DUF4383 - PFAM28P - GREMLIN Contacts

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DUF4383 - Domain of unknown function (DUF4383)

PFAM:	PF14325	Sequences: RTAALVFGAVFLLVGILGFIPGITTPYDGLSFAGHTSGGKLLGLFQVNGLHNLVHLLFGVAGLAAARSAAAARTYLLGFGVVYLLLAVLGLIVGGGSLGLLPLNGADNWLHLVLGLVMLALGLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (118)
Sequences:	7257 (4793)
Seq/√Len:	441.2
META:	0.868

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_G	75_Y	4.536	1.00
84_L	115_G	3.521	1.00
58_F	83_Y	2.909	1.00
87_A	112_L	2.851	1.00
11_F	114_L	2.705	1.00
68_S	71_A	2.472	1.00
45_F	110_L	1.920	1.00
73_R	77_L	1.903	1.00
77_L	123_L	1.896	1.00
5_L	66_A	1.891	1.00
3_A	76_L	1.837	1.00
87_A	115_G	1.735	1.00
40_K	46_Q	1.731	1.00
89_L	93_V	1.728	1.00
87_A	91_L	1.696	1.00
8_G	63_L	1.675	1.00
58_F	79_F	1.639	1.00
16_I	20_I	1.630	1.00
27_Y	30_L	1.550	1.00
106_A	109_W	1.540	1.00
60_V	64_A	1.520	1.00
77_L	122_G	1.512	1.00
19_F	52_N	1.480	1.00
80_G	115_G	1.460	1.00
32_F	35_H	1.413	1.00
51_H	107_D	1.411	1.00
12_L	59_G	1.381	1.00
10_V	14_V	1.359	1.00
74_T	78_G	1.352	1.00
105_G	109_W	1.344	1.00
80_G	119_L	1.342	1.00
93_V	96_G	1.340	1.00
65_A	71_A	1.315	1.00
3_A	118_M	1.308	1.00
5_L	63_L	1.301	1.00
62_G	118_M	1.296	1.00
119_L	123_L	1.290	1.00
55_H	111_H	1.276	1.00
11_F	58_F	1.265	1.00
3_A	121_L	1.260	1.00
58_F	114_L	1.243	1.00
2_T	6_V	1.224	1.00
91_L	108_N	1.218	1.00
12_L	63_L	1.217	1.00
76_L	118_M	1.215	1.00
38_G	46_Q	1.209	1.00
15_G	56_L	1.202	1.00
103_L	108_N	1.165	1.00
28_D	31_S	1.157	1.00
70_A	74_T	1.152	1.00
114_L	118_M	1.142	1.00
109_W	113_V	1.135	1.00
61_A	65_A	1.113	1.00
81_V	85_L	1.107	1.00
91_L	112_L	1.053	1.00
87_A	109_W	1.047	1.00
54_V	86_L	1.042	1.00
5_L	9_A	1.038	1.00
49_G	53_L	1.038	1.00
104_N	107_D	1.008	1.00
105_G	108_N	0.998	1.00
93_V	97_S	0.995	1.00
71_A	74_T	0.988	1.00
8_G	59_G	0.969	1.00
31_S	35_H	0.959	1.00
2_T	5_L	0.957	1.00
62_G	65_A	0.949	1.00
46_Q	102_P	0.941	1.00
31_S	36_T	0.941	1.00
69_A	73_R	0.940	1.00
31_S	34_G	0.938	1.00
12_L	56_L	0.924	1.00
46_Q	104_N	0.918	1.00
18_G	52_N	0.917	1.00
27_Y	31_S	0.913	1.00
107_D	111_H	0.897	1.00
15_G	59_G	0.891	1.00
67_R	71_A	0.888	1.00
41_L	47_V	0.883	1.00
115_G	119_L	0.867	1.00
33_A	36_T	0.867	1.00
116_L	120_A	0.866	1.00
28_D	33_A	0.864	1.00
65_A	75_Y	0.863	1.00
65_A	68_S	0.858	1.00
50_L	54_V	0.854	1.00
51_H	55_H	0.834	1.00
78_G	82_V	0.830	1.00
74_T	77_L	0.825	1.00
17_L	41_L	0.819	1.00
90_G	108_N	0.802	1.00
70_A	73_R	0.802	1.00
9_A	13_L	0.801	1.00
1_R	69_A	0.790	1.00
55_H	83_Y	0.786	1.00
4_A	76_L	0.776	1.00
6_V	10_V	0.774	1.00
58_F	82_V	0.765	1.00
7_F	76_L	0.757	1.00
48_N	102_P	0.756	1.00
67_R	70_A	0.750	1.00
30_L	34_G	0.749	1.00
120_A	123_L	0.741	1.00
51_H	83_Y	0.737	1.00
30_L	36_T	0.735	1.00
95_G	108_N	0.728	1.00
27_Y	32_F	0.727	1.00
19_F	49_G	0.722	1.00
52_N	55_H	0.722	1.00
28_D	32_F	0.721	1.00
44_L	106_A	0.718	1.00
29_G	32_F	0.717	1.00
107_D	110_L	0.713	1.00
38_G	41_L	0.709	1.00
2_T	69_A	0.705	1.00
79_F	83_Y	0.702	1.00
64_A	67_R	0.702	1.00
11_F	83_Y	0.701	1.00
113_V	117_V	0.700	1.00
75_Y	79_F	0.697	1.00
65_A	72_A	0.696	1.00
51_H	111_H	0.692	1.00
85_L	89_L	0.688	1.00
7_F	118_M	0.688	1.00
61_A	82_V	0.686	1.00
106_A	110_L	0.685	1.00
40_K	104_N	0.682	1.00
65_A	78_G	0.681	1.00
47_V	55_H	0.679	1.00
30_L	33_A	0.676	1.00
14_V	55_H	0.670	1.00
86_L	90_G	0.669	1.00
14_V	83_Y	0.669	1.00
93_V	99_G	0.663	1.00
89_L	95_G	0.663	1.00
30_L	35_H	0.661	1.00
78_G	122_G	0.654	1.00
8_G	62_G	0.648	0.99
2_T	66_A	0.642	0.99
32_F	36_T	0.641	0.99
61_A	75_Y	0.631	0.99
51_H	54_V	0.620	0.99
53_L	57_L	0.617	0.99
46_Q	49_G	0.615	0.99
29_G	38_G	0.613	0.99
30_L	39_G	0.609	0.99
48_N	98_L	0.608	0.99
47_V	52_N	0.608	0.99
76_L	121_L	0.605	0.99
82_V	85_L	0.604	0.99
91_L	105_G	0.602	0.99
4_A	62_G	0.588	0.99
3_A	7_F	0.586	0.99
31_S	37_S	0.576	0.99
28_D	36_T	0.576	0.99
118_M	121_L	0.573	0.99
38_G	104_N	0.571	0.99
79_F	118_M	0.563	0.99
7_F	11_F	0.561	0.99
28_D	38_G	0.558	0.98
13_L	17_L	0.558	0.98
37_S	40_K	0.555	0.98
102_P	105_G	0.546	0.98
17_L	20_I	0.545	0.98
50_L	101_L	0.541	0.98
14_V	51_H	0.539	0.98
12_L	60_V	0.539	0.98
27_Y	33_A	0.537	0.98
97_S	103_L	0.533	0.98
45_F	107_D	0.532	0.98
29_G	40_K	0.528	0.98
24_T	52_N	0.522	0.98
113_V	120_A	0.515	0.97
32_F	38_G	0.507	0.97
76_L	80_G	0.507	0.97
94_G	97_S	0.501	0.97
7_F	117_V	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
3pjzA	2	0.8952	6.1	0.9	Contact Map
2ww9B	1	0.2661	3	0.914	Contact Map
1rh5B	1	0.2661	2.9	0.915	Contact Map
3mp7B	1	0.25	2.2	0.92	Contact Map
4w252	1	0.2823	1.8	0.924	Contact Map
2mpnA	2	0.2823	1.5	0.927	Contact Map
4p79A	1	0.5565	1.4	0.928	Contact Map
1qleC	1	0.7581	1.3	0.93	Contact Map
1m56C	2	0.7581	1.3	0.93	Contact Map
1fftC	1	0.7823	1.3	0.93	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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