DUF3305 - PFAM28P - GREMLIN Contacts

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DUF3305 - Protein of unknown function (DUF3305)

PFAM:	PF11749	Sequences: PVGVVMERRKADSRWADWRWRPVAVLPDGAPDAAWRVLREDGDATQFLAGGFELELHRDETEGYRLNLSSGAPSVFVVLRPDDDGEPPAEPVLVTASPNEAERWLDAGEDVEAVPMPPEIRAWVEAFVAEHYVPEPFKKRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	141 (139)
Sequences:	4229 (2710)
Seq/√Len:	229.9
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_V	40_E	3.686	1.00
37_V	45_T	3.681	1.00
61_T	132_Y	3.345	1.00
74_S	113_A	3.228	1.00
40_E	45_T	2.959	1.00
75_V	96_A	2.784	1.00
125_E	129_A	2.535	1.00
41_D	44_A	2.478	1.00
39_R	46_Q	2.455	1.00
56_L	124_V	2.318	1.00
9_R	19_R	2.253	1.00
52_F	91_P	2.154	1.00
78_V	104_W	2.020	1.00
80_R	110_D	2.007	1.00
121_R	125_E	1.964	1.00
93_L	104_W	1.917	1.00
126_A	130_E	1.871	1.00
13_S	16_A	1.841	1.00
96_A	124_V	1.835	1.00
103_R	106_D	1.818	1.00
37_V	47_F	1.803	1.00
7_E	44_A	1.783	1.00
2_V	54_L	1.760	1.00
96_A	116_M	1.701	1.00
16_A	19_R	1.696	1.00
62_E	99_N	1.526	1.00
11_A	17_D	1.487	1.00
66_L	99_N	1.482	1.00
63_G	99_N	1.479	1.00
10_K	43_D	1.478	1.00
63_G	97_S	1.463	1.00
11_A	16_A	1.463	1.00
4_V	25_V	1.431	1.00
118_P	121_R	1.417	1.00
107_A	110_D	1.394	1.00
79_L	89_A	1.312	1.00
122_A	125_E	1.303	1.00
48_L	51_G	1.295	1.00
52_F	94_V	1.294	1.00
7_E	21_R	1.277	1.00
116_M	124_V	1.269	1.00
62_E	66_L	1.264	1.00
80_R	92_V	1.252	1.00
29_G	33_A	1.249	1.00
11_A	19_R	1.249	1.00
65_R	69_S	1.239	1.00
133_V	136_P	1.228	1.00
135_E	138_K	1.222	1.00
78_V	93_L	1.221	1.00
9_R	21_R	1.221	1.00
127_F	131_H	1.214	1.00
75_V	116_M	1.200	1.00
7_E	46_Q	1.190	1.00
7_E	23_V	1.187	1.00
5_V	38_L	1.166	1.00
25_V	75_V	1.161	1.00
117_P	120_I	1.135	1.00
8_R	45_T	1.129	1.00
29_G	32_D	1.119	1.00
80_R	109_E	1.119	1.00
22_P	112_E	1.105	1.00
54_L	96_A	1.101	1.00
8_R	18_W	1.100	1.00
67_N	98_P	1.079	1.00
75_V	94_V	1.079	1.00
77_V	114_V	1.078	1.00
26_L	48_L	1.078	1.00
23_V	46_Q	1.074	1.00
25_V	114_V	1.073	1.00
116_M	120_I	1.064	1.00
99_N	102_E	1.063	1.00
83_D	87_P	1.061	1.00
61_T	128_V	1.041	1.00
102_E	106_D	1.013	1.00
10_K	13_S	0.988	1.00
31_P	34_A	0.974	1.00
40_E	43_D	0.973	1.00
70_S	74_S	0.967	1.00
124_V	128_V	0.957	1.00
106_D	109_E	0.957	1.00
122_A	129_A	0.937	1.00
24_A	46_Q	0.929	1.00
3_G	48_L	0.928	1.00
35_W	49_A	0.922	1.00
65_R	128_V	0.907	0.99
28_D	31_P	0.905	0.99
116_M	121_R	0.901	0.99
4_V	94_V	0.897	0.99
122_A	126_A	0.888	0.99
30_A	33_A	0.862	0.99
119_E	122_A	0.855	0.99
13_S	17_D	0.853	0.99
83_D	86_E	0.842	0.99
118_P	122_A	0.838	0.99
12_D	19_R	0.830	0.99
60_E	100_E	0.828	0.99
6_M	89_A	0.821	0.99
5_V	26_L	0.813	0.99
54_L	75_V	0.811	0.99
9_R	44_A	0.804	0.99
60_E	97_S	0.797	0.99
39_R	44_A	0.790	0.99
81_P	89_A	0.789	0.99
5_V	46_Q	0.788	0.99
60_E	63_G	0.788	0.99
11_A	18_W	0.786	0.99
58_R	131_H	0.780	0.98
13_S	18_W	0.775	0.98
10_K	14_R	0.770	0.98
51_G	91_P	0.764	0.98
102_E	105_L	0.764	0.98
137_F	140_R	0.763	0.98
58_R	127_F	0.762	0.98
60_E	99_N	0.752	0.98
2_V	94_V	0.750	0.98
76_F	113_A	0.745	0.98
50_G	91_P	0.739	0.98
59_D	97_S	0.733	0.98
67_N	70_S	0.727	0.98
36_R	50_G	0.722	0.97
57_H	99_N	0.714	0.97
84_D	87_P	0.712	0.97
68_L	124_V	0.708	0.97
138_K	141_K	0.706	0.97
101_A	110_D	0.704	0.97
97_S	107_A	0.702	0.97
10_K	18_W	0.699	0.97
134_P	137_F	0.684	0.97
12_D	43_D	0.679	0.96
66_L	70_S	0.671	0.96
14_R	17_D	0.670	0.96
36_R	48_L	0.668	0.96
75_V	120_I	0.666	0.96
60_E	76_F	0.656	0.96
22_P	114_V	0.654	0.96
6_M	49_A	0.651	0.95
27_P	119_E	0.647	0.95
105_L	113_A	0.644	0.95
54_L	94_V	0.641	0.95
62_E	106_D	0.638	0.95
121_R	129_A	0.634	0.95
119_E	123_W	0.629	0.94
16_A	38_L	0.625	0.94
97_S	103_R	0.624	0.94
119_E	128_V	0.622	0.94
22_P	77_V	0.621	0.94
103_R	107_A	0.618	0.94
65_R	134_P	0.616	0.94
65_R	125_E	0.615	0.94
109_E	113_A	0.611	0.94
6_M	79_L	0.609	0.93
33_A	50_G	0.606	0.93
35_W	88_P	0.605	0.93
128_V	132_Y	0.604	0.93
89_A	92_V	0.602	0.93
99_N	103_R	0.599	0.93
127_F	138_K	0.597	0.93
78_V	111_V	0.597	0.93
61_T	127_F	0.594	0.93
95_T	100_E	0.592	0.93
9_R	23_V	0.589	0.92
124_V	127_F	0.588	0.92
95_T	104_W	0.583	0.92
2_V	120_I	0.578	0.92
24_A	27_P	0.573	0.91
12_D	18_W	0.573	0.91
40_E	44_A	0.573	0.91
27_P	30_A	0.570	0.91
56_L	123_W	0.567	0.91
105_L	111_V	0.566	0.91
61_T	99_N	0.565	0.91
63_G	66_L	0.565	0.91
38_L	46_Q	0.563	0.91
76_F	101_A	0.557	0.90
63_G	103_R	0.553	0.90
132_Y	135_E	0.553	0.90
6_M	20_W	0.545	0.89
68_L	121_R	0.543	0.89
26_L	38_L	0.540	0.89
62_E	134_P	0.539	0.89
61_T	65_R	0.539	0.89
22_P	89_A	0.536	0.88
31_P	35_W	0.534	0.88
35_W	87_P	0.533	0.88
6_M	22_P	0.532	0.88
67_N	73_P	0.528	0.88
66_L	105_L	0.526	0.87
65_R	97_S	0.523	0.87
109_E	120_I	0.523	0.87
6_M	10_K	0.522	0.87
46_Q	74_S	0.522	0.87
79_L	91_P	0.519	0.87
106_D	112_E	0.516	0.86
126_A	129_A	0.515	0.86
81_P	87_P	0.515	0.86
79_L	110_D	0.513	0.86
11_A	20_W	0.513	0.86
70_S	73_P	0.512	0.86
74_S	115_P	0.509	0.86
58_R	99_N	0.509	0.86
22_P	99_N	0.509	0.86
92_V	104_W	0.508	0.86
63_G	109_E	0.508	0.86
26_L	115_P	0.505	0.85
22_P	113_A	0.503	0.85
84_D	90_E	0.502	0.85
35_W	47_F	0.501	0.85
38_L	49_A	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
2kkeA	2	0.3759	5.4	0.952	Contact Map
4qlaA	2	0.9007	4.3	0.954	Contact Map
4me7E	2	0.2411	3.4	0.956	Contact Map
4eo1A	1	0.1986	3.2	0.957	Contact Map
3bidA	2	0.4326	2.8	0.958	Contact Map
3bqoB	1	0.0496	2.7	0.958	Contact Map
2lnuA	1	0.9007	2.6	0.959	Contact Map
4r1zA	2	0.3688	2.4	0.959	Contact Map
2k5jA	2	0.2908	2.4	0.959	Contact Map
2mdvA	2	0.227	2.3	0.96	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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