UPF0262 - PFAM28P - GREMLIN Contacts

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UPF0262 - Uncharacterised protein family (UPF0262)

PFAM:	PF06793	Sequences: QRLVAITLDEASIGRRSPDIEHERAVAIFDLLEENSFAPVGRPGGPYRLHLSIEENRLVFDIRDEDGEPLATHILSLTPFRRIVKDYFLICESYYEAIRTATPSQIEAIDMGRRGLHNEGSELLRERLEGKVEVDFDTARRLFTLICVLHWR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	152 (152)
Sequences:	3814 (1879)
Seq/√Len:	152.4
META:	0.898

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
108_A	112_G	3.977	1.00
118_N	122_E	3.423	1.00
5_A	48_R	3.396	1.00
38_A	133_E	3.317	1.00
64_D	68_E	3.009	1.00
122_E	125_R	2.704	1.00
48_R	67_G	2.616	1.00
122_E	136_F	2.532	1.00
54_E	72_T	2.445	1.00
7_T	50_H	2.390	1.00
50_H	63_R	2.349	1.00
64_D	70_L	2.230	1.00
3_L	49_L	2.195	1.00
1_Q	38_A	2.122	1.00
29_F	33_E	2.047	1.00
121_S	136_F	1.935	1.00
34_E	137_D	1.935	1.00
61_D	72_T	1.931	1.00
4_V	48_R	1.919	1.00
9_D	12_S	1.848	1.00
48_R	65_E	1.846	1.00
122_E	126_E	1.832	1.00
61_D	69_P	1.797	1.00
101_A	105_Q	1.759	1.00
111_M	115_G	1.759	1.00
73_H	132_V	1.726	1.00
28_I	32_L	1.725	1.00
88_F	147_C	1.700	1.00
39_P	42_R	1.668	1.00
13_I	16_R	1.662	1.00
90_I	116_L	1.649	1.00
63_R	67_G	1.623	1.00
59_V	74_I	1.508	1.00
90_I	112_G	1.485	1.00
3_L	6_I	1.463	1.00
39_P	70_L	1.428	1.00
76_S	79_P	1.403	1.00
86_D	119_E	1.399	1.00
69_P	72_T	1.395	1.00
80_F	123_L	1.388	1.00
98_I	106_I	1.345	1.00
42_R	64_D	1.298	1.00
29_F	98_I	1.298	1.00
22_H	26_V	1.297	1.00
92_E	96_E	1.294	1.00
42_R	70_L	1.290	1.00
42_R	47_Y	1.281	1.00
126_E	129_E	1.274	1.00
26_V	29_F	1.230	1.00
125_R	136_F	1.229	1.00
63_R	69_P	1.229	1.00
118_N	137_D	1.219	1.00
59_V	72_T	1.213	1.00
6_I	32_L	1.209	1.00
7_T	48_R	1.187	1.00
9_D	13_I	1.183	1.00
100_T	105_Q	1.182	1.00
51_L	60_F	1.180	1.00
32_L	35_N	1.173	1.00
83_I	120_G	1.162	1.00
57_R	74_I	1.128	1.00
95_Y	99_R	1.105	0.99
44_G	47_Y	1.083	0.99
85_K	89_L	1.081	0.99
53_I	77_L	1.070	0.99
129_E	133_E	1.061	0.99
41_G	71_A	1.057	0.99
42_R	71_A	1.051	0.99
15_R	25_A	1.051	0.99
16_R	20_I	1.047	0.99
40_V	130_G	1.039	0.99
52_S	72_T	1.036	0.99
39_P	43_P	1.036	0.99
80_F	146_I	1.024	0.99
1_Q	36_S	1.006	0.99
125_R	134_V	1.003	0.99
44_G	64_D	0.991	0.99
90_I	93_S	0.990	0.99
37_F	62_I	0.986	0.99
6_I	49_L	0.983	0.99
84_V	88_F	0.978	0.99
82_R	85_K	0.960	0.98
18_P	25_A	0.947	0.98
10_E	16_R	0.939	0.98
79_P	127_R	0.929	0.98
62_I	132_V	0.928	0.98
19_D	33_E	0.924	0.98
102_T	105_Q	0.915	0.98
40_V	133_E	0.912	0.98
91_C	95_Y	0.911	0.98
109_I	115_G	0.906	0.98
21_E	24_R	0.906	0.98
148_V	151_W	0.903	0.98
96_E	100_T	0.900	0.98
83_I	123_L	0.897	0.98
118_N	136_F	0.895	0.98
41_G	44_G	0.873	0.97
22_H	29_F	0.868	0.97
53_I	150_H	0.866	0.97
96_E	99_R	0.856	0.97
147_C	150_H	0.852	0.97
52_S	61_D	0.844	0.97
84_V	147_C	0.844	0.97
16_R	21_E	0.843	0.96
48_R	63_R	0.840	0.96
78_T	81_R	0.840	0.96
39_P	47_Y	0.839	0.96
50_H	61_D	0.835	0.96
43_P	64_D	0.817	0.96
112_G	115_G	0.812	0.96
64_D	67_G	0.811	0.96
17_S	22_H	0.802	0.95
19_D	22_H	0.801	0.95
12_S	16_R	0.800	0.95
6_I	31_L	0.793	0.95
96_E	101_A	0.790	0.95
98_I	102_T	0.788	0.95
104_S	112_G	0.786	0.95
105_Q	108_A	0.783	0.95
54_E	59_V	0.766	0.94
75_L	127_R	0.753	0.94
25_A	29_F	0.749	0.93
139_A	146_I	0.749	0.93
4_V	7_T	0.745	0.93
71_A	76_S	0.744	0.93
14_G	151_W	0.735	0.93
18_P	22_H	0.734	0.93
11_A	16_R	0.732	0.93
96_E	105_Q	0.728	0.92
15_R	20_I	0.722	0.92
49_L	127_R	0.717	0.92
120_G	146_I	0.716	0.92
97_A	106_I	0.716	0.92
23_E	92_E	0.712	0.91
31_L	34_E	0.712	0.91
94_Y	99_R	0.704	0.91
88_F	120_G	0.703	0.91
87_Y	117_H	0.702	0.91
3_L	151_W	0.697	0.91
89_L	112_G	0.696	0.91
122_E	129_E	0.693	0.90
60_F	73_H	0.685	0.90
94_Y	98_I	0.681	0.90
1_Q	44_G	0.680	0.90
63_R	70_L	0.676	0.89
16_R	151_W	0.675	0.89
13_I	20_I	0.667	0.89
120_G	147_C	0.665	0.88
140_R	143_F	0.661	0.88
4_V	65_E	0.658	0.88
130_G	134_V	0.658	0.88
90_I	115_G	0.656	0.88
25_A	84_V	0.655	0.88
44_G	70_L	0.641	0.87
84_V	107_E	0.638	0.86
56_N	78_T	0.635	0.86
104_S	115_G	0.635	0.86
97_A	109_I	0.630	0.86
82_R	89_L	0.629	0.86
86_D	89_L	0.626	0.85
102_T	109_I	0.625	0.85
142_L	145_L	0.625	0.85
27_A	37_F	0.624	0.85
72_T	82_R	0.623	0.85
39_P	62_I	0.621	0.85
130_G	133_E	0.602	0.83
129_E	132_V	0.600	0.83
32_L	95_Y	0.600	0.83
1_Q	39_P	0.600	0.83
27_A	144_T	0.599	0.83
71_A	148_V	0.598	0.83
40_V	129_E	0.594	0.82
84_V	151_W	0.586	0.81
108_A	111_M	0.586	0.81
121_S	124_L	0.584	0.81
10_E	14_G	0.582	0.81
77_L	128_L	0.581	0.81
52_S	74_I	0.581	0.81
39_P	79_P	0.580	0.81
137_D	146_I	0.579	0.81
125_R	129_E	0.578	0.80
20_I	151_W	0.574	0.80
91_C	102_T	0.569	0.79
119_E	122_E	0.568	0.79
1_Q	5_A	0.568	0.79
51_L	120_G	0.567	0.79
124_L	134_V	0.565	0.79
22_H	53_I	0.561	0.78
23_E	107_E	0.559	0.78
127_R	131_K	0.559	0.78
84_V	150_H	0.557	0.78
15_R	21_E	0.555	0.78
104_S	116_L	0.554	0.78
99_R	105_Q	0.554	0.78
59_V	69_P	0.552	0.77
73_H	78_T	0.550	0.77
36_S	44_G	0.550	0.77
19_D	121_S	0.549	0.77
8_L	16_R	0.548	0.77
7_T	36_S	0.547	0.77
33_E	98_I	0.547	0.77
126_E	136_F	0.545	0.76
29_F	102_T	0.543	0.76
80_F	83_I	0.541	0.76
15_R	18_P	0.540	0.76
16_R	152_R	0.538	0.76
29_F	106_I	0.537	0.75
3_L	14_G	0.536	0.75
123_L	126_E	0.533	0.75
58_L	77_L	0.532	0.75
25_A	102_T	0.527	0.74
14_G	18_P	0.526	0.74
9_D	28_I	0.523	0.74
108_A	121_S	0.521	0.73
27_A	113_R	0.520	0.73
59_V	86_D	0.519	0.73
56_N	59_V	0.514	0.72
112_G	122_E	0.513	0.72
93_S	115_G	0.513	0.72
20_I	148_V	0.510	0.72
48_R	66_D	0.508	0.71
35_N	95_Y	0.505	0.71
7_T	11_A	0.505	0.71
62_I	73_H	0.503	0.71
121_S	134_V	0.503	0.71
29_F	78_T	0.500	0.70
8_L	28_I	0.500	0.70
36_S	133_E	0.500	0.70

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
1njhA	2	0.4276	14.6	0.945	Contact Map
4doxA	1	0.8816	11.5	0.948	Contact Map
4kwyA	1	0.8224	8.9	0.95	Contact Map
1ry9A	2	0.5724	7.9	0.951	Contact Map
2xgaA	2	0.5724	7.6	0.952	Contact Map
2fvnA	1	0.4671	6.9	0.953	Contact Map
1nv8A	1	0.625	4	0.958	Contact Map
1i60A	1	0.5066	3.3	0.959	Contact Map
5a2tA	12	0.8947	3.3	0.96	Contact Map
2l5aA	1	0.3618	3.1	0.96	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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