DUF3014 - PFAM28P - GREMLIN Contacts

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DUF3014 - Protein of unknown function (DUF3014)

PFAM:	PF11219	Sequences: LIRRFVATVDNLARGKVPARLLPVLPPPGRFAVTGRGGRLVIDPANYARYDPYVDAVESVDAAALAALYRRLYPLFQQAYRELGYPDGYFNDRLVEAIDHLLATPEVEGPIALVRPKVLYEFADPALEALSAGQKQLLRMGPENARRVKAKLRELR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	156 (156)
Sequences:	4649 (3375)
Seq/√Len:	270.2
META:	0.945

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
100_H	131_S	3.168	1.00
58_E	147_R	3.166	1.00
73_Y	91_N	2.653	1.00
151_K	154_E	2.634	1.00
60_V	65_L	2.580	1.00
130_L	138_L	2.485	1.00
140_M	148_V	2.374	1.00
106_E	149_K	2.311	1.00
39_R	112_A	2.150	1.00
48_A	51_D	2.000	1.00
62_A	151_K	1.999	1.00
42_I	113_L	1.997	1.00
107_V	111_I	1.864	1.00
97_A	100_H	1.846	1.00
89_Y	92_D	1.770	1.00
62_A	66_A	1.747	1.00
3_R	82_E	1.745	1.00
130_L	134_Q	1.741	1.00
112_A	123_A	1.735	1.00
27_P	53_Y	1.721	1.00
40_L	113_L	1.700	1.00
114_V	121_E	1.689	1.00
81_R	88_G	1.682	1.00
104_T	134_Q	1.678	1.00
145_A	149_K	1.673	1.00
34_T	43_D	1.610	1.00
7_A	11_N	1.609	1.00
81_R	87_D	1.580	1.00
10_D	14_R	1.579	1.00
7_A	21_L	1.569	1.00
31_F	42_I	1.547	1.00
51_D	55_D	1.508	1.00
54_V	148_V	1.492	1.00
98_I	102_L	1.480	1.00
98_I	152_L	1.475	1.00
35_G	40_L	1.448	1.00
17_V	22_L	1.447	1.00
9_V	90_F	1.429	1.00
57_V	148_V	1.383	1.00
104_T	138_L	1.356	1.00
62_A	154_E	1.354	1.00
64_A	67_A	1.345	1.00
33_V	40_L	1.334	1.00
117_K	121_E	1.320	1.00
126_A	130_L	1.318	1.00
2_I	76_F	1.302	1.00
66_A	155_L	1.276	1.00
142_P	146_R	1.267	1.00
79_A	82_E	1.262	1.00
73_Y	89_Y	1.253	1.00
53_Y	57_V	1.253	1.00
54_V	58_E	1.248	1.00
1_L	5_F	1.232	1.00
100_H	134_Q	1.225	1.00
115_R	118_V	1.220	1.00
13_A	100_H	1.218	1.00
137_L	140_M	1.211	1.00
143_E	147_R	1.206	1.00
101_L	152_L	1.197	1.00
80_Y	93_R	1.197	1.00
61_D	64_A	1.196	1.00
41_V	112_A	1.189	1.00
10_D	85_Y	1.162	1.00
121_E	128_E	1.147	1.00
51_D	144_N	1.145	1.00
32_A	43_D	1.139	1.00
55_D	143_E	1.134	1.00
62_A	155_L	1.133	1.00
78_Q	82_E	1.126	1.00
141_G	144_N	1.118	1.00
40_L	115_R	1.117	1.00
42_I	47_Y	1.114	1.00
55_D	147_R	1.102	1.00
99_D	156_R	1.099	1.00
116_P	119_L	1.097	1.00
77_Q	89_Y	1.086	1.00
95_V	99_D	1.086	1.00
68_L	72_L	1.079	1.00
5_F	9_V	1.075	1.00
45_A	48_A	1.073	1.00
72_L	76_F	1.056	1.00
57_V	151_K	1.048	1.00
102_L	153_R	1.046	1.00
104_T	145_A	1.045	1.00
55_D	58_E	1.045	1.00
19_A	22_L	1.042	1.00
111_I	138_L	1.040	1.00
128_E	135_K	1.034	1.00
32_A	46_N	1.032	1.00
101_L	133_G	1.026	1.00
69_Y	91_N	1.017	1.00
100_H	104_T	1.005	1.00
75_L	78_Q	1.004	1.00
58_E	151_K	1.003	1.00
47_Y	142_P	0.997	1.00
35_G	41_V	0.995	1.00
151_K	155_L	0.987	1.00
105_P	134_Q	0.982	1.00
114_V	123_A	0.977	1.00
85_Y	88_G	0.962	1.00
89_Y	95_V	0.962	1.00
104_T	137_L	0.960	1.00
42_I	122_F	0.948	1.00
99_D	103_A	0.943	1.00
40_L	120_Y	0.937	1.00
5_F	76_F	0.929	1.00
35_G	39_R	0.928	1.00
76_F	94_L	0.918	1.00
107_V	145_A	0.900	1.00
17_V	21_L	0.894	1.00
91_N	95_V	0.874	1.00
13_A	97_A	0.872	1.00
90_F	94_L	0.858	1.00
35_G	38_G	0.847	1.00
95_V	156_R	0.841	1.00
140_M	145_A	0.835	0.99
42_I	111_I	0.831	0.99
80_Y	85_Y	0.829	0.99
27_P	136_Q	0.821	0.99
77_Q	81_R	0.819	0.99
92_D	95_V	0.819	0.99
6_V	10_D	0.814	0.99
36_R	39_R	0.814	0.99
124_D	127_L	0.808	0.99
138_L	145_A	0.804	0.99
144_N	147_R	0.796	0.99
132_A	135_K	0.790	0.99
22_L	27_P	0.790	0.99
54_V	57_V	0.780	0.99
34_T	44_P	0.774	0.99
36_R	41_V	0.774	0.99
54_V	140_M	0.773	0.99
34_T	45_A	0.768	0.99
118_V	121_E	0.765	0.99
150_A	154_E	0.760	0.99
6_V	76_F	0.760	0.99
113_L	123_A	0.756	0.99
78_Q	81_R	0.756	0.99
47_Y	111_I	0.752	0.99
76_F	90_F	0.752	0.99
140_M	144_N	0.750	0.99
17_V	136_Q	0.742	0.99
116_P	121_E	0.738	0.99
107_V	127_L	0.728	0.99
104_T	149_K	0.725	0.99
147_R	150_A	0.724	0.99
11_N	21_L	0.722	0.99
56_A	59_S	0.719	0.98
93_R	96_E	0.718	0.98
54_V	147_R	0.716	0.98
32_A	45_A	0.709	0.98
143_E	146_R	0.705	0.98
12_L	133_G	0.703	0.98
34_T	41_V	0.702	0.98
4_R	8_T	0.694	0.98
108_E	146_R	0.693	0.98
19_A	26_P	0.691	0.98
80_Y	90_F	0.691	0.98
43_D	47_Y	0.690	0.98
80_Y	86_P	0.689	0.98
67_A	71_R	0.688	0.98
77_Q	90_F	0.682	0.98
113_L	116_P	0.678	0.98
18_P	21_L	0.677	0.98
131_S	134_Q	0.676	0.98
73_Y	77_Q	0.676	0.98
25_L	53_Y	0.674	0.98
64_A	68_L	0.673	0.98
67_A	70_R	0.668	0.98
69_Y	73_Y	0.664	0.97
66_A	70_R	0.664	0.97
52_P	55_D	0.660	0.97
147_R	151_K	0.658	0.97
42_I	46_N	0.657	0.97
81_R	89_Y	0.656	0.97
55_D	59_S	0.655	0.97
126_A	129_A	0.655	0.97
33_V	120_Y	0.654	0.97
36_R	40_L	0.651	0.97
10_D	93_R	0.647	0.97
142_P	145_A	0.643	0.97
76_F	91_N	0.633	0.97
9_V	93_R	0.632	0.97
94_L	98_I	0.622	0.96
41_V	110_P	0.619	0.96
51_D	143_E	0.617	0.96
65_L	68_L	0.614	0.96
73_Y	95_V	0.614	0.96
100_H	103_A	0.613	0.96
73_Y	92_D	0.612	0.96
38_G	41_V	0.609	0.96
127_L	138_L	0.602	0.96
133_G	136_Q	0.597	0.95
138_L	142_P	0.595	0.95
63_A	67_A	0.593	0.95
8_T	11_N	0.593	0.95
22_L	26_P	0.591	0.95
115_R	121_E	0.591	0.95
11_N	18_P	0.589	0.95
90_F	93_R	0.587	0.95
107_V	138_L	0.585	0.95
41_V	111_I	0.583	0.95
18_P	22_L	0.581	0.95
14_R	85_Y	0.578	0.94
97_A	101_L	0.576	0.94
61_D	151_K	0.567	0.94
144_N	148_V	0.557	0.93
106_E	146_R	0.552	0.93
8_T	22_L	0.552	0.93
23_P	136_Q	0.550	0.93
99_D	102_L	0.549	0.93
145_A	148_V	0.549	0.93
33_V	113_L	0.546	0.93
62_A	65_L	0.546	0.93
79_A	84_G	0.545	0.93
5_F	23_P	0.541	0.92
51_D	54_V	0.539	0.92
13_A	93_R	0.536	0.92
101_L	145_A	0.533	0.92
15_G	25_L	0.530	0.91
81_R	86_P	0.529	0.91
13_A	16_K	0.527	0.91
23_P	26_P	0.525	0.91
106_E	145_A	0.522	0.91
46_N	54_V	0.519	0.91
22_L	53_Y	0.518	0.91
53_Y	155_L	0.516	0.90
10_D	16_K	0.516	0.90
8_T	12_L	0.515	0.90
38_G	112_A	0.511	0.90
107_V	110_P	0.507	0.90
146_R	150_A	0.502	0.89
12_L	97_A	0.501	0.89
19_A	27_P	0.500	0.89

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
3c1yA	5	0.8782	21.3	0.943	Contact Map
2d0tA	1	0.8333	20.1	0.943	Contact Map
3ktaB	1	0.5705	15.1	0.946	Contact Map
4ka7A	1	0.7564	10.4	0.95	Contact Map
1y791	1	0.7628	9.1	0.952	Contact Map
4nqwA	1	0.6795	7.9	0.953	Contact Map
2wtgA	2	0.5128	7.9	0.953	Contact Map
2b1eA	1	0.8141	6.9	0.954	Contact Map
3i10A	1	0.609	6.4	0.955	Contact Map
1mvfD	1	0.2692	6.2	0.955	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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