0.95
175_F	179_Y	0.618	0.95
158_F	188_E	0.617	0.95
29_A	32_D	0.614	0.95
149_A	152_D	0.607	0.95
102_G	127_H	0.604	0.95
157_A	188_E	0.603	0.95
127_H	136_V	0.602	0.95
25_G	138_A	0.599	0.94
91_V	94_G	0.598	0.94
79_T	167_P	0.597	0.94
49_D	60_V	0.595	0.94
35_A	137_A	0.590	0.94
80_V	104_V	0.590	0.94
20_A	59_G	0.580	0.93
71_P	78_L	0.578	0.93
25_G	29_A	0.577	0.93
158_F	187_P	0.574	0.93
6_V	22_A	0.571	0.93
88_G	117_V	0.567	0.93
4_F	57_R	0.565	0.92
23_V	139_A	0.564	0.92
25_G	135_L	0.561	0.92
161_D	164_S	0.557	0.92
176_L	200_A	0.556	0.92
151_V	155_A	0.550	0.91
86_A	90_V	0.544	0.91
39_R	128_G	0.543	0.91
20_A	63_V	0.542	0.91
46_A	49_D	0.540	0.91
163_G	166_Y	0.538	0.91
75_M	78_L	0.538	0.91
148_D	166_Y	0.537	0.90
142_V	146_A	0.536	0.90
99_V	125_A	0.536	0.90
98_Y	126_E	0.535	0.90
9_A	21_A	0.535	0.90
153_A	157_A	0.534	0.90
103_D	125_A	0.533	0.90
20_A	86_A	0.532	0.90
87_L	117_V	0.528	0.90
80_V	125_A	0.528	0.90
124_T	133_Y	0.527	0.90
14_V	194_W	0.526	0.90
83_Q	99_V	0.523	0.89
175_F	178_A	0.520	0.89
52_V	142_V	0.516	0.89
117_V	123_V	0.515	0.89
27_P	30_V	0.508	0.88
25_G	55_S	0.508	0.88
26_D	56_M	0.507	0.88
185_E	190_A	0.506	0.88
25_G	56_M	0.501	0.87
14_V	176_L	0.501	0.87
53_R	92_A	0.500	0.87

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
1uaxA	1	0.9623	100	0.129	Contact Map
1io2A	1	0.9717	100	0.138	Contact Map
1ekeA	2	0.9717	100	0.141	Contact Map
1i39A	1	0.9198	100	0.174	Contact Map
3kioA	1	0.9387	100	0.209	Contact Map
2etjA	1	0.8302	100	0.213	Contact Map
4py5A	1	0.8679	100	0.217	Contact Map
2d0bA	1	0.9623	100	0.229	Contact Map
3vn5A	1	0.8349	100	0.28	Contact Map
1c8bA	3	0.3915	37.7	0.947	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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