RTA1 - PFAM28P - GREMLIN Contacts

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RTA1 - RTA1 like protein

PFAM:	PF04479	Sequences: FVIGGLLEVIGYIGRILSHKNFPPWSLGPFIIQIVLLLLAPAFFAAAIYMILGRIIRYLGPEYSRIRPRWYTKIFVTGDVISLLLQAAGGGLAASASSSSSAKTGENIMLAGLALQVVFFGLFVVLAADFHRRVRPSRRWRLFLYALYIASLLILIRSIYRVVELAQGWDGYLITHEWYFYVLDALPMLLAMVLLNVFHPGRLLPG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	206 (202)
Sequences:	2492 (1981)
Seq/√Len:	139.4
META:	0.116

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
178_W	182_V	4.414	1.00
13_I	17_L	3.755	1.00
5_G	192_M	3.684	1.00
131_H	148_Y	3.150	1.00
65_R	129_D	3.106	1.00
172_Y	176_H	2.947	1.00
129_D	133_R	2.830	1.00
26_S	29_P	2.718	1.00
121_G	155_L	2.425	1.00
114_A	118_V	2.377	1.00
82_S	115_L	2.348	1.00
114_A	166_A	2.284	1.00
17_L	29_P	2.219	1.00
159_I	163_V	2.111	1.00
114_A	162_V	2.101	1.00
176_H	179_Y	2.050	1.00
28_G	32_I	2.049	1.00
7_L	40_A	2.027	1.00
78_G	115_L	2.023	1.00
78_G	119_F	2.009	1.00
167_Q	171_G	1.994	1.00
178_W	183_L	1.989	1.00
21_N	25_W	1.986	1.00
14_G	32_I	1.980	1.00
84_L	88_A	1.979	1.00
189_L	193_V	1.930	1.00
128_A	132_R	1.916	1.00
14_G	17_L	1.906	1.00
107_N	111_A	1.898	1.00
27_L	31_I	1.834	1.00
31_I	35_V	1.820	1.00
87_A	91_G	1.816	1.00
149_I	194_L	1.775	1.00
91_G	95_S	1.754	1.00
48_I	150_A	1.708	1.00
145_Y	149_I	1.702	1.00
146_A	198_F	1.692	1.00
103_K	107_N	1.690	1.00
110_L	166_A	1.619	1.00
152_L	156_I	1.613	1.00
10_I	32_I	1.586	1.00
56_I	64_S	1.582	1.00
104_T	107_N	1.553	1.00
28_G	31_I	1.526	1.00
3_I	7_L	1.525	1.00
8_E	44_F	1.468	1.00
173_L	179_Y	1.458	1.00
52_L	56_I	1.432	1.00
103_K	106_E	1.426	1.00
21_N	26_S	1.420	1.00
69_R	73_K	1.410	1.00
127_A	144_L	1.405	1.00
38_L	109_M	1.386	1.00
124_V	151_S	1.384	1.00
10_I	36_L	1.381	1.00
85_L	115_L	1.370	1.00
146_A	194_L	1.353	1.00
82_S	119_F	1.352	1.00
149_I	153_L	1.338	1.00
93_A	109_M	1.316	1.00
92_L	104_T	1.289	1.00
79_D	86_Q	1.285	1.00
67_R	70_W	1.259	1.00
70_W	73_K	1.240	1.00
50_M	76_V	1.220	1.00
60_G	63_Y	1.207	1.00
154_I	158_S	1.202	1.00
10_I	14_G	1.199	1.00
90_G	94_A	1.179	1.00
156_I	187_P	1.173	1.00
45_A	120_F	1.170	0.99
52_L	127_A	1.164	0.99
31_I	94_A	1.156	0.99
181_Y	186_L	1.151	0.99
111_A	118_V	1.141	0.99
88_A	92_L	1.136	0.99
172_Y	179_Y	1.134	0.99
78_G	82_S	1.130	0.99
160_Y	173_L	1.124	0.99
44_F	192_M	1.124	0.99
61_P	68_P	1.122	0.99
9_V	13_I	1.109	0.99
111_A	115_L	1.108	0.99
117_V	155_L	1.093	0.99
35_V	39_L	1.086	0.99
104_T	108_I	1.085	0.99
7_L	39_L	1.081	0.99
154_I	188_M	1.066	0.99
117_V	162_V	1.063	0.99
173_L	183_L	1.062	0.99
186_L	190_L	1.054	0.99
169_W	174_I	1.026	0.99
14_G	29_P	1.022	0.99
153_L	187_P	1.017	0.99
87_A	90_G	1.016	0.99
130_F	144_L	1.009	0.98
182_V	186_L	1.007	0.98
4_G	44_F	1.004	0.98
42_A	83_L	0.998	0.98
38_L	165_L	0.992	0.98
46_A	79_D	0.984	0.98
81_I	115_L	0.979	0.98
44_F	188_M	0.979	0.98
64_S	68_P	0.977	0.98
12_Y	185_A	0.977	0.98
6_L	10_I	0.977	0.98
100_S	104_T	0.974	0.98
131_H	135_R	0.957	0.98
101_S	104_T	0.957	0.98
39_L	83_L	0.955	0.98
124_V	128_A	0.954	0.98
196_N	199_H	0.951	0.98
81_I	85_L	0.948	0.98
150_A	195_L	0.947	0.98
146_A	150_A	0.939	0.98
71_Y	126_L	0.934	0.98
7_L	36_L	0.933	0.97
93_A	169_W	0.929	0.97
120_F	151_S	0.923	0.97
72_T	76_V	0.917	0.97
49_Y	79_D	0.914	0.97
149_I	190_L	0.910	0.97
181_Y	185_A	0.910	0.97
38_L	113_L	0.900	0.97
76_V	80_V	0.899	0.97
33_Q	37_L	0.894	0.97
70_W	74_I	0.887	0.97
17_L	20_K	0.883	0.96
75_F	79_D	0.877	0.96
99_S	103_K	0.877	0.96
59_L	134_V	0.870	0.96
14_G	33_Q	0.865	0.96
153_L	194_L	0.861	0.96
121_G	125_V	0.860	0.96
157_R	161_R	0.855	0.96
40_A	47_A	0.853	0.96
40_A	109_M	0.853	0.96
98_S	101_S	0.849	0.96
50_M	54_R	0.847	0.96
96_A	100_S	0.847	0.96
14_G	28_G	0.846	0.96
21_N	24_P	0.843	0.95
50_M	72_T	0.842	0.95
27_L	98_S	0.840	0.95
60_G	64_S	0.820	0.95
7_L	10_I	0.818	0.95
35_V	83_L	0.817	0.95
11_G	37_L	0.809	0.94
179_Y	183_L	0.808	0.94
132_R	135_R	0.805	0.94
38_L	90_G	0.802	0.94
52_L	130_F	0.801	0.94
127_A	148_Y	0.801	0.94
46_A	76_V	0.798	0.94
90_G	164_E	0.794	0.94
28_G	36_L	0.791	0.94
79_D	164_E	0.779	0.93
167_Q	172_Y	0.775	0.93
8_E	40_A	0.769	0.93
167_Q	173_L	0.769	0.93
142_L	198_F	0.769	0.93
168_G	171_G	0.766	0.93
113_L	162_V	0.765	0.92
135_R	141_R	0.765	0.92
171_G	176_H	0.760	0.92
142_L	202_R	0.754	0.92
18_S	33_Q	0.753	0.92
4_G	7_L	0.751	0.92
122_L	126_L	0.749	0.92
45_A	151_S	0.744	0.91
57_R	68_P	0.744	0.91
86_Q	112_G	0.743	0.91
77_T	81_I	0.739	0.91
55_I	143_F	0.739	0.91
185_A	189_L	0.736	0.91
42_A	49_Y	0.735	0.91
21_N	29_P	0.732	0.91
113_L	120_F	0.728	0.90
98_S	104_T	0.726	0.90
8_E	12_Y	0.726	0.90
17_L	21_N	0.725	0.90
109_M	158_S	0.725	0.90
137_S	141_R	0.724	0.90
51_I	147_L	0.712	0.90
92_L	98_S	0.707	0.89
73_K	77_T	0.707	0.89
5_G	9_V	0.706	0.89
37_L	110_L	0.703	0.89
181_Y	184_D	0.696	0.88
86_Q	157_R	0.696	0.88
150_A	191_A	0.694	0.88
16_I	20_K	0.692	0.88
30_F	39_L	0.688	0.88
39_L	42_A	0.687	0.88
88_A	104_T	0.682	0.87
43_F	83_L	0.680	0.87
46_A	86_Q	0.679	0.87
18_S	24_P	0.674	0.87
110_L	114_A	0.671	0.87
172_Y	178_W	0.670	0.86
91_G	94_A	0.670	0.86
160_Y	180_F	0.660	0.86
128_A	145_Y	0.655	0.85
153_L	190_L	0.649	0.85
6_L	13_I	0.649	0.85
135_R	145_Y	0.648	0.85
105_G	184_D	0.648	0.85
32_I	36_L	0.647	0.85
198_F	203_L	0.646	0.84
42_A	158_S	0.645	0.84
39_L	87_A	0.643	0.84
106_E	117_V	0.640	0.84
53_G	72_T	0.635	0.83
159_I	166_A	0.631	0.83
7_L	35_V	0.626	0.83
102_A	106_E	0.626	0.83
82_S	86_Q	0.626	0.83
115_L	119_F	0.622	0.82
131_H	141_R	0.620	0.82
195_L	200_P	0.620	0.82
81_I	132_R	0.619	0.82
194_L	197_V	0.618	0.82
52_L	113_L	0.618	0.82
54_R	57_R	0.616	0.82
145_Y	197_V	0.615	0.81
35_V	38_L	0.615	0.81
180_F	184_D	0.613	0.81
84_L	87_A	0.609	0.81
90_G	165_L	0.608	0.81
5_G	44_F	0.607	0.81
79_D	82_S	0.606	0.81
186_L	189_L	0.605	0.80
49_Y	157_R	0.598	0.80
61_P	64_S	0.597	0.80
37_L	120_F	0.596	0.79
136_P	139_R	0.593	0.79
40_A	195_L	0.591	0.79
37_L	169_W	0.588	0.79
44_F	85_L	0.586	0.78
136_P	141_R	0.581	0.78
106_E	169_W	0.580	0.78
12_Y	37_L	0.580	0.78
64_S	129_D	0.578	0.77
13_I	16_I	0.577	0.77
140_W	204_L	0.577	0.77
180_F	185_A	0.576	0.77
144_L	148_Y	0.576	0.77
95_S	100_S	0.576	0.77
164_E	173_L	0.573	0.77
17_L	32_I	0.569	0.76
7_L	43_F	0.568	0.76
162_V	166_A	0.567	0.76
183_L	187_P	0.565	0.76
134_V	184_D	0.565	0.76
171_G	175_T	0.564	0.76
20_K	149_I	0.562	0.75
165_L	171_G	0.561	0.75
63_Y	134_V	0.558	0.75
79_D	157_R	0.558	0.75
13_I	145_Y	0.557	0.75
39_L	160_Y	0.557	0.75
102_A	152_L	0.555	0.74
129_D	132_R	0.552	0.74
63_Y	184_D	0.552	0.74
99_S	104_T	0.547	0.73
189_L	199_H	0.547	0.73
34_I	93_A	0.542	0.73
45_A	48_I	0.541	0.73
2_V	62_E	0.540	0.72
2_V	5_G	0.538	0.72
127_A	131_H	0.537	0.72
187_P	190_L	0.535	0.72
167_Q	174_I	0.534	0.72
6_L	9_V	0.532	0.71
167_Q	179_Y	0.530	0.71
76_V	79_D	0.529	0.71
88_A	108_I	0.528	0.71
116_Q	164_E	0.527	0.71
178_W	181_Y	0.527	0.71
104_T	111_A	0.525	0.70
98_S	163_V	0.524	0.70
55_I	196_N	0.521	0.70
68_P	126_L	0.518	0.69
160_Y	179_Y	0.518	0.69
143_F	198_F	0.518	0.69
124_V	148_Y	0.516	0.69
3_I	35_V	0.516	0.69
4_G	8_E	0.515	0.69
139_R	190_L	0.514	0.69
56_I	91_G	0.513	0.69
31_I	34_I	0.513	0.69
170_D	175_T	0.512	0.68
3_I	43_F	0.512	0.68
98_S	107_N	0.512	0.68
48_I	195_L	0.511	0.68
128_A	131_H	0.510	0.68
124_V	155_L	0.509	0.68
115_L	118_V	0.507	0.68
31_I	36_L	0.507	0.68
12_Y	110_L	0.506	0.68
165_L	174_I	0.503	0.67
138_R	142_L	0.502	0.67
81_I	88_A	0.500	0.67

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
2jwaA	2	0.2136	3	0.961	Contact Map
3wxwA	1	0.8738	2.4	0.963	Contact Map
2ks1B	1	0.2136	2	0.964	Contact Map
2l2tA	2	0.2136	2	0.964	Contact Map
4p79A	1	0.4612	2	0.964	Contact Map
4pd6A	3	0.4272	2	0.964	Contact Map
3x29A	1	0.4466	1.6	0.966	Contact Map
2ys2A	1	0.1117	1.5	0.966	Contact Map
3rqwA	4	0.4078	1.3	0.968	Contact Map
4o6yA	2	0.8981	1.3	0.968	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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