DUF4010 - PFAM28P - GREMLIN Contacts

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DUF4010 - Domain of unknown function (DUF4010)

PFAM:	PF13194	Sequences: VLISGISFAGYVAVRLLGARRGLLLTGLLGGLVSSTATTLSLARRSREEPALARALAAGILLASAVMFLRVLVLVAVLNPALLRALALPLLAMALVALAAAALLYRRARRAEAEAEPELGNPFELKPALKFALLFAVVLLASAAAQEYFGDAGLYALAALSGLTDVDAITLSLARLAAAGGLSAAVAALAILIAALSNTLVKAGLALVLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	210 (209)
Sequences:	9494 (7252)
Seq/√Len:	501.7
META:	0.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_K	130_K	3.574	1.00
102_A	106_R	3.293	1.00
173_L	190_A	3.130	1.00
144_A	148_Y	2.968	1.00
76_A	83_L	2.894	1.00
71_V	195_A	2.892	1.00
30_G	38_T	2.884	1.00
143_A	146_Q	2.687	1.00
75_V	86_L	2.600	1.00
143_A	147_E	2.521	1.00
159_A	193_I	2.390	1.00
89_P	92_A	2.329	1.00
158_A	190_A	2.144	1.00
155_Y	193_I	2.143	1.00
204_G	208_V	2.068	1.00
72_L	83_L	1.987	1.00
79_N	177_A	1.960	1.00
65_A	97_A	1.955	1.00
80_P	84_R	1.952	1.00
159_A	197_S	1.944	1.00
42_L	59_G	1.881	1.00
177_A	187_A	1.865	1.00
154_L	190_A	1.823	1.00
99_A	103_L	1.790	1.00
142_S	160_L	1.755	1.00
46_S	56_L	1.749	1.00
12_V	16_L	1.710	1.00
103_L	107_R	1.669	1.00
129_L	133_L	1.663	1.00
75_V	174_A	1.653	1.00
145_A	157_L	1.632	1.00
81_A	84_R	1.626	1.00
53_A	57_A	1.619	1.00
45_R	48_E	1.609	1.00
36_T	201_V	1.593	1.00
175_R	178_A	1.573	1.00
155_Y	189_L	1.555	1.00
76_A	80_P	1.545	1.00
71_V	170_T	1.536	1.00
42_L	56_L	1.527	1.00
169_I	194_A	1.525	1.00
154_L	173_L	1.508	1.00
27_G	31_G	1.479	1.00
201_V	205_L	1.473	1.00
39_T	206_A	1.472	1.00
87_A	91_L	1.467	1.00
205_L	209_L	1.456	1.00
144_A	147_E	1.451	1.00
85_A	188_A	1.412	1.00
84_R	87_A	1.404	1.00
67_M	199_T	1.389	1.00
46_S	53_A	1.380	1.00
43_A	60_I	1.337	1.00
158_A	173_L	1.332	1.00
145_A	148_Y	1.325	1.00
45_R	49_E	1.324	1.00
69_L	94_A	1.323	1.00
170_T	174_A	1.321	1.00
28_L	66_V	1.289	1.00
49_E	52_L	1.281	1.00
68_F	195_A	1.271	1.00
201_V	204_G	1.264	1.00
24_L	58_A	1.254	1.00
75_V	82_L	1.246	1.00
17_L	25_L	1.234	1.00
154_L	182_L	1.228	1.00
56_L	59_G	1.227	1.00
123_F	127_P	1.225	1.00
184_A	188_A	1.207	1.00
124_E	127_P	1.197	1.00
40_L	209_L	1.191	1.00
98_L	102_A	1.184	1.00
88_L	92_A	1.183	1.00
167_D	202_K	1.181	1.00
163_L	201_V	1.173	1.00
11_Y	121_N	1.165	1.00
133_L	137_V	1.153	1.00
68_F	93_M	1.152	1.00
174_A	187_A	1.147	1.00
155_Y	186_V	1.147	1.00
94_A	101_A	1.132	1.00
67_M	195_A	1.124	1.00
72_L	90_L	1.121	1.00
44_R	48_E	1.121	1.00
186_V	189_L	1.111	1.00
23_L	55_A	1.110	1.00
106_R	109_R	1.109	1.00
54_R	107_R	1.105	1.00
125_L	129_L	1.101	1.00
142_S	146_Q	1.100	1.00
173_L	187_A	1.086	1.00
69_L	72_L	1.083	1.00
131_F	135_F	1.081	1.00
177_A	184_A	1.078	1.00
166_V	195_A	1.077	1.00
161_S	169_I	1.077	1.00
100_A	104_L	1.068	1.00
185_A	189_L	1.068	1.00
74_L	77_V	1.067	1.00
186_V	190_A	1.060	1.00
165_D	198_N	1.055	1.00
33_V	119_L	1.046	1.00
103_L	106_R	1.042	1.00
81_A	85_A	1.032	1.00
90_L	94_A	1.028	1.00
70_R	167_D	1.025	1.00
7_S	11_Y	1.018	1.00
183_S	186_V	1.014	1.00
38_T	42_L	1.010	1.00
52_L	56_L	1.005	1.00
138_V	157_L	1.005	1.00
39_T	60_I	1.000	1.00
140_L	144_A	0.999	1.00
106_R	110_R	0.995	1.00
146_Q	151_D	0.993	1.00
181_G	185_A	0.991	1.00
23_L	56_L	0.990	1.00
78_L	171_L	0.986	1.00
86_L	191_I	0.985	1.00
50_P	53_A	0.982	1.00
44_R	47_R	0.982	1.00
24_L	27_G	0.981	1.00
27_G	55_A	0.980	1.00
13_A	29_L	0.976	1.00
79_N	178_A	0.973	1.00
82_L	174_A	0.970	1.00
62_L	101_A	0.964	1.00
67_M	70_R	0.962	1.00
31_G	38_T	0.962	1.00
145_A	149_F	0.961	1.00
159_A	200_L	0.961	1.00
40_L	205_L	0.960	1.00
91_L	95_L	0.957	1.00
152_A	156_A	0.950	1.00
66_V	167_D	0.933	1.00
72_L	76_A	0.930	1.00
153_G	156_A	0.926	1.00
91_L	94_A	0.925	1.00
59_G	123_F	0.922	1.00
205_L	208_V	0.920	1.00
153_G	157_L	0.917	1.00
35_S	67_M	0.915	1.00
96_V	100_A	0.905	1.00
158_A	169_I	0.898	1.00
196_L	200_L	0.895	1.00
94_A	97_A	0.892	1.00
18_G	22_G	0.890	1.00
163_L	197_S	0.881	1.00
74_L	78_L	0.881	1.00
24_L	62_L	0.877	1.00
134_L	138_V	0.876	1.00
105_Y	109_R	0.872	1.00
89_P	93_M	0.868	1.00
11_Y	122_P	0.861	1.00
142_S	157_L	0.858	1.00
94_A	98_L	0.857	1.00
102_A	105_Y	0.856	1.00
5_G	9_A	0.852	1.00
192_L	195_A	0.851	1.00
95_L	99_A	0.851	1.00
157_L	161_S	0.845	1.00
10_G	29_L	0.840	1.00
58_A	105_Y	0.840	1.00
162_G	197_S	0.838	1.00
182_L	187_A	0.829	1.00
13_A	16_L	0.829	1.00
98_L	101_A	0.827	1.00
4_S	8_F	0.822	1.00
71_V	166_V	0.822	1.00
90_L	93_M	0.819	1.00
22_G	26_T	0.816	1.00
145_A	153_G	0.813	1.00
141_A	157_L	0.812	1.00
39_T	64_S	0.811	1.00
145_A	160_L	0.810	1.00
2_L	78_L	0.809	1.00
65_A	98_L	0.797	1.00
83_L	87_A	0.787	1.00
28_L	62_L	0.785	1.00
78_L	174_A	0.785	1.00
75_V	170_T	0.783	1.00
66_V	70_R	0.780	1.00
74_L	174_A	0.773	1.00
61_L	97_A	0.770	1.00
203_A	207_L	0.770	1.00
161_S	164_T	0.769	1.00
137_V	141_A	0.769	1.00
196_L	199_T	0.762	1.00
7_S	127_P	0.761	1.00
130_K	134_L	0.753	1.00
158_A	162_G	0.743	1.00
2_L	77_V	0.742	1.00
3_I	131_F	0.742	1.00
90_L	192_L	0.741	1.00
149_F	156_A	0.740	1.00
3_I	128_A	0.739	1.00
94_A	105_Y	0.739	1.00
14_V	29_L	0.737	1.00
13_A	17_L	0.736	1.00
70_R	122_P	0.732	1.00
82_L	191_I	0.728	1.00
70_R	73_V	0.724	1.00
92_A	95_L	0.724	1.00
55_A	59_G	0.724	1.00
105_Y	108_A	0.724	1.00
65_A	101_A	0.717	1.00
4_S	128_A	0.716	1.00
138_V	161_S	0.715	1.00
60_I	206_A	0.710	1.00
172_S	175_R	0.710	1.00
182_L	186_V	0.710	1.00
8_F	123_F	0.708	1.00
18_G	21_R	0.708	1.00
75_V	83_L	0.697	1.00
104_L	108_A	0.692	1.00
84_R	88_L	0.691	1.00
67_M	166_V	0.689	1.00
66_V	98_L	0.687	1.00
189_L	193_I	0.686	1.00
38_T	41_S	0.679	1.00
142_S	176_L	0.676	1.00
173_L	191_I	0.675	1.00
100_A	103_L	0.672	1.00
110_R	113_A	0.672	1.00
42_L	60_I	0.664	1.00
64_S	97_A	0.662	1.00
99_A	102_A	0.659	1.00
8_F	121_N	0.659	1.00
71_V	167_D	0.657	1.00
2_L	10_G	0.657	1.00
150_G	153_G	0.657	1.00
61_L	64_S	0.657	1.00
27_G	58_A	0.644	1.00
199_T	203_A	0.637	1.00
35_S	63_A	0.634	1.00
4_S	132_A	0.634	1.00
79_N	174_A	0.633	1.00
2_L	6_I	0.632	1.00
93_M	192_L	0.630	1.00
167_D	198_N	0.630	1.00
4_S	135_F	0.630	1.00
85_A	184_A	0.620	1.00
57_A	61_L	0.619	1.00
41_S	45_R	0.618	1.00
136_A	140_L	0.615	1.00
37_A	41_S	0.613	1.00
93_M	97_A	0.612	1.00
86_L	188_A	0.607	0.99
73_V	77_V	0.601	0.99
56_L	60_I	0.600	0.99
54_R	110_R	0.599	0.99
11_Y	15_R	0.598	0.99
142_S	145_A	0.594	0.99
203_A	206_A	0.591	0.99
52_L	55_A	0.587	0.99
41_S	44_R	0.586	0.99
72_L	86_L	0.585	0.99
64_S	67_M	0.585	0.99
85_A	185_A	0.584	0.99
204_G	207_L	0.583	0.99
73_V	76_A	0.582	0.99
135_F	171_L	0.582	0.99
197_S	200_L	0.581	0.99
171_L	175_R	0.579	0.99
39_T	43_A	0.575	0.99
206_A	210_G	0.572	0.99
55_A	58_A	0.571	0.99
141_A	145_A	0.569	0.99
200_L	204_G	0.568	0.99
58_A	62_L	0.564	0.99
119_L	122_P	0.562	0.99
161_S	168_A	0.562	0.99
133_L	136_A	0.561	0.99
130_K	133_L	0.561	0.99
29_L	145_A	0.561	0.99
85_A	88_L	0.560	0.99
71_V	165_D	0.555	0.99
155_Y	190_A	0.553	0.99
17_L	21_R	0.548	0.99
166_V	194_A	0.547	0.99
176_L	182_L	0.541	0.99
14_V	17_L	0.540	0.99
135_F	142_S	0.539	0.99
19_A	52_L	0.538	0.99
88_L	91_L	0.537	0.99
183_S	189_L	0.537	0.99
109_R	115_A	0.534	0.99
82_L	85_A	0.533	0.99
164_T	201_V	0.532	0.99
192_L	196_L	0.532	0.99
92_A	96_V	0.530	0.99
176_L	180_G	0.530	0.99
36_T	167_D	0.524	0.98
90_L	97_A	0.523	0.98
134_L	137_V	0.523	0.98
185_A	188_A	0.521	0.98
32_L	70_R	0.520	0.98
91_L	98_L	0.520	0.98
57_A	60_I	0.519	0.98
74_L	142_S	0.517	0.98
81_A	184_A	0.512	0.98
96_V	103_L	0.511	0.98
143_A	148_Y	0.508	0.98
11_Y	144_A	0.508	0.98
40_L	44_R	0.508	0.98
11_Y	119_L	0.507	0.98
32_L	73_V	0.506	0.98
151_D	186_V	0.505	0.98
58_A	101_A	0.503	0.98
38_T	63_A	0.503	0.98
169_I	173_L	0.502	0.98
149_F	160_L	0.501	0.98
135_F	164_T	0.500	0.98
1_V	4_S	0.500	0.98

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
3zuxA	1	0.4952	27.5	0.932	Contact Map
4f35D	2	0.8952	26	0.933	Contact Map
2cfqA	1	0.5667	20.4	0.936	Contact Map
1pw4A	1	0.5714	12.4	0.942	Contact Map
4n7wA	2	0.5095	9.8	0.944	Contact Map
4ikvA	1	0.5095	8.8	0.946	Contact Map
2xq2A	2	0.4762	6.9	0.948	Contact Map
4cofA	3	0.481	6.6	0.949	Contact Map
4b19A	1	0.1429	4.9	0.951	Contact Map
4xnjA	1	0.481	4.7	0.952	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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