RNH2 - SULSO - GREMLIN Contacts

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RNH2 - Ribonuclease HII

UniProt:	Q97W56	Sequences: MRVGIDEAGRGALIGPMIVAGVVISDTKLKFLKGIGVKDSKQLTRERREKLFDIVANTVEAFTVVKVFPYEIDNYNLNDLTYDAVSKIILSLSSFNPEIVTVDKVGDEKPVIELINKLGYKSNVVHKADVLFVEASAASIIAKVIRDNYIDELKQVYGDFGSGYPADPRTIKWLKSFYEKNPNPPPIIRRSWKILRSTAPLYYISKEGRRLW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	212 (181)
Sequences:	4954 (3304)
Seq/√Len:	245.6

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
154_K	163_G	4.814	1.00
159_D	182_P	3.477	1.00
99_I	123_N	2.618	1.00
38_K	130_V	2.552	1.00
153_L	187_I	2.501	1.00
52_F	56_A	2.470	1.00
62_F	141_I	2.449	1.00
161_G	172_K	2.318	1.00
73_D	191_S	2.299	1.00
18_I	66_K	2.266	1.00
38_K	42_Q	2.254	1.00
63_T	91_S	2.215	1.00
128_A	135_A	2.165	1.00
49_E	148_N	2.067	1.00
19_V	84_A	2.055	1.00
47_R	50_K	2.052	1.00
56_A	62_F	1.925	1.00
162_S	165_P	1.903	1.00
193_K	197_S	1.891	1.00
175_K	181_N	1.891	1.00
54_I	58_T	1.791	1.00
52_F	148_N	1.770	1.00
52_F	144_V	1.749	1.00
45_R	151_D	1.740	1.00
78_N	105_V	1.712	1.00
125_V	131_L	1.688	1.00
66_K	149_Y	1.673	1.00
164_Y	172_K	1.640	1.00
21_G	88_I	1.617	1.00
52_F	145_I	1.610	1.00
71_E	83_D	1.586	1.00
45_R	166_A	1.552	1.00
14_I	162_S	1.536	1.00
42_Q	130_V	1.534	1.00
75_Y	83_D	1.531	1.00
101_T	135_A	1.521	1.00
127_K	130_V	1.491	1.00
71_E	87_K	1.480	1.00
67_V	87_K	1.466	1.00
172_K	176_S	1.431	1.00
171_I	175_K	1.401	1.00
83_D	87_K	1.392	1.00
161_G	176_S	1.384	1.00
154_K	159_D	1.382	1.00
64_V	145_I	1.379	1.00
79_D	82_Y	1.379	1.00
13_L	174_L	1.361	1.00
115_I	122_S	1.359	1.00
55_V	59_V	1.357	1.00
25_S	28_K	1.319	1.00
66_K	145_I	1.300	1.00
152_E	155_Q	1.290	1.00
177_F	184_P	1.281	1.00
99_I	121_K	1.268	1.00
45_R	49_E	1.256	1.00
18_I	145_I	1.245	1.00
3_V	23_V	1.243	1.00
72_I	77_L	1.231	1.00
68_F	71_E	1.229	1.00
19_V	81_T	1.223	1.00
37_V	136_S	1.217	1.00
86_S	90_L	1.216	1.00
37_V	140_I	1.200	1.00
49_E	144_V	1.198	1.00
16_P	66_K	1.193	1.00
105_V	114_L	1.192	1.00
3_V	21_G	1.171	1.00
89_I	100_V	1.151	1.00
149_Y	153_L	1.139	1.00
16_P	149_Y	1.136	1.00
100_V	120_Y	1.134	1.00
61_A	93_S	1.127	1.00
5_I	81_T	1.126	1.00
161_G	164_Y	1.125	1.00
174_L	178_Y	1.114	1.00
28_K	34_G	1.106	1.00
65_V	88_I	1.100	1.00
28_K	58_T	1.100	1.00
67_V	84_A	1.094	1.00
86_S	117_K	1.090	1.00
43_L	140_I	1.075	1.00
184_P	190_R	1.074	1.00
105_V	124_V	1.066	1.00
8_A	144_V	1.062	1.00
162_S	187_I	1.058	1.00
156_V	187_I	1.053	1.00
115_I	118_L	1.042	1.00
71_E	74_N	1.039	1.00
157_Y	187_I	1.036	1.00
5_I	100_V	1.034	1.00
44_T	47_R	1.030	1.00
43_L	47_R	1.027	1.00
165_P	176_S	1.025	1.00
161_G	165_P	1.023	1.00
13_L	169_R	1.017	1.00
3_V	97_P	1.006	1.00
50_K	54_I	1.004	1.00
20_A	64_V	0.997	1.00
37_V	137_A	0.995	1.00
75_Y	79_D	0.994	1.00
82_Y	105_V	0.984	1.00
69_P	73_D	0.980	1.00
76_N	79_D	0.980	1.00
125_V	132_F	0.978	1.00
53_D	56_A	0.967	1.00
53_D	148_N	0.966	1.00
54_I	57_N	0.960	1.00
193_K	196_R	0.957	1.00
36_G	47_R	0.956	1.00
175_K	178_Y	0.955	1.00
151_D	155_Q	0.953	1.00
56_A	141_I	0.952	1.00
132_F	136_S	0.951	1.00
14_I	187_I	0.944	1.00
65_V	84_A	0.941	1.00
71_E	75_Y	0.940	1.00
67_V	71_E	0.938	1.00
125_V	135_A	0.933	1.00
5_I	89_I	0.930	1.00
101_T	132_F	0.929	1.00
43_L	51_L	0.926	1.00
149_Y	152_E	0.917	1.00
76_N	81_T	0.912	1.00
21_G	92_L	0.909	1.00
171_I	174_L	0.906	1.00
3_V	89_I	0.905	1.00
10_R	81_T	0.904	1.00
174_L	194_I	0.899	1.00
159_D	176_S	0.893	1.00
151_D	166_A	0.884	1.00
56_A	145_I	0.881	1.00
49_E	151_D	0.873	0.99
18_I	149_Y	0.871	0.99
92_L	97_P	0.864	0.99
67_V	83_D	0.864	0.99
14_I	150_I	0.861	0.99
53_D	57_N	0.856	0.99
86_S	118_L	0.842	0.99
70_Y	74_N	0.840	0.99
3_V	100_V	0.840	0.99
115_I	124_V	0.839	0.99
145_I	149_Y	0.838	0.99
172_K	175_K	0.836	0.99
19_V	65_V	0.834	0.99
127_K	131_L	0.830	0.99
37_V	133_V	0.829	0.99
100_V	118_L	0.818	0.99
60_E	95_F	0.816	0.99
17_M	77_L	0.814	0.99
64_V	141_I	0.810	0.99
13_L	195_L	0.800	0.99
178_Y	197_S	0.797	0.99
125_V	128_A	0.797	0.99
145_I	148_N	0.795	0.99
144_V	148_N	0.788	0.99
63_T	88_I	0.785	0.99
24_I	37_V	0.776	0.99
25_S	33_K	0.773	0.99
78_N	114_L	0.769	0.99
104_K	124_V	0.768	0.99
23_V	61_A	0.762	0.99
104_K	126_H	0.759	0.99
83_D	86_S	0.753	0.98
162_S	185_P	0.744	0.98
5_I	102_V	0.743	0.98
8_A	52_F	0.742	0.98
5_I	85_V	0.742	0.98
78_N	82_Y	0.735	0.98
47_R	51_L	0.734	0.98
100_V	122_S	0.732	0.98
3_V	92_L	0.725	0.98
133_V	136_S	0.721	0.98
178_Y	181_N	0.719	0.98
34_G	58_T	0.717	0.98
13_L	194_I	0.714	0.98
82_Y	114_L	0.711	0.98
51_L	140_I	0.710	0.98
63_T	92_L	0.706	0.98
70_Y	190_R	0.706	0.98
23_V	92_L	0.706	0.98
70_Y	186_P	0.703	0.98
8_A	19_V	0.701	0.98
164_Y	170_T	0.696	0.97
65_V	87_K	0.696	0.97
16_P	68_F	0.694	0.97
36_G	51_L	0.694	0.97
81_T	85_V	0.692	0.97
148_N	152_E	0.691	0.97
69_P	187_I	0.688	0.97
8_A	141_I	0.681	0.97
184_P	195_L	0.680	0.97
38_K	136_S	0.678	0.97
22_V	137_A	0.676	0.97
78_N	81_T	0.664	0.97
19_V	63_T	0.663	0.97
24_I	59_V	0.660	0.96
129_D	136_S	0.658	0.96
52_F	141_I	0.653	0.96
73_D	190_R	0.652	0.96
24_I	133_V	0.651	0.96
46_E	50_K	0.649	0.96
177_F	195_L	0.644	0.96
165_P	170_T	0.641	0.96
61_A	95_F	0.640	0.96
55_V	60_E	0.636	0.96
126_H	135_A	0.636	0.96
184_P	194_I	0.633	0.96
17_M	81_T	0.628	0.95
169_R	174_L	0.628	0.95
33_K	133_V	0.622	0.95
82_Y	104_K	0.612	0.95
82_Y	86_S	0.611	0.95
86_S	115_I	0.605	0.94
50_K	53_D	0.605	0.94
114_L	117_K	0.603	0.94
26_D	33_K	0.600	0.94
157_Y	186_P	0.597	0.94
165_P	172_K	0.597	0.94
90_L	118_L	0.596	0.94
118_L	122_S	0.596	0.94
22_V	59_V	0.595	0.94
82_Y	116_N	0.592	0.94
51_L	55_V	0.591	0.94
148_N	151_D	0.591	0.94
173_W	183_N	0.589	0.94
14_I	188_I	0.583	0.93
8_A	166_A	0.583	0.93
65_V	91_S	0.582	0.93
156_V	186_P	0.581	0.93
28_K	33_K	0.577	0.93
185_P	188_I	0.575	0.93
16_P	69_P	0.574	0.93
105_V	126_H	0.571	0.92
22_V	138_A	0.571	0.92
89_I	118_L	0.570	0.92
14_I	185_P	0.570	0.92
42_Q	127_K	0.560	0.92
150_I	162_S	0.559	0.92
23_V	97_P	0.558	0.92
24_I	134_E	0.558	0.92
82_Y	124_V	0.557	0.92
154_K	166_A	0.554	0.91
49_E	52_F	0.552	0.91
162_S	188_I	0.552	0.91
51_L	54_I	0.551	0.91
24_I	28_K	0.547	0.91
5_I	21_G	0.546	0.91
24_I	137_A	0.544	0.91
88_I	92_L	0.544	0.91
162_S	167_D	0.537	0.90
165_P	168_P	0.537	0.90
52_F	64_V	0.536	0.90
131_L	134_E	0.533	0.90
101_T	134_E	0.531	0.89
177_F	194_I	0.530	0.89
8_A	20_A	0.530	0.89
2_R	98_E	0.528	0.89
157_Y	185_P	0.527	0.89
27_T	35_I	0.526	0.89
159_D	163_G	0.525	0.89
101_T	125_V	0.524	0.89
114_L	118_L	0.524	0.89
159_D	185_P	0.524	0.89
34_G	51_L	0.515	0.88
123_N	132_F	0.515	0.88
22_V	55_V	0.510	0.88
76_N	80_L	0.508	0.87
76_N	85_V	0.507	0.87
56_A	148_N	0.505	0.87
177_F	183_N	0.504	0.87
114_L	122_S	0.501	0.87
23_V	60_E	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
1io2A	1	0.967	100	0.137	Contact Map
1ekeA	2	0.9575	100	0.142	Contact Map
1uaxA	1	0.9575	100	0.144	Contact Map
1i39A	1	0.9057	100	0.168	Contact Map
3kioA	1	0.9717	100	0.176	Contact Map
2etjA	1	0.8396	100	0.18	Contact Map
2d0bA	1	0.9387	100	0.221	Contact Map
4py5A	1	0.8726	100	0.237	Contact Map
3vn5A	1	0.8443	100	0.276	Contact Map
4lhsA	2	0.6698	12	0.958	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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