DUF4199 - PFAM28P - GREMLIN Contacts

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DUF4199 - Protein of unknown function (DUF4199)

PFAM:	PF13858	Sequences: KYGLILGLISIVLMLLILYFLGLHEIFDTGPLLGYLSLLLFLLTIVLIFFGIKSYRDNNLGGFISFGQAFKVGLLISLIASLIYVIFWYIYFNFIDPDFMEKYIEAAIEKMEASGASAAEEEAIGMTEEQIEEAMEMMKPLFNALMTFIESLPVGLIISLISAAILKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	168 (163)
Sequences:	11891 (10209)
Seq/√Len:	799.7
META:	0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_I	69_A	2.943	1.00
11_I	87_F	2.582	1.00
53_K	57_D	2.447	1.00
6_L	80_A	2.392	1.00
51_G	76_I	2.246	1.00
77_S	155_G	2.187	1.00
127_T	130_Q	2.089	1.00
91_Y	96_D	2.050	1.00
54_S	58_N	1.959	1.00
108_I	112_E	1.955	1.00
89_Y	93_N	1.933	1.00
73_G	159_S	1.921	1.00
105_E	109_E	1.861	1.00
46_V	50_F	1.851	1.00
128_E	132_E	1.828	1.00
101_E	105_E	1.823	1.00
105_E	108_I	1.785	1.00
7_G	83_I	1.749	1.00
68_Q	71_K	1.706	1.00
98_D	102_K	1.705	1.00
102_K	105_E	1.687	1.00
109_E	112_E	1.665	1.00
55_Y	72_V	1.662	1.00
65_S	68_Q	1.653	1.00
98_D	101_E	1.652	1.00
90_I	94_F	1.637	1.00
52_I	166_L	1.627	1.00
106_A	109_E	1.623	1.00
40_L	43_L	1.618	1.00
106_A	110_K	1.616	1.00
52_I	162_S	1.593	1.00
126_M	130_Q	1.539	1.00
104_I	108_I	1.528	1.00
109_E	113_A	1.509	1.00
69_A	163_A	1.500	1.00
130_Q	133_E	1.480	1.00
70_F	156_L	1.464	1.00
158_I	162_S	1.455	1.00
49_F	53_K	1.446	1.00
38_L	41_F	1.445	1.00
129_E	133_E	1.441	1.00
110_K	113_A	1.433	1.00
4_L	8_L	1.431	1.00
66_F	70_F	1.415	1.00
107_A	111_M	1.401	1.00
77_S	81_S	1.369	1.00
125_G	128_E	1.347	1.00
31_P	35_Y	1.347	1.00
140_P	143_N	1.324	1.00
6_L	47_L	1.313	1.00
77_S	159_S	1.308	1.00
117_S	120_E	1.295	1.00
125_G	129_E	1.294	1.00
107_A	110_K	1.279	1.00
121_E	124_I	1.267	1.00
121_E	125_G	1.265	1.00
127_T	131_I	1.261	1.00
103_Y	107_A	1.235	1.00
17_I	20_F	1.221	1.00
31_P	34_G	1.202	1.00
101_E	104_I	1.197	1.00
53_K	166_L	1.189	1.00
162_S	166_L	1.189	1.00
52_I	73_G	1.186	1.00
87_F	91_Y	1.174	1.00
133_E	137_M	1.174	1.00
118_A	121_E	1.171	1.00
66_F	160_L	1.167	1.00
50_F	54_S	1.154	1.00
89_Y	94_F	1.146	1.00
14_M	87_F	1.145	1.00
85_V	144_A	1.139	1.00
38_L	42_L	1.125	1.00
124_I	127_T	1.116	1.00
3_G	7_G	1.096	1.00
91_Y	99_F	1.094	1.00
39_L	42_L	1.088	1.00
133_E	136_E	1.086	1.00
132_E	136_E	1.085	1.00
136_E	139_K	1.065	1.00
128_E	131_I	1.061	1.00
123_A	126_M	1.054	1.00
56_R	168_K	1.054	1.00
111_M	114_S	1.050	1.00
135_M	139_K	1.033	1.00
148_F	152_L	1.032	1.00
33_L	37_S	1.026	1.00
146_M	150_E	1.022	1.00
7_G	11_I	1.022	1.00
123_A	127_T	1.019	1.00
18_L	21_L	1.017	1.00
34_G	37_S	1.015	1.00
17_I	21_L	1.007	1.00
72_V	76_I	1.006	1.00
55_Y	60_L	1.003	1.00
124_I	128_E	0.999	1.00
54_S	57_D	0.991	1.00
15_L	87_F	0.986	1.00
89_Y	144_A	0.986	1.00
104_I	107_A	0.969	1.00
147_T	151_S	0.962	1.00
3_G	79_I	0.958	1.00
49_F	162_S	0.949	1.00
2_Y	54_S	0.946	1.00
82_L	148_F	0.940	1.00
102_K	106_A	0.939	1.00
131_I	134_A	0.937	1.00
131_I	135_M	0.924	1.00
111_M	115_G	0.923	1.00
140_P	144_A	0.912	1.00
60_L	64_I	0.910	1.00
53_K	56_R	0.908	1.00
19_Y	22_G	0.906	1.00
126_M	129_E	0.905	1.00
51_G	72_V	0.901	1.00
150_E	154_V	0.900	1.00
21_L	24_H	0.897	1.00
122_E	125_G	0.891	1.00
85_V	148_F	0.891	1.00
146_M	149_I	0.882	1.00
67_G	71_K	0.880	1.00
10_S	80_A	0.879	1.00
134_A	138_M	0.878	1.00
14_M	84_Y	0.877	1.00
100_M	104_I	0.873	1.00
2_Y	51_G	0.871	1.00
132_E	135_M	0.869	1.00
115_G	118_A	0.847	1.00
10_S	84_Y	0.845	1.00
81_S	151_S	0.844	1.00
18_L	23_L	0.840	1.00
81_S	85_V	0.839	1.00
89_Y	92_F	0.822	1.00
6_L	10_S	0.821	1.00
96_D	102_K	0.821	1.00
71_K	74_L	0.817	1.00
48_I	52_I	0.814	1.00
71_K	75_L	0.809	1.00
110_K	114_S	0.809	1.00
4_L	83_I	0.803	1.00
13_L	18_L	0.796	1.00
121_E	127_T	0.793	1.00
81_S	155_G	0.792	1.00
74_L	156_L	0.791	1.00
124_I	131_I	0.781	1.00
84_Y	88_W	0.777	1.00
5_I	9_I	0.768	1.00
66_F	164_A	0.765	1.00
128_E	135_M	0.765	1.00
48_I	77_S	0.765	1.00
116_A	120_E	0.763	1.00
108_I	111_M	0.761	1.00
134_A	137_M	0.761	1.00
64_I	166_L	0.759	1.00
20_F	23_L	0.756	1.00
81_S	148_F	0.744	1.00
17_I	22_G	0.736	1.00
142_F	146_M	0.733	1.00
50_F	53_K	0.732	1.00
19_Y	23_L	0.731	1.00
27_F	106_A	0.730	1.00
88_W	92_F	0.729	1.00
91_Y	94_F	0.725	1.00
135_M	138_M	0.719	1.00
122_E	126_M	0.709	1.00
103_Y	106_A	0.704	1.00
99_F	103_Y	0.701	1.00
70_F	163_A	0.699	1.00
39_L	43_L	0.689	1.00
78_L	152_L	0.685	1.00
91_Y	95_I	0.685	1.00
10_S	14_M	0.685	1.00
32_L	36_L	0.684	1.00
164_A	167_K	0.683	1.00
48_I	162_S	0.679	1.00
76_I	80_A	0.676	1.00
48_I	73_G	0.676	1.00
55_Y	59_N	0.673	1.00
83_I	87_F	0.673	1.00
8_L	12_V	0.665	1.00
52_I	72_V	0.664	1.00
60_L	63_F	0.663	1.00
60_L	68_Q	0.662	1.00
100_M	103_Y	0.660	1.00
17_I	23_L	0.658	1.00
57_D	62_G	0.658	1.00
142_F	145_L	0.656	1.00
66_F	163_A	0.654	1.00
2_Y	72_V	0.651	1.00
70_F	74_L	0.648	1.00
129_E	132_E	0.646	1.00
67_G	70_F	0.644	1.00
72_V	75_L	0.642	1.00
151_S	154_V	0.642	1.00
66_F	165_I	0.635	1.00
11_I	15_L	0.633	1.00
29_T	32_L	0.633	1.00
49_F	166_L	0.629	1.00
97_P	101_E	0.628	1.00
74_L	77_S	0.627	1.00
94_F	97_P	0.627	1.00
155_G	159_S	0.624	1.00
48_I	51_G	0.614	1.00
56_R	62_G	0.613	1.00
115_G	119_A	0.612	1.00
28_D	31_P	0.612	1.00
92_F	99_F	0.603	1.00
11_I	14_M	0.601	1.00
144_A	148_F	0.598	1.00
116_A	119_A	0.595	1.00
92_F	100_M	0.593	1.00
7_G	10_S	0.589	1.00
75_L	79_I	0.589	1.00
38_L	43_L	0.588	1.00
47_L	51_G	0.585	1.00
10_S	151_S	0.580	1.00
80_A	84_Y	0.571	1.00
161_I	164_A	0.568	1.00
63_F	67_G	0.568	1.00
32_L	37_S	0.564	1.00
154_V	158_I	0.563	1.00
2_Y	6_L	0.559	1.00
122_E	127_T	0.559	1.00
29_T	33_L	0.559	1.00
127_T	135_M	0.554	1.00
128_E	134_A	0.552	1.00
130_Q	134_A	0.550	1.00
90_I	95_I	0.549	1.00
156_L	159_S	0.545	1.00
115_G	120_E	0.539	1.00
30_G	33_L	0.536	1.00
18_L	24_H	0.533	1.00
52_I	69_A	0.530	1.00
124_I	134_A	0.528	1.00
75_L	78_L	0.527	1.00
147_T	150_E	0.525	1.00
84_Y	151_S	0.523	1.00
16_L	19_Y	0.522	1.00
79_I	82_L	0.515	1.00
125_G	131_I	0.511	1.00
125_G	130_Q	0.509	1.00
9_I	13_L	0.508	1.00
141_L	145_L	0.502	1.00
2_Y	5_I	0.500	1.00

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
2l9uA	2	0.1845	8.1	0.907	Contact Map
1iijA	1	0.2024	5.2	0.915	Contact Map
4i0uA	4	0.3393	5.2	0.915	Contact Map
4ev6A	3	0.3512	3.8	0.921	Contact Map
3rvyA	3	0.5298	3.7	0.921	Contact Map
2l2tA	2	0.2143	3.5	0.921	Contact Map
4xp4A	1	0.9702	3.5	0.922	Contact Map
2m20A	2	0.1726	3.4	0.922	Contact Map
4av3A	2	0.5119	3.3	0.922	Contact Map
3j1zP	8	0.9464	3.2	0.923	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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