DUF2993 - PFAM28P - GREMLIN Contacts

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DUF2993 - Protein of unknown function (DUF2993)

PFAM:	PF11209	Sequences: VADRVAAAYAERRAADALRSQLGLAEDPDVSIGGFPFLTQLLSGRYDSVDVSARGVTVDGGGLRIASLDATLDDVRLDLSSLLSGKLSLATAGSATGTATLTYADLNRALGSPLVRLGGGLLISDLQIGDLGNGTVELTGDTVLLGGLPVSVTATLTVVVGDGTLRLTPTDVTLGGGGPSQPLPPALLDALLDALDFTLDLPGLPFGLRLTSVEVTPGGLVITAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	225 (211)
Sequences:	4336 (3413)
Seq/√Len:	235.0
META:	0.612

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_D	93_G	5.902	1.00
33_G	50_D	3.301	1.00
4_R	7_A	3.036	1.00
52_S	69_D	2.867	1.00
13_R	17_A	2.855	1.00
7_A	11_E	2.643	1.00
48_S	71_T	2.547	1.00
53_A	56_V	2.273	1.00
64_R	105_D	2.155	1.00
8_A	12_R	2.122	1.00
36_P	39_T	2.087	1.00
9_Y	13_R	2.081	1.00
24_L	28_P	2.054	1.00
5_V	9_Y	2.008	1.00
102_T	105_D	1.979	1.00
13_R	16_D	1.974	1.00
153_T	156_L	1.967	1.00
50_D	71_T	1.958	1.00
3_D	7_A	1.941	1.00
160_V	163_G	1.905	1.00
216_T	221_V	1.899	1.00
76_R	93_G	1.876	1.00
19_R	27_D	1.874	1.00
15_A	19_R	1.822	1.00
69_D	98_T	1.792	1.00
123_I	127_Q	1.770	1.00
103_Y	218_G	1.764	1.00
72_L	95_A	1.746	1.00
103_Y	215_V	1.729	1.00
131_L	134_G	1.719	1.00
33_G	48_S	1.716	1.00
214_E	221_V	1.708	1.00
17_A	20_S	1.697	1.00
72_L	75_V	1.605	1.00
98_T	221_V	1.604	1.00
97_G	224_A	1.596	1.00
150_V	156_L	1.593	1.00
11_E	32_I	1.571	1.00
121_L	124_S	1.554	1.00
66_A	102_T	1.533	1.00
130_D	133_N	1.514	1.00
121_L	126_L	1.511	1.00
135_T	139_T	1.506	1.00
35_F	39_T	1.486	1.00
189_D	193_D	1.486	1.00
212_S	223_T	1.481	1.00
121_L	125_D	1.481	1.00
73_D	94_S	1.468	1.00
175_G	178_G	1.463	1.00
134_G	139_T	1.463	1.00
38_L	42_L	1.461	1.00
98_T	223_T	1.460	1.00
48_S	73_D	1.453	1.00
216_T	219_G	1.453	1.00
12_R	16_D	1.449	1.00
105_D	108_R	1.438	1.00
124_S	127_Q	1.415	1.00
132_G	137_E	1.410	1.00
5_V	8_A	1.406	1.00
103_Y	219_G	1.367	1.00
34_G	40_Q	1.366	1.00
122_L	125_D	1.364	1.00
41_L	46_Y	1.350	1.00
165_L	169_P	1.335	1.00
134_G	140_G	1.314	1.00
55_G	64_R	1.306	1.00
107_N	110_L	1.305	1.00
3_D	11_E	1.294	1.00
191_L	195_L	1.259	1.00
2_A	5_V	1.257	1.00
151_S	156_L	1.251	1.00
154_A	158_V	1.235	1.00
40_Q	47_D	1.225	1.00
132_G	140_G	1.218	1.00
132_G	135_T	1.200	1.00
46_Y	206_F	1.197	1.00
129_G	133_N	1.195	1.00
147_G	156_L	1.192	1.00
131_L	140_G	1.182	1.00
39_T	43_S	1.181	1.00
133_N	139_T	1.172	1.00
16_D	20_S	1.171	1.00
123_I	126_L	1.170	1.00
133_N	140_G	1.170	1.00
62_G	65_I	1.168	1.00
132_G	139_T	1.166	1.00
8_A	11_E	1.154	1.00
152_V	156_L	1.148	1.00
146_G	149_P	1.145	1.00
147_G	154_A	1.132	1.00
79_L	82_L	1.127	1.00
131_L	137_E	1.120	1.00
150_V	153_T	1.120	1.00
100_T	219_G	1.113	1.00
32_I	49_V	1.111	1.00
26_E	55_G	1.106	1.00
46_Y	49_V	1.088	1.00
131_L	135_T	1.069	1.00
174_L	178_G	1.062	1.00
134_G	141_D	1.061	1.00
107_N	111_G	1.054	1.00
148_L	154_A	1.044	1.00
2_A	6_A	1.033	1.00
40_Q	46_Y	1.029	1.00
11_E	15_A	1.024	1.00
39_T	99_A	1.023	1.00
104_A	108_R	1.021	1.00
167_L	197_F	1.020	1.00
15_A	18_L	1.011	1.00
103_Y	107_N	1.009	1.00
45_R	76_R	1.001	1.00
142_T	145_L	0.997	1.00
3_D	10_A	0.994	1.00
150_V	154_A	0.992	1.00
204_L	207_G	0.989	1.00
24_L	27_D	0.985	1.00
25_A	28_P	0.982	1.00
149_P	155_T	0.981	1.00
146_G	154_A	0.975	1.00
149_P	153_T	0.973	1.00
122_L	127_Q	0.967	1.00
159_V	163_G	0.961	1.00
165_L	213_V	0.961	1.00
156_L	160_V	0.960	1.00
135_T	141_D	0.956	1.00
67_S	100_T	0.948	1.00
15_A	30_V	0.945	1.00
149_P	156_L	0.935	1.00
122_L	126_L	0.933	1.00
183_L	187_L	0.931	1.00
195_L	198_T	0.931	1.00
7_A	32_I	0.930	1.00
134_G	138_L	0.921	1.00
15_A	28_P	0.919	1.00
188_L	192_L	0.915	1.00
151_S	155_T	0.915	1.00
44_G	79_L	0.913	1.00
150_V	155_T	0.911	1.00
169_P	173_T	0.907	1.00
149_P	154_A	0.902	1.00
76_R	90_A	0.883	0.99
100_T	221_V	0.882	0.99
129_G	132_G	0.879	0.99
45_R	93_G	0.876	0.99
157_T	170_T	0.873	0.99
169_P	172_V	0.871	0.99
132_G	138_L	0.864	0.99
74_D	92_A	0.861	0.99
3_D	37_F	0.858	0.99
45_R	74_D	0.857	0.99
164_T	200_D	0.856	0.99
121_L	127_Q	0.855	0.99
139_T	142_T	0.851	0.99
61_G	64_R	0.849	0.99
10_A	32_I	0.848	0.99
181_Q	184_P	0.843	0.99
35_F	40_Q	0.840	0.99
73_D	96_T	0.840	0.99
174_L	177_G	0.837	0.99
136_V	145_L	0.835	0.99
131_L	139_T	0.834	0.99
29_D	52_S	0.829	0.99
159_V	168_T	0.829	0.99
221_V	224_A	0.824	0.99
6_A	38_L	0.819	0.99
130_D	136_V	0.815	0.99
34_G	39_T	0.814	0.99
192_L	195_L	0.810	0.99
36_P	40_Q	0.808	0.99
132_G	136_V	0.801	0.99
134_G	137_E	0.799	0.99
7_A	14_A	0.788	0.99
190_A	193_D	0.787	0.99
6_A	10_A	0.787	0.99
14_A	17_A	0.786	0.99
87_L	91_T	0.784	0.99
9_Y	12_R	0.783	0.99
28_P	37_F	0.783	0.99
77_L	87_L	0.782	0.99
28_P	53_A	0.766	0.98
37_F	46_Y	0.766	0.98
55_G	66_A	0.764	0.98
157_T	168_T	0.763	0.98
208_L	224_A	0.758	0.98
159_V	162_D	0.756	0.98
184_P	188_L	0.753	0.98
68_L	99_A	0.752	0.98
18_L	53_A	0.749	0.98
63_L	109_A	0.743	0.98
81_S	86_K	0.742	0.98
130_D	134_G	0.741	0.98
55_G	105_D	0.733	0.98
193_D	196_D	0.724	0.98
189_D	192_L	0.718	0.98
166_R	169_P	0.717	0.98
138_L	143_V	0.710	0.97
3_D	34_G	0.703	0.97
76_R	91_T	0.702	0.97
55_G	67_S	0.701	0.97
184_P	191_L	0.700	0.97
151_S	154_A	0.697	0.97
195_L	199_L	0.696	0.97
4_R	39_T	0.694	0.97
30_V	51_V	0.686	0.97
218_G	221_V	0.685	0.97
28_P	36_P	0.677	0.97
22_L	53_A	0.677	0.97
133_N	145_L	0.672	0.96
6_A	19_R	0.672	0.96
148_L	151_S	0.671	0.96
169_P	177_G	0.669	0.96
188_L	191_L	0.667	0.96
41_L	44_G	0.666	0.96
161_G	166_R	0.665	0.96
13_R	18_L	0.662	0.96
188_L	197_F	0.661	0.96
44_G	77_L	0.661	0.96
131_L	138_L	0.655	0.96
129_G	140_G	0.648	0.96
206_F	210_L	0.647	0.96
7_A	39_T	0.645	0.95
138_L	141_D	0.642	0.95
65_I	110_L	0.637	0.95
32_I	37_F	0.635	0.95
204_L	208_L	0.634	0.95
178_G	183_L	0.634	0.95
11_E	14_A	0.634	0.95
19_R	24_L	0.632	0.95
31_S	50_D	0.631	0.95
6_A	37_F	0.627	0.95
19_R	28_P	0.627	0.95
129_G	138_L	0.626	0.95
153_T	173_T	0.624	0.95
73_D	92_A	0.623	0.95
47_D	74_D	0.619	0.94
163_G	168_T	0.619	0.94
75_V	92_A	0.618	0.94
76_R	80_S	0.618	0.94
32_I	39_T	0.616	0.94
147_G	151_S	0.615	0.94
211_T	224_A	0.615	0.94
42_L	79_L	0.615	0.94
172_V	175_G	0.614	0.94
37_F	40_Q	0.613	0.94
63_L	68_L	0.612	0.94
12_R	15_A	0.610	0.94
190_A	196_D	0.609	0.94
134_G	145_L	0.607	0.94
25_A	53_A	0.606	0.94
7_A	43_S	0.606	0.94
31_S	52_S	0.603	0.94
56_V	105_D	0.603	0.94
77_L	99_A	0.600	0.93
191_L	194_A	0.599	0.93
17_A	21_Q	0.595	0.93
57_T	62_G	0.593	0.93
25_A	34_G	0.592	0.93
78_D	89_L	0.588	0.93
43_S	50_D	0.587	0.93
148_L	152_V	0.587	0.93
21_Q	32_I	0.585	0.93
57_T	187_L	0.584	0.92
34_G	37_F	0.584	0.92
130_D	140_G	0.584	0.92
101_L	106_L	0.582	0.92
133_N	138_L	0.582	0.92
49_V	75_V	0.581	0.92
46_Y	75_V	0.579	0.92
14_A	18_L	0.576	0.92
214_E	223_T	0.573	0.92
4_R	103_Y	0.570	0.92
19_R	22_L	0.568	0.91
66_A	105_D	0.564	0.91
213_V	222_I	0.563	0.91
46_Y	72_L	0.561	0.91
129_G	136_V	0.561	0.91
7_A	20_S	0.560	0.91
68_L	72_L	0.560	0.91
54_R	67_S	0.558	0.91
205_P	210_L	0.557	0.91
192_L	196_D	0.554	0.90
104_A	107_N	0.553	0.90
194_A	198_T	0.553	0.90
173_T	194_A	0.552	0.90
164_T	198_T	0.551	0.90
135_T	138_L	0.551	0.90
159_V	166_R	0.550	0.90
151_S	160_V	0.545	0.90
76_R	92_A	0.542	0.89
74_D	81_S	0.541	0.89
185_P	189_D	0.537	0.89
40_Q	49_V	0.536	0.89
166_R	198_T	0.536	0.89
74_D	91_T	0.536	0.89
126_L	135_T	0.533	0.89
147_G	153_T	0.532	0.89
19_R	23_G	0.532	0.89
104_A	218_G	0.532	0.89
34_G	47_D	0.531	0.88
58_V	200_D	0.531	0.88
110_L	169_P	0.529	0.88
167_L	173_T	0.528	0.88
78_D	81_S	0.524	0.88
56_V	68_L	0.521	0.87
138_L	142_T	0.521	0.87
47_D	222_I	0.520	0.87
108_R	112_S	0.516	0.87
16_D	19_R	0.516	0.87
66_A	219_G	0.512	0.87
54_R	66_A	0.512	0.87
68_L	74_D	0.512	0.87
55_G	102_T	0.509	0.86
31_S	55_G	0.503	0.86
70_A	92_A	0.502	0.86
184_P	189_D	0.501	0.85
207_G	213_V	0.500	0.85

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
3l6iA	2	0.5778	82	0.871	Contact Map
3oa1A	1	0.4222	7.9	0.931	Contact Map
4k3lA	2	0.4133	5.8	0.935	Contact Map
1vyiA	1	0.44	5	0.937	Contact Map
3t0pA	2	0.4711	4.1	0.939	Contact Map
4alzA	1	0.4267	3.9	0.94	Contact Map
2yjlA	1	0.3022	3.6	0.941	Contact Map
4trtA	2	0.4444	3.6	0.941	Contact Map
2wzlA	1	0.4489	3.6	0.941	Contact Map
4m4dA	1	0.8667	3.2	0.943	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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