DUF3043 - PFAM28P - GREMLIN Contacts

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DUF3043 - Protein of unknown function (DUF3043)

PFAM:	PF11241	Sequences: GKGRPTPKRKEAEAARRRPLKAPADRKEARKRAREARRAARARQREAMAAGDERYLPARDRGPVRRFVRDYVDSRRNVGEFFLPLALVVLVLTFLSFVPNPAVQLYASLLMLVLLLVVVVDGVLLGRRLKRLVAERFPEDESTRGLGWYAAMRALQMRRLRLPKPQVKRGD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (169)
Sequences:	2951 (1907)
Seq/√Len:	146.7
META:	0.732

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_R	166_Q	3.778	1.00
37_R	41_R	3.035	1.00
46_E	50_A	2.626	1.00
82_F	86_A	2.603	1.00
53_E	66_R	2.540	1.00
25_D	28_E	2.459	1.00
8_K	11_E	2.420	1.00
47_A	50_A	2.335	1.00
26_R	30_R	2.246	1.00
70_D	166_Q	2.240	1.00
45_R	49_A	2.233	1.00
68_V	150_A	2.171	1.00
128_R	132_L	2.144	1.00
132_L	135_E	2.000	1.00
28_E	32_R	1.911	1.00
76_R	169_R	1.901	1.00
42_A	46_E	1.874	1.00
68_V	146_L	1.868	1.00
168_K	171_D	1.860	1.00
25_D	29_A	1.843	1.00
132_L	136_R	1.834	1.00
147_G	151_A	1.775	1.00
39_A	43_R	1.749	1.00
67_F	132_L	1.741	1.00
76_R	81_F	1.731	1.00
71_Y	128_R	1.706	1.00
10_K	13_E	1.705	1.00
47_A	55_Y	1.653	1.00
67_F	137_F	1.651	1.00
77_N	121_D	1.609	1.00
81_F	84_P	1.598	1.00
35_E	39_A	1.596	1.00
129_L	150_A	1.585	1.00
22_A	25_D	1.565	1.00
129_L	133_V	1.544	1.00
36_A	39_A	1.531	1.00
99_P	104_Q	1.509	1.00
133_V	146_L	1.484	1.00
40_A	44_Q	1.441	1.00
126_G	147_G	1.416	1.00
28_E	31_K	1.396	1.00
1_G	4_R	1.391	1.00
157_M	160_L	1.373	1.00
77_N	125_L	1.372	1.00
123_V	127_R	1.371	1.00
35_E	38_R	1.367	1.00
87_L	90_L	1.359	1.00
105_L	109_L	1.344	1.00
18_R	21_K	1.331	1.00
13_E	16_R	1.316	1.00
67_F	71_Y	1.285	1.00
64_V	143_T	1.276	1.00
32_R	36_A	1.267	1.00
40_A	43_R	1.255	1.00
13_E	17_R	1.252	1.00
113_V	117_V	1.251	1.00
86_A	90_L	1.246	1.00
48_M	162_L	1.246	1.00
138_P	142_S	1.230	1.00
109_L	113_V	1.226	1.00
87_L	91_V	1.213	1.00
120_V	124_L	1.196	1.00
53_E	61_R	1.176	1.00
127_R	131_R	1.173	1.00
36_A	40_A	1.170	1.00
32_R	35_E	1.157	1.00
128_R	131_R	1.147	1.00
64_V	141_E	1.136	0.99
26_R	29_A	1.128	0.99
65_R	146_L	1.125	0.99
130_K	134_A	1.117	0.99
41_R	44_Q	1.115	0.99
15_A	19_P	1.112	0.99
100_N	103_V	1.110	0.99
84_P	88_V	1.110	0.99
125_L	154_A	1.105	0.99
22_A	26_R	1.100	0.99
15_A	18_R	1.094	0.99
39_A	42_A	1.093	0.99
50_A	55_Y	1.084	0.99
27_K	30_R	1.081	0.99
152_M	155_L	1.067	0.99
43_R	55_Y	1.064	0.99
2_K	5_P	1.064	0.99
33_A	37_R	1.061	0.99
124_L	128_R	1.056	0.99
48_M	57_P	1.053	0.99
147_G	150_A	1.045	0.99
34_R	38_R	1.042	0.99
106_Y	110_L	1.039	0.99
22_A	32_R	1.030	0.99
101_P	104_Q	1.026	0.99
64_V	133_V	1.025	0.99
25_D	31_K	1.019	0.99
152_M	156_Q	1.006	0.99
27_K	33_A	1.003	0.99
122_G	155_L	0.980	0.98
138_P	143_T	0.979	0.98
95_L	98_V	0.963	0.98
83_L	87_L	0.953	0.98
124_L	127_R	0.952	0.98
37_R	40_A	0.951	0.98
58_A	61_R	0.951	0.98
62_G	66_R	0.943	0.98
52_D	55_Y	0.937	0.98
23_P	26_R	0.932	0.98
108_S	112_L	0.931	0.98
112_L	116_L	0.925	0.98
74_S	77_N	0.921	0.98
46_E	49_A	0.920	0.98
49_A	164_K	0.913	0.98
89_V	111_M	0.911	0.98
71_Y	129_L	0.899	0.97
167_V	170_G	0.899	0.97
116_L	120_V	0.899	0.97
10_K	14_A	0.886	0.97
2_K	6_T	0.885	0.97
130_K	147_G	0.873	0.97
68_V	133_V	0.868	0.97
121_D	125_L	0.865	0.97
82_F	118_V	0.858	0.96
142_S	145_G	0.856	0.96
134_A	143_T	0.855	0.96
138_P	141_E	0.849	0.96
44_Q	47_A	0.836	0.96
22_A	27_K	0.832	0.96
100_N	104_Q	0.831	0.96
133_V	147_G	0.822	0.95
34_R	37_R	0.817	0.95
25_D	32_R	0.817	0.95
126_G	151_A	0.817	0.95
30_R	33_A	0.809	0.95
143_T	146_L	0.805	0.95
43_R	47_A	0.804	0.95
156_Q	160_L	0.796	0.95
23_P	29_A	0.785	0.94
12_A	16_R	0.784	0.94
148_W	152_M	0.775	0.94
141_E	144_R	0.768	0.94
53_E	62_G	0.767	0.93
78_V	117_V	0.762	0.93
141_E	145_G	0.762	0.93
55_Y	61_R	0.760	0.93
107_A	110_L	0.760	0.93
119_V	123_V	0.756	0.93
98_V	103_V	0.754	0.93
77_N	154_A	0.754	0.93
160_L	164_K	0.753	0.93
8_K	12_A	0.744	0.92
103_V	106_Y	0.740	0.92
23_P	28_E	0.739	0.92
29_A	32_R	0.739	0.92
126_G	130_K	0.732	0.92
79_G	121_D	0.724	0.91
80_E	169_R	0.723	0.91
38_R	42_A	0.719	0.91
71_Y	132_L	0.719	0.91
13_E	18_R	0.713	0.91
4_R	11_E	0.709	0.90
22_A	29_A	0.708	0.90
92_L	107_A	0.706	0.90
78_V	85_L	0.706	0.90
89_V	107_A	0.703	0.90
72_V	125_L	0.703	0.90
95_L	100_N	0.702	0.90
67_F	136_R	0.697	0.90
47_A	57_P	0.697	0.90
74_S	132_L	0.689	0.89
19_P	22_A	0.688	0.89
127_R	134_A	0.686	0.89
109_L	116_L	0.684	0.89
88_V	92_L	0.680	0.89
52_D	56_L	0.679	0.89
64_V	67_F	0.678	0.88
68_V	137_F	0.677	0.88
24_A	28_E	0.676	0.88
140_D	143_T	0.675	0.88
125_L	129_L	0.674	0.88
44_Q	50_A	0.669	0.88
103_V	168_K	0.667	0.88
134_A	138_P	0.659	0.87
16_R	20_L	0.656	0.87
142_S	146_L	0.652	0.86
71_Y	80_E	0.652	0.86
115_L	155_L	0.648	0.86
38_R	41_R	0.648	0.86
43_R	46_E	0.647	0.86
3_G	6_T	0.644	0.86
2_K	9_R	0.643	0.86
45_R	93_T	0.639	0.85
14_A	19_P	0.638	0.85
27_K	31_K	0.636	0.85
6_T	9_R	0.634	0.85
115_L	160_L	0.630	0.85
23_P	27_K	0.628	0.84
79_G	154_A	0.627	0.84
118_V	155_L	0.626	0.84
152_M	160_L	0.626	0.84
71_Y	125_L	0.625	0.84
53_E	56_L	0.624	0.84
92_L	103_V	0.623	0.84
158_R	161_R	0.618	0.83
49_A	162_L	0.609	0.83
59_R	62_G	0.606	0.82
17_R	21_K	0.605	0.82
99_P	103_V	0.605	0.82
105_L	108_S	0.604	0.82
47_A	54_R	0.603	0.82
102_A	106_Y	0.602	0.82
15_A	20_L	0.600	0.82
30_R	34_R	0.600	0.82
59_R	65_R	0.588	0.80
22_A	28_E	0.587	0.80
90_L	114_L	0.587	0.80
10_K	15_A	0.586	0.80
12_A	19_P	0.584	0.80
127_R	135_E	0.584	0.80
157_M	162_L	0.582	0.80
111_M	122_G	0.580	0.79
59_R	154_A	0.578	0.79
159_R	168_K	0.577	0.79
130_K	143_T	0.572	0.78
126_G	129_L	0.569	0.78
79_G	122_G	0.567	0.78
14_A	18_R	0.566	0.78
76_R	170_G	0.566	0.78
82_F	111_M	0.565	0.78
49_A	53_E	0.562	0.77
77_N	80_E	0.562	0.77
117_V	120_V	0.561	0.77
8_K	14_A	0.558	0.77
127_R	159_R	0.556	0.76
78_V	92_L	0.553	0.76
53_E	60_D	0.551	0.76
24_A	31_K	0.549	0.76
111_M	115_L	0.547	0.75
71_Y	74_S	0.541	0.75
47_A	52_D	0.541	0.75
60_D	66_R	0.539	0.74
18_R	22_A	0.534	0.74
74_S	167_V	0.532	0.73
131_R	135_E	0.527	0.73
50_A	54_R	0.524	0.72
122_G	126_G	0.522	0.72
42_A	47_A	0.521	0.72
119_V	148_W	0.519	0.71
126_G	150_A	0.516	0.71
43_R	52_D	0.516	0.71
100_N	107_A	0.514	0.71
148_W	151_A	0.514	0.71
88_V	168_K	0.504	0.69
44_Q	55_Y	0.504	0.69
154_A	157_M	0.502	0.69
122_G	151_A	0.500	0.69

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
4jweC	1	0.0585	5.8	0.961	Contact Map
4cylA	1	0	5.5	0.962	Contact Map
1pi7A	1	0.1111	3.9	0.965	Contact Map
1wazA	1	0.2632	3.7	0.965	Contact Map
2m7gA	1	0.3567	3.4	0.965	Contact Map
3uwpA	1	0	3.2	0.966	Contact Map
1mhsA	2	0.7368	2.9	0.967	Contact Map
2f93B	2	0.2105	2.5	0.968	Contact Map
3aaeX	1	0.076	2.5	0.968	Contact Map
2hi2A	1	0.4795	2.3	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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