DUF4396 - PFAM28P - GREMLIN Contacts

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DUF4396 - Domain of unknown function (DUF4396)

PFAM:	PF14342	Sequences: TWRQAASATLHCLTGCAIGEVLGMVIGTLTGIALGWSNLATIALAIVLAFLFGYALTTLPLLRARGLSLRAALRTALAADTLSIAVMEIVDNAVMLLVPGAMDAALGLGDPLFWGSLAIALAVGFVTAYPVNRWLIARGKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	141 (131)
Sequences:	6310 (3004)
Seq/√Len:	262.4
META:	0.894

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_G	41_T	3.858	1.00
122_A	126_V	2.996	1.00
6_A	129_Y	2.684	1.00
68_S	71_A	2.666	1.00
51_L	55_A	2.426	1.00
59_L	63_R	2.406	1.00
50_F	81_T	2.342	1.00
62_L	69_L	2.323	1.00
86_V	131_V	2.314	1.00
46_I	85_A	2.270	1.00
26_I	34_L	2.173	1.00
82_L	131_V	2.045	1.00
94_V	98_V	2.007	1.00
36_W	40_A	1.899	1.00
94_V	119_I	1.895	1.00
70_R	74_R	1.821	1.00
23_G	48_L	1.751	1.00
115_G	119_I	1.739	1.00
50_F	77_L	1.724	1.00
133_R	137_A	1.713	1.00
58_T	72_A	1.628	1.00
22_L	52_F	1.609	1.00
91_D	120_A	1.572	1.00
24_M	45_A	1.508	1.00
71_A	74_R	1.505	1.00
6_A	125_F	1.500	1.00
18_I	56_L	1.487	1.00
42_I	96_L	1.486	1.00
111_P	115_G	1.486	1.00
85_A	89_I	1.475	1.00
6_A	10_L	1.461	1.00
26_I	48_L	1.417	1.00
54_Y	81_T	1.405	1.00
10_L	14_T	1.378	1.00
90_V	123_V	1.344	1.00
93_A	96_L	1.295	1.00
94_V	123_V	1.279	1.00
73_L	77_L	1.266	1.00
107_G	110_D	1.261	1.00
25_V	28_T	1.233	1.00
99_P	102_M	1.232	1.00
119_I	123_V	1.228	1.00
47_V	51_L	1.223	1.00
100_G	103_D	1.206	1.00
90_V	127_T	1.198	1.00
8_A	60_P	1.190	1.00
86_V	127_T	1.172	1.00
61_L	67_L	1.149	1.00
7_S	10_L	1.137	1.00
125_F	129_Y	1.131	1.00
39_L	43_A	1.128	1.00
126_V	129_Y	1.115	1.00
58_T	73_L	1.110	1.00
56_L	59_L	1.101	1.00
43_A	47_V	1.100	1.00
49_A	89_I	1.097	1.00
71_A	75_T	1.092	1.00
129_Y	133_R	1.091	1.00
55_A	59_L	1.089	1.00
37_S	40_A	1.071	1.00
57_T	76_A	1.064	1.00
19_G	23_G	1.063	1.00
99_P	103_D	1.057	1.00
33_A	108_L	1.046	1.00
67_L	75_T	1.033	1.00
27_G	44_L	1.033	1.00
68_S	74_R	1.021	1.00
26_I	44_L	1.016	1.00
39_L	42_I	1.006	1.00
126_V	130_P	1.002	1.00
127_T	130_P	0.998	1.00
17_A	121_L	0.988	1.00
98_V	116_S	0.982	1.00
50_F	54_Y	0.980	1.00
58_T	69_L	0.973	1.00
64_A	67_L	0.972	1.00
14_T	17_A	0.967	1.00
134_W	137_A	0.965	1.00
62_L	66_G	0.955	1.00
112_L	115_G	0.947	1.00
58_T	62_L	0.935	1.00
40_A	43_A	0.925	1.00
67_L	71_A	0.921	1.00
88_E	92_N	0.918	1.00
36_W	39_L	0.918	1.00
94_V	115_G	0.916	1.00
69_L	73_L	0.910	1.00
23_G	44_L	0.899	1.00
38_N	42_I	0.896	1.00
61_L	75_T	0.894	1.00
22_L	25_V	0.870	1.00
94_V	116_S	0.870	1.00
16_C	20_E	0.867	1.00
62_L	68_S	0.862	1.00
10_L	125_F	0.860	1.00
14_T	18_I	0.852	1.00
77_L	81_T	0.846	0.99
45_A	92_N	0.844	0.99
90_V	94_V	0.838	0.99
5_A	129_Y	0.836	0.99
93_A	97_L	0.833	0.99
62_L	72_A	0.809	0.99
5_A	133_R	0.808	0.99
97_L	101_A	0.805	0.99
48_L	52_F	0.799	0.99
134_W	138_R	0.782	0.99
72_A	75_T	0.767	0.99
82_L	86_V	0.766	0.99
17_A	21_V	0.765	0.99
26_I	33_A	0.762	0.99
95_M	120_A	0.761	0.99
101_A	116_S	0.759	0.99
112_L	116_S	0.754	0.99
115_G	118_A	0.753	0.99
74_R	77_L	0.752	0.99
28_T	108_L	0.744	0.99
59_L	74_R	0.744	0.99
42_I	92_N	0.743	0.99
100_G	104_A	0.740	0.99
9_T	125_F	0.735	0.99
122_A	125_F	0.730	0.98
121_L	130_P	0.728	0.98
54_Y	73_L	0.727	0.98
12_C	16_C	0.723	0.98
125_F	128_A	0.708	0.98
20_E	24_M	0.707	0.98
67_L	72_A	0.700	0.98
95_M	117_L	0.699	0.98
42_I	46_I	0.689	0.98
23_G	27_G	0.684	0.98
4_Q	8_A	0.684	0.98
55_A	60_P	0.677	0.98
21_V	117_L	0.675	0.97
58_T	74_R	0.674	0.97
45_A	120_A	0.673	0.97
75_T	79_A	0.673	0.97
57_T	79_A	0.666	0.97
98_V	113_F	0.664	0.97
24_M	102_M	0.664	0.97
74_R	82_L	0.662	0.97
53_G	80_D	0.656	0.97
96_L	102_M	0.656	0.97
102_M	116_S	0.634	0.96
12_C	15_G	0.633	0.96
28_T	109_G	0.626	0.96
19_G	88_E	0.625	0.96
37_S	41_T	0.625	0.96
89_I	93_A	0.623	0.96
24_M	95_M	0.621	0.96
15_G	19_G	0.621	0.96
95_M	116_S	0.613	0.96
57_T	80_D	0.612	0.96
26_I	40_A	0.612	0.96
36_W	41_T	0.612	0.96
15_G	83_S	0.611	0.96
25_V	108_L	0.608	0.95
116_S	119_I	0.607	0.95
16_C	88_E	0.607	0.95
18_I	22_L	0.605	0.95
7_S	14_T	0.604	0.95
46_I	50_F	0.597	0.95
8_A	136_I	0.596	0.95
4_Q	7_S	0.595	0.95
90_V	119_I	0.595	0.95
58_T	61_L	0.592	0.95
11_H	53_G	0.591	0.95
38_N	103_D	0.590	0.95
58_T	76_A	0.589	0.95
24_M	41_T	0.588	0.95
62_L	71_A	0.587	0.94
60_P	63_R	0.584	0.94
24_M	28_T	0.582	0.94
74_R	78_A	0.581	0.94
70_R	77_L	0.581	0.94
125_F	134_W	0.574	0.94
3_R	7_S	0.572	0.94
9_T	128_A	0.570	0.94
98_V	114_W	0.569	0.94
79_A	135_L	0.568	0.93
26_I	36_W	0.563	0.93
7_S	59_L	0.555	0.93
25_V	109_G	0.555	0.93
50_F	84_I	0.550	0.92
68_S	72_A	0.548	0.92
90_V	95_M	0.545	0.92
78_A	140_K	0.541	0.92
40_A	44_L	0.533	0.91
59_L	62_L	0.532	0.91
103_D	111_P	0.531	0.91
61_L	72_A	0.529	0.91
35_G	40_A	0.525	0.90
44_L	48_L	0.524	0.90
134_W	140_K	0.508	0.89
19_G	50_F	0.506	0.89
42_I	45_A	0.505	0.89
34_L	44_L	0.500	0.88

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
3aqpA	1	0.9078	59	0.901	Contact Map
3ne5A	3	0.922	48.5	0.907	Contact Map
3w9iA	3	0.922	43.2	0.91	Contact Map
4dx5A	3	0.8936	42.7	0.91	Contact Map
4k0jA	3	0.8794	38.8	0.912	Contact Map
4mt1A	3	0.9504	27.9	0.919	Contact Map
4httA	1	0.5177	21.8	0.923	Contact Map
4b4aA	1	0.6028	9.8	0.934	Contact Map
1zcdA	1	0.4255	8.5	0.936	Contact Map
2gfpA	2	0.9716	7.1	0.938	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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