DUF4381 - PFAM28P - GREMLIN Contacts

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DUF4381 - Domain of unknown function (DUF4381)

PFAM:	PF14316	Sequences: AQLRDIHLPPPVSWWPPAPGWWLLAALLLLLALLALALWRRRRRRRYRREALAELDRLRAAAADPAALLAALSELLRRVALAAYPREEVASLTGEAWLAFLDRTGPTPEFSEGARLLLEAPYRPDELDDADLEALLALARRWIRH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	145 (143)
Sequences:	6167 (5165)
Seq/√Len:	431.9
META:	0.843

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_R	47_Y	3.516	1.00
35_A	39_W	3.357	1.00
36_L	40_R	3.219	1.00
37_A	41_R	2.752	1.00
59_R	140_R	2.664	1.00
4_R	7_H	2.405	1.00
54_E	78_R	2.346	1.00
84_Y	100_F	2.333	1.00
110_F	113_G	2.267	1.00
118_L	121_P	2.205	1.00
68_L	136_L	2.090	1.00
64_D	67_A	2.065	1.00
34_L	38_L	2.052	1.00
38_L	42_R	1.988	1.00
131_D	134_A	1.959	1.00
128_D	131_D	1.915	1.00
56_D	140_R	1.868	1.00
72_L	139_A	1.804	1.00
54_E	57_R	1.792	1.00
41_R	45_R	1.751	1.00
119_E	123_R	1.744	1.00
79_V	143_I	1.739	1.00
59_R	136_L	1.730	1.00
80_A	100_F	1.729	1.00
95_E	99_A	1.656	1.00
33_L	37_A	1.639	1.00
32_A	36_L	1.613	1.00
17_P	25_A	1.609	1.00
98_L	102_D	1.585	1.00
102_D	110_F	1.575	1.00
96_A	99_A	1.560	1.00
73_S	97_W	1.545	1.00
56_D	59_R	1.542	1.00
81_L	85_P	1.495	1.00
67_A	71_A	1.489	1.00
18_A	21_W	1.464	1.00
77_R	93_T	1.451	1.00
81_L	90_A	1.432	1.00
36_L	39_W	1.413	1.00
100_F	104_T	1.410	1.00
92_L	100_F	1.394	1.00
73_S	77_R	1.391	1.00
79_V	83_A	1.382	1.00
19_P	23_L	1.369	1.00
50_E	54_E	1.368	1.00
94_G	97_W	1.353	1.00
35_A	38_L	1.328	1.00
19_P	22_W	1.327	1.00
117_L	121_P	1.301	1.00
99_A	103_R	1.293	1.00
115_R	119_E	1.289	1.00
58_L	71_A	1.254	1.00
86_R	90_A	1.240	1.00
39_W	42_R	1.225	1.00
76_L	139_A	1.223	1.00
68_L	132_L	1.208	1.00
18_A	22_W	1.193	1.00
36_L	42_R	1.155	1.00
37_A	40_R	1.144	1.00
140_R	144_R	1.136	1.00
15_W	18_A	1.124	1.00
86_R	89_V	1.113	1.00
38_L	41_R	1.109	1.00
73_S	121_P	1.069	1.00
52_L	140_R	1.066	1.00
58_L	75_L	1.050	1.00
74_E	78_R	1.047	1.00
73_S	120_A	1.039	1.00
33_L	36_L	1.032	1.00
69_L	120_A	1.021	1.00
84_Y	104_T	1.004	1.00
14_W	17_P	0.998	1.00
52_L	144_R	0.973	1.00
64_D	68_L	0.972	1.00
21_W	24_L	0.972	1.00
110_F	114_A	0.948	1.00
48_R	52_L	0.944	1.00
43_R	46_R	0.938	1.00
136_L	140_R	0.934	1.00
81_L	89_V	0.929	1.00
133_E	137_A	0.922	1.00
55_L	75_L	0.919	1.00
108_P	112_E	0.917	1.00
21_W	25_A	0.912	1.00
13_S	16_P	0.902	1.00
80_A	89_V	0.885	1.00
31_L	35_A	0.878	1.00
132_L	136_L	0.876	1.00
77_R	121_P	0.876	1.00
13_S	17_P	0.872	1.00
32_A	35_A	0.868	1.00
20_G	23_L	0.863	1.00
102_D	113_G	0.861	1.00
89_V	92_L	0.841	1.00
109_E	114_A	0.833	1.00
108_P	111_S	0.832	1.00
98_L	118_L	0.831	1.00
116_L	119_E	0.829	1.00
72_L	136_L	0.826	1.00
97_W	100_F	0.816	1.00
33_L	41_R	0.811	1.00
72_L	135_L	0.811	1.00
59_R	133_E	0.810	1.00
23_L	26_A	0.809	1.00
39_W	43_R	0.809	1.00
81_L	86_R	0.802	1.00
55_L	59_R	0.797	1.00
69_L	135_L	0.796	1.00
66_A	70_A	0.788	1.00
42_R	45_R	0.783	1.00
15_W	22_W	0.783	1.00
7_H	77_R	0.779	1.00
35_A	42_R	0.775	1.00
17_P	22_W	0.758	1.00
51_A	79_V	0.752	1.00
114_A	138_L	0.749	1.00
109_E	138_L	0.749	1.00
115_R	118_L	0.748	1.00
20_G	24_L	0.743	1.00
8_L	11_P	0.741	1.00
37_A	44_R	0.734	1.00
76_L	101_L	0.732	1.00
79_V	142_W	0.732	1.00
40_R	43_R	0.730	1.00
58_L	68_L	0.728	1.00
51_A	54_E	0.725	1.00
116_L	120_A	0.717	1.00
60_A	63_A	0.714	1.00
16_P	21_W	0.709	1.00
65_P	132_L	0.704	1.00
78_R	82_A	0.704	1.00
111_S	114_A	0.703	1.00
105_G	109_E	0.703	1.00
102_D	111_S	0.703	1.00
52_L	56_D	0.701	1.00
2_Q	8_L	0.692	1.00
80_A	142_W	0.691	1.00
35_A	41_R	0.689	1.00
118_L	122_Y	0.684	1.00
85_P	88_E	0.684	1.00
107_T	110_F	0.683	1.00
68_L	71_A	0.681	1.00
77_R	100_F	0.665	1.00
109_E	113_G	0.664	1.00
54_E	58_L	0.658	0.99
51_A	143_I	0.651	0.99
47_Y	83_A	0.650	0.99
116_L	130_A	0.649	0.99
130_A	133_E	0.646	0.99
109_E	112_E	0.645	0.99
92_L	97_W	0.640	0.99
120_A	123_R	0.640	0.99
41_R	44_R	0.637	0.99
68_L	72_L	0.636	0.99
102_D	112_E	0.631	0.99
110_F	138_L	0.630	0.99
127_L	130_A	0.629	0.99
107_T	111_S	0.627	0.99
54_E	71_A	0.626	0.99
22_W	26_A	0.626	0.99
35_A	40_R	0.625	0.99
5_D	8_L	0.623	0.99
71_A	74_E	0.617	0.99
12_V	16_P	0.614	0.99
14_W	18_A	0.611	0.99
62_A	65_P	0.611	0.99
54_E	75_L	0.604	0.99
15_W	19_P	0.603	0.99
105_G	138_L	0.600	0.99
84_Y	89_V	0.600	0.99
140_R	143_I	0.598	0.99
102_D	138_L	0.597	0.99
115_R	120_A	0.594	0.99
105_G	108_P	0.594	0.99
127_L	131_D	0.592	0.99
121_P	124_P	0.592	0.99
55_L	72_L	0.591	0.99
98_L	115_R	0.590	0.99
137_A	141_R	0.589	0.99
34_L	37_A	0.586	0.99
37_A	42_R	0.586	0.99
105_G	141_R	0.582	0.99
51_A	55_L	0.577	0.99
9_P	12_V	0.575	0.99
65_P	129_D	0.574	0.99
61_A	65_P	0.571	0.99
73_S	117_L	0.569	0.99
70_A	121_P	0.559	0.98
8_L	12_V	0.559	0.98
95_E	115_R	0.556	0.98
93_T	96_A	0.552	0.98
14_W	21_W	0.550	0.98
4_R	14_W	0.547	0.98
73_S	76_L	0.545	0.98
33_L	42_R	0.541	0.98
122_Y	125_D	0.540	0.98
138_L	141_R	0.536	0.98
132_L	137_A	0.533	0.98
68_L	73_S	0.532	0.98
70_A	74_E	0.530	0.98
128_D	132_L	0.528	0.98
52_L	75_L	0.525	0.98
7_H	22_W	0.524	0.98
99_A	102_D	0.520	0.97
92_L	98_L	0.517	0.97
102_D	114_A	0.515	0.97
79_V	84_Y	0.514	0.97
32_A	39_W	0.512	0.97
13_S	18_A	0.510	0.97
97_W	101_L	0.508	0.97
42_R	47_Y	0.507	0.97
109_E	141_R	0.507	0.97
7_H	11_P	0.501	0.97
26_A	33_L	0.500	0.97

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
2l2tA	2	0.2897	48.4	0.881	Contact Map
3j6da	3	0	48.3	0.881	Contact Map
4tllB	2	0.2759	43.8	0.884	Contact Map
4p02B	1	0.3103	38.3	0.888	Contact Map
2m20A	2	0.4069	33.6	0.891	Contact Map
4v3iA	2	0.0828	33.3	0.891	Contact Map
4tllA	1	0.1655	32.3	0.892	Contact Map
2kluA	1	0.4552	27.4	0.896	Contact Map
5a2fA	1	0	26.5	0.897	Contact Map
2ks1B	1	0.3034	24.3	0.899	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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