UPF0179 - PFAM28P - GREMLIN Contacts

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UPF0179 - Uncharacterised protein family (UPF0179)

PFAM:	PF03684	Sequences: KITLIGERLAKEGLEFVYLGPAPECEGCKLKKVCLNLEPGRRYRIVGVRDKATHECPVHEGGVRVVEVEEAPIEAAIPSKKAIEGSKITFEPPECDETDCPNYELCHPEGLKEGDKYKIVKVLGDPPHCPKGRSLKLVEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (137)
Sequences:	1201 (811)
Seq/√Len:	69.3
META:	0.872

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_E	44_R	4.771	1.00
47_G	67_E	3.834	1.00
15_E	42_R	3.061	1.00
100_C	129_C	2.860	1.00
100_C	106_C	2.747	1.00
5_I	45_I	2.707	1.00
44_R	69_E	2.400	1.00
7_E	53_T	2.372	1.00
6_G	59_H	2.329	1.00
18_Y	35_L	2.329	1.00
84_E	121_K	2.282	1.00
76_A	126_P	2.219	1.00
30_L	54_H	2.119	1.00
12_E	47_G	1.922	1.00
74_E	137_L	1.850	1.00
38_E	70_E	1.830	1.00
59_H	62_G	1.804	1.00
7_E	64_R	1.751	1.00
46_V	69_E	1.740	1.00
103_Y	107_H	1.735	1.00
4_L	63_V	1.731	1.00
121_K	139_E	1.706	1.00
105_L	137_L	1.680	1.00
54_H	65_V	1.677	1.00
8_R	60_E	1.661	0.99
92_P	113_E	1.642	0.99
14_L	45_I	1.634	0.99
79_S	136_K	1.563	0.99
22_A	35_L	1.541	0.99
9_L	14_L	1.529	0.99
95_C	106_C	1.528	0.99
82_A	122_V	1.499	0.99
111_L	117_Y	1.472	0.99
93_P	107_H	1.452	0.99
123_L	137_L	1.424	0.98
74_E	139_E	1.416	0.98
17_V	42_R	1.404	0.98
125_D	136_K	1.370	0.98
3_T	68_V	1.358	0.98
6_G	9_L	1.355	0.98
31_K	36_N	1.342	0.98
124_G	137_L	1.329	0.97
97_E	130_P	1.325	0.97
87_K	118_K	1.307	0.97
78_P	91_E	1.303	0.97
27_G	57_P	1.263	0.96
21_P	35_L	1.229	0.96
76_A	105_L	1.223	0.96
6_G	62_G	1.200	0.95
101_P	128_H	1.198	0.95
122_V	136_K	1.198	0.95
51_K	54_H	1.197	0.95
72_P	139_E	1.172	0.95
53_T	62_G	1.151	0.94
53_T	64_R	1.118	0.93
49_R	66_V	1.111	0.93
13_G	16_F	1.099	0.93
3_T	6_G	1.089	0.92
39_P	124_G	1.082	0.92
38_E	110_G	1.059	0.91
74_E	123_L	1.052	0.91
22_A	58_V	1.051	0.91
102_N	126_P	1.010	0.89
111_L	115_D	1.009	0.89
18_Y	33_V	1.008	0.89
77_I	82_A	1.006	0.89
41_R	71_A	0.999	0.88
7_E	61_G	0.996	0.88
106_C	129_C	0.994	0.88
78_P	81_K	0.985	0.88
87_K	116_K	0.973	0.87
82_A	108_P	0.972	0.87
5_I	9_L	0.964	0.87
75_A	117_Y	0.957	0.86
49_R	65_V	0.952	0.86
40_G	124_G	0.950	0.86
38_E	41_R	0.949	0.86
44_R	72_P	0.937	0.85
25_C	28_C	0.934	0.85
102_N	124_G	0.926	0.84
40_G	82_A	0.918	0.84
83_I	86_S	0.918	0.84
2_I	65_V	0.904	0.83
41_R	111_L	0.897	0.82
71_A	110_G	0.881	0.81
55_E	62_G	0.877	0.81
81_K	88_I	0.874	0.81
82_A	88_I	0.839	0.78
41_R	115_D	0.838	0.78
96_D	131_K	0.837	0.78
71_A	79_S	0.834	0.77
2_I	36_N	0.829	0.77
93_P	133_R	0.829	0.77
79_S	125_D	0.822	0.76
80_K	85_G	0.820	0.76
77_I	119_I	0.819	0.76
75_A	90_F	0.817	0.76
31_K	70_E	0.816	0.76
121_K	125_D	0.815	0.76
4_L	29_K	0.807	0.75
82_A	138_V	0.795	0.74
30_L	71_A	0.790	0.74
8_R	77_I	0.777	0.72
122_V	138_V	0.776	0.72
67_E	106_C	0.772	0.72
126_P	137_L	0.768	0.71
28_C	34_C	0.766	0.71
95_C	100_C	0.765	0.71
21_P	24_E	0.761	0.71
46_V	71_A	0.749	0.70
86_S	117_Y	0.745	0.69
95_C	129_C	0.729	0.67
58_V	135_L	0.727	0.67
90_F	133_R	0.727	0.67
10_A	13_G	0.722	0.67
110_G	115_D	0.722	0.67
123_L	139_E	0.721	0.67
22_A	86_S	0.715	0.66
5_I	10_A	0.712	0.66
85_G	112_K	0.712	0.66
32_K	36_N	0.711	0.66
18_Y	36_N	0.707	0.65
48_V	57_P	0.702	0.65
72_P	112_K	0.701	0.64
46_V	49_R	0.700	0.64
93_P	97_E	0.692	0.63
59_H	110_G	0.686	0.63
24_E	103_Y	0.684	0.63
55_E	59_H	0.683	0.62
24_E	83_I	0.681	0.62
70_E	127_P	0.680	0.62
90_F	93_P	0.679	0.62
88_I	136_K	0.669	0.61
124_G	127_P	0.658	0.60
18_Y	31_K	0.653	0.59
4_L	10_A	0.653	0.59
122_V	125_D	0.651	0.59
41_R	110_G	0.650	0.59
4_L	30_L	0.649	0.59
12_E	44_R	0.648	0.58
31_K	54_H	0.648	0.58
16_F	43_Y	0.646	0.58
78_P	92_P	0.645	0.58
41_R	73_I	0.643	0.58
65_V	112_K	0.643	0.58
8_R	61_G	0.643	0.58
10_A	16_F	0.639	0.57
101_P	105_L	0.632	0.57
6_G	14_L	0.631	0.56
55_E	63_V	0.617	0.55
7_E	62_G	0.614	0.54
107_H	110_G	0.613	0.54
81_K	119_I	0.608	0.54
92_P	107_H	0.608	0.54
82_A	119_I	0.604	0.53
67_E	95_C	0.604	0.53
41_R	48_V	0.599	0.53
102_N	127_P	0.596	0.52
60_E	65_V	0.596	0.52
39_P	101_P	0.589	0.51
92_P	115_D	0.589	0.51
71_A	115_D	0.589	0.51
11_K	14_L	0.586	0.51
31_K	84_E	0.584	0.51
31_K	75_A	0.583	0.51
49_R	54_H	0.582	0.51
5_I	14_L	0.582	0.51
9_L	21_P	0.582	0.51
5_I	21_P	0.582	0.51
60_E	63_V	0.581	0.50
5_I	8_R	0.581	0.50
113_E	124_G	0.577	0.50
45_I	132_G	0.574	0.50
14_L	57_P	0.574	0.50
91_E	113_E	0.573	0.49
23_P	32_K	0.572	0.49
102_N	106_C	0.565	0.48
75_A	124_G	0.565	0.48
92_P	110_G	0.562	0.48
108_P	111_L	0.556	0.47
91_E	96_D	0.554	0.47
59_H	66_V	0.553	0.47
30_L	63_V	0.552	0.47
44_R	71_A	0.551	0.47
19_L	79_S	0.545	0.46
40_G	84_E	0.542	0.46
136_K	139_E	0.540	0.45
17_V	111_L	0.537	0.45
108_P	115_D	0.536	0.45
19_L	109_E	0.533	0.45
36_N	65_V	0.527	0.44
11_K	19_L	0.526	0.44
96_D	130_P	0.522	0.43
36_N	86_S	0.521	0.43
8_R	119_I	0.520	0.43
58_V	93_P	0.513	0.42
30_L	35_L	0.512	0.42
94_E	113_E	0.510	0.42
59_H	63_V	0.509	0.42
21_P	26_E	0.509	0.42
26_E	39_P	0.508	0.42
29_K	49_R	0.508	0.42
58_V	117_Y	0.507	0.42
20_G	31_K	0.504	0.41
89_T	116_K	0.500	0.41
73_I	98_T	0.500	0.41

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
1d2vC	2	0.3357	10.3	0.944	Contact Map
4j80A	2	0.8	7.3	0.947	Contact Map
2p28B	1	0.4786	5.7	0.95	Contact Map
2zwsA	2	0.3286	2.9	0.956	Contact Map
1wspA	3	0.4	2.8	0.957	Contact Map
2lx9A	1	0.4143	2.7	0.957	Contact Map
1c3gA	2	0.5143	2.4	0.958	Contact Map
2gcxA	1	0.4143	2	0.96	Contact Map
1kg2A	1	0.3429	1.6	0.962	Contact Map
3i38A	5	0.5286	1.6	0.962	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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