DUF4013 - PFAM28P - GREMLIN Contacts

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DUF4013 - Protein of unknown function (DUF4013)

PFAM:	PF13197	Sequences: ILGLLLLIPIIGWFLLLGYLLRVLRNVIAGEEELPEWDDWGELFVDGLKLFVVGLVYALLPLIIALLILLVALAALAGGDSAGAAAGLGALLGLLLALLGLLLGLLLALLLPAALARFARTGSFGAAFNFGEIFRLIRANIGNYLIALLVLLVAGFIAGLIGILLCI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	167 (162)
Sequences:	6034 (5334)
Seq/√Len:	419.0
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_V	127_A	4.229	1.00
9_P	12_G	3.908	1.00
22_R	43_L	3.694	1.00
129_N	132_E	3.430	1.00
49_K	118_F	2.856	1.00
53_V	118_F	2.692	1.00
25_R	46_D	2.285	1.00
126_A	129_N	2.280	1.00
117_R	121_T	2.144	1.00
121_T	126_A	2.143	1.00
39_D	42_E	2.104	1.00
46_D	49_K	2.043	1.00
21_L	50_L	2.029	1.00
10_I	13_W	2.029	1.00
28_I	120_R	2.020	1.00
6_L	9_P	2.018	1.00
42_E	46_D	1.998	1.00
123_S	126_A	1.969	1.00
34_L	37_W	1.949	1.00
45_V	48_L	1.881	1.00
26_N	31_E	1.865	1.00
123_S	129_N	1.845	1.00
22_R	42_E	1.823	1.00
45_V	49_K	1.806	1.00
161_I	165_L	1.790	1.00
6_L	12_G	1.784	1.00
14_F	51_F	1.776	1.00
25_R	122_G	1.738	1.00
52_V	124_F	1.736	1.00
21_L	118_F	1.704	1.00
22_R	46_D	1.630	1.00
134_F	138_R	1.624	1.00
117_R	132_E	1.620	1.00
117_R	129_N	1.606	1.00
22_R	26_N	1.597	1.00
162_G	165_L	1.595	1.00
117_R	120_R	1.516	1.00
7_L	12_G	1.509	1.00
57_Y	114_A	1.471	1.00
140_N	143_N	1.434	1.00
117_R	136_L	1.419	1.00
28_I	116_A	1.395	1.00
143_N	146_I	1.385	1.00
9_P	13_W	1.361	1.00
24_L	116_A	1.349	1.00
117_R	126_A	1.320	1.00
17_L	51_F	1.289	1.00
62_L	107_L	1.288	1.00
93_G	96_L	1.285	1.00
94_L	98_L	1.280	1.00
14_F	44_F	1.277	1.00
21_L	119_A	1.275	1.00
69_L	72_A	1.266	1.00
49_K	124_F	1.213	1.00
8_I	12_G	1.206	1.00
72_A	75_A	1.199	1.00
43_L	46_D	1.194	1.00
71_V	75_A	1.192	1.00
113_A	136_L	1.187	1.00
158_A	161_I	1.170	1.00
109_L	112_P	1.158	1.00
118_F	127_A	1.153	1.00
50_L	115_L	1.151	1.00
53_V	128_F	1.128	1.00
133_I	137_I	1.126	1.00
75_A	79_G	1.103	1.00
70_L	73_L	1.085	1.00
160_L	164_L	1.069	1.00
56_V	128_F	1.067	1.00
4_L	9_P	1.058	1.00
25_R	29_A	1.045	1.00
116_A	120_R	1.044	1.00
15_L	43_L	1.037	1.00
149_L	153_V	1.032	1.00
15_L	40_W	1.029	1.00
135_R	138_R	1.024	1.00
7_L	13_W	1.023	1.00
57_Y	133_I	1.010	1.00
56_V	124_F	1.009	1.00
23_V	35_P	1.008	1.00
4_L	7_L	1.006	1.00
72_A	76_L	1.000	1.00
113_A	137_I	0.997	1.00
110_L	134_F	0.970	1.00
93_G	97_A	0.962	1.00
66_L	69_L	0.955	1.00
158_A	165_L	0.954	1.00
73_L	77_A	0.949	1.00
37_W	43_L	0.949	1.00
19_Y	23_V	0.948	1.00
53_V	124_F	0.934	1.00
5_L	8_I	0.933	1.00
23_V	27_V	0.932	1.00
98_L	102_L	0.932	1.00
22_R	39_D	0.915	1.00
114_A	127_A	0.911	1.00
15_L	44_F	0.904	1.00
22_R	38_D	0.903	1.00
131_G	135_R	0.902	1.00
46_D	122_G	0.897	1.00
6_L	10_I	0.875	1.00
108_A	148_L	0.872	1.00
125_G	131_G	0.865	1.00
54_G	111_L	0.863	1.00
155_G	159_G	0.856	1.00
69_L	73_L	0.854	1.00
21_L	25_R	0.850	1.00
156_F	160_L	0.846	1.00
67_L	71_V	0.837	1.00
137_I	144_Y	0.829	1.00
100_G	104_G	0.812	1.00
109_L	137_I	0.799	1.00
58_A	61_P	0.799	1.00
44_F	47_G	0.796	1.00
144_Y	148_L	0.795	1.00
77_A	80_D	0.794	1.00
108_A	112_P	0.789	1.00
18_G	47_G	0.787	1.00
84_A	88_L	0.787	1.00
73_L	80_D	0.784	1.00
87_G	91_L	0.782	1.00
56_V	61_P	0.780	1.00
77_A	81_S	0.779	1.00
117_R	133_I	0.778	1.00
40_W	43_L	0.777	1.00
68_I	72_A	0.771	1.00
21_L	46_D	0.770	1.00
49_K	53_V	0.769	1.00
94_L	97_A	0.766	1.00
27_V	32_E	0.765	1.00
113_A	144_Y	0.765	1.00
116_A	119_A	0.760	1.00
12_G	16_L	0.759	1.00
10_I	14_F	0.752	1.00
114_A	133_I	0.750	1.00
73_L	76_L	0.746	1.00
79_G	82_A	0.744	1.00
148_L	151_L	0.743	1.00
124_F	128_F	0.741	1.00
57_Y	110_L	0.731	1.00
3_G	7_L	0.730	1.00
156_F	161_I	0.727	1.00
75_A	78_G	0.725	1.00
69_L	77_A	0.720	1.00
62_L	100_G	0.719	1.00
100_G	103_L	0.718	1.00
49_K	52_V	0.710	1.00
17_L	50_L	0.692	1.00
57_Y	127_A	0.690	1.00
136_L	144_Y	0.686	1.00
111_L	114_A	0.686	1.00
76_L	83_G	0.679	1.00
70_L	76_L	0.678	1.00
133_I	136_L	0.676	1.00
159_G	163_I	0.671	1.00
147_A	151_L	0.671	1.00
86_A	90_A	0.669	1.00
12_G	15_L	0.668	0.99
88_L	91_L	0.665	0.99
90_A	94_L	0.662	0.99
74_A	77_A	0.657	0.99
130_F	134_F	0.657	0.99
11_I	15_L	0.656	0.99
97_A	100_G	0.655	0.99
117_R	128_F	0.654	0.99
161_I	164_L	0.652	0.99
102_L	105_L	0.651	0.99
103_L	107_L	0.645	0.99
70_L	74_A	0.645	0.99
53_V	57_Y	0.645	0.99
91_L	95_L	0.642	0.99
78_G	83_G	0.642	0.99
122_G	126_A	0.640	0.99
38_D	43_L	0.639	0.99
65_A	69_L	0.636	0.99
7_L	10_I	0.632	0.99
120_R	123_S	0.630	0.99
14_F	48_L	0.626	0.99
42_E	45_V	0.625	0.99
3_G	12_G	0.623	0.99
53_V	114_A	0.622	0.99
130_F	133_I	0.622	0.99
158_A	162_G	0.621	0.99
46_D	118_F	0.617	0.99
103_L	106_L	0.615	0.99
75_A	81_S	0.613	0.99
142_G	146_I	0.612	0.99
116_A	136_L	0.612	0.99
65_A	72_A	0.606	0.99
19_Y	34_L	0.606	0.99
66_L	72_A	0.605	0.99
100_G	105_L	0.604	0.99
95_L	99_L	0.602	0.99
132_E	136_L	0.602	0.99
84_A	89_G	0.600	0.99
71_V	76_L	0.599	0.99
77_A	83_G	0.599	0.99
58_A	111_L	0.597	0.99
113_A	116_A	0.596	0.99
159_G	162_G	0.589	0.99
17_L	54_G	0.589	0.99
26_N	32_E	0.585	0.99
74_A	81_S	0.585	0.99
49_K	122_G	0.583	0.99
86_A	89_G	0.583	0.99
16_L	20_L	0.581	0.99
6_L	13_W	0.581	0.99
41_G	45_V	0.577	0.99
136_L	139_A	0.577	0.99
74_A	78_G	0.575	0.99
7_L	14_F	0.574	0.98
5_L	15_L	0.571	0.98
67_L	76_L	0.571	0.98
118_F	124_F	0.566	0.98
81_S	84_A	0.566	0.98
80_D	83_G	0.565	0.98
146_I	149_L	0.563	0.98
76_L	80_D	0.562	0.98
71_V	74_A	0.553	0.98
65_A	68_I	0.547	0.98
66_L	70_L	0.547	0.98
145_L	149_L	0.545	0.98
109_L	144_Y	0.545	0.98
134_F	137_I	0.541	0.98
160_L	163_I	0.538	0.98
85_A	88_L	0.535	0.98
51_F	55_L	0.532	0.98
67_L	70_L	0.532	0.98
121_T	129_N	0.531	0.97
68_I	75_A	0.528	0.97
107_L	114_A	0.528	0.97
109_L	148_L	0.527	0.97
58_A	107_L	0.527	0.97
78_G	82_A	0.526	0.97
15_L	37_W	0.525	0.97
3_G	13_W	0.525	0.97
68_I	81_S	0.514	0.97
142_G	152_L	0.511	0.97
60_L	63_I	0.504	0.97
3_G	6_L	0.504	0.97
109_L	145_L	0.503	0.97
24_L	119_A	0.501	0.96
61_P	64_I	0.500	0.96

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
3tx3A	2	0.8084	14.1	0.89	Contact Map
3ayfA	2	0.1976	4.8	0.911	Contact Map
3ne5A	3	0.8623	4.3	0.913	Contact Map
3aqpA	1	0.6407	4.1	0.914	Contact Map
4k0jA	3	0.7904	3.3	0.918	Contact Map
4ldeA	1	0.6527	2.8	0.921	Contact Map
3rqwA	4	0.3054	2.6	0.922	Contact Map
4n6hA	1	0.7305	2.6	0.922	Contact Map
4yayA	1	0.6527	2.1	0.926	Contact Map
3mktA	1	0.8982	2	0.927	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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