DUF3333 - PFAM28P - GREMLIN Contacts

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DUF3333 - Domain of unknown function (DUF3333)

PFAM:	PF11812	Sequences: EARLKRRYAAERRFRAYGLAAIALALLFLAFLLGSIVSKGYSAFTQTYITLDVTFDPAVLDPDGRPRDPEALATADYRGLVRAALRAAFPEVTGRRDKRALYGLVSSGAAFQLRDMVLADPSLIGTTVTVWLPASDDVDMYLKGRIDRDLPE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	152 (148)
Sequences:	5161 (3900)
Seq/√Len:	320.6
META:	0.867

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_D	129_T	3.324	1.00
50_T	129_T	2.883	1.00
50_T	131_W	2.827	1.00
116_M	123_L	2.788	1.00
30_A	34_G	2.658	1.00
55_F	128_V	2.449	1.00
16_A	19_L	2.336	1.00
94_G	97_D	2.316	1.00
13_R	17_Y	2.181	1.00
47_T	142_L	2.051	1.00
34_G	38_S	2.046	1.00
86_R	102_Y	2.004	1.00
10_A	13_R	1.988	1.00
23_A	27_L	1.975	1.00
37_V	41_Y	1.926	1.00
9_A	13_R	1.898	1.00
54_T	57_P	1.831	1.00
81_V	105_V	1.807	1.00
35_S	39_K	1.771	1.00
20_A	24_L	1.722	1.00
68_D	71_A	1.717	1.00
16_A	20_A	1.695	1.00
84_A	88_A	1.691	1.00
83_A	87_A	1.651	1.00
111_F	115_D	1.590	1.00
82_R	102_Y	1.569	1.00
116_M	120_D	1.567	1.00
19_L	23_A	1.514	1.00
12_R	15_R	1.513	1.00
49_I	134_A	1.511	1.00
41_Y	45_T	1.484	1.00
147_D	150_L	1.477	1.00
27_L	31_F	1.465	1.00
54_T	127_T	1.447	1.00
47_T	134_A	1.430	1.00
112_Q	133_P	1.423	1.00
78_R	110_A	1.409	1.00
24_L	28_F	1.394	1.00
140_M	145_R	1.386	1.00
116_M	130_V	1.385	1.00
114_R	118_L	1.371	1.00
42_S	45_T	1.367	1.00
86_R	98_K	1.358	1.00
11_E	14_F	1.343	1.00
134_A	138_V	1.316	1.00
13_R	16_A	1.312	1.00
117_V	123_L	1.307	1.00
5_K	9_A	1.292	1.00
123_L	126_T	1.275	1.00
117_V	124_I	1.268	1.00
139_D	143_K	1.267	1.00
8_Y	12_R	1.256	1.00
15_R	19_L	1.245	1.00
61_D	67_R	1.242	1.00
120_D	123_L	1.227	1.00
33_L	37_V	1.222	1.00
48_Y	131_W	1.219	1.00
116_M	128_V	1.217	1.00
98_K	102_Y	1.205	1.00
78_R	82_R	1.183	1.00
29_L	33_L	1.183	1.00
4_L	8_Y	1.171	1.00
72_L	77_Y	1.166	1.00
10_A	17_Y	1.160	1.00
52_D	127_T	1.159	1.00
55_F	116_M	1.148	1.00
51_L	84_A	1.142	1.00
63_D	66_P	1.140	1.00
45_T	48_Y	1.131	1.00
97_D	100_A	1.130	1.00
141_Y	148_R	1.124	1.00
115_D	119_A	1.122	1.00
26_L	30_A	1.106	1.00
79_G	83_A	1.099	1.00
55_F	123_L	1.082	1.00
76_D	79_G	1.057	1.00
22_I	26_L	1.043	1.00
57_P	125_G	1.031	1.00
85_L	105_V	1.022	1.00
56_D	59_V	1.017	1.00
20_A	23_A	1.016	1.00
61_D	64_G	0.999	1.00
48_Y	133_P	0.995	1.00
34_G	37_V	0.992	1.00
69_P	73_A	0.972	1.00
62_P	67_R	0.967	1.00
92_V	101_L	0.966	1.00
59_V	79_G	0.942	1.00
17_Y	20_A	0.939	1.00
38_S	42_S	0.939	1.00
55_F	60_L	0.931	1.00
77_Y	117_V	0.928	1.00
112_Q	116_M	0.926	1.00
100_A	103_G	0.915	1.00
59_V	83_A	0.914	1.00
83_A	86_R	0.909	1.00
54_T	87_A	0.905	1.00
138_V	142_L	0.902	1.00
40_G	44_F	0.896	1.00
120_D	126_T	0.895	1.00
25_A	29_L	0.885	1.00
95_R	98_K	0.884	1.00
38_S	41_Y	0.883	1.00
89_F	92_V	0.882	1.00
73_A	118_L	0.872	1.00
52_D	56_D	0.861	1.00
12_R	16_A	0.858	1.00
66_P	71_A	0.852	1.00
81_V	109_A	0.840	1.00
115_D	118_L	0.835	1.00
69_P	118_L	0.833	1.00
53_V	84_A	0.812	1.00
28_F	32_L	0.809	1.00
47_T	139_D	0.803	1.00
122_S	126_T	0.803	1.00
66_P	69_P	0.799	1.00
53_V	81_V	0.799	1.00
55_F	130_V	0.797	1.00
104_L	138_V	0.797	1.00
23_A	26_L	0.791	1.00
53_V	80_L	0.790	1.00
137_D	140_M	0.784	1.00
32_L	36_I	0.774	1.00
82_R	86_R	0.772	1.00
25_A	28_F	0.769	1.00
40_G	45_T	0.763	0.99
22_I	25_A	0.746	0.99
93_T	97_D	0.736	0.99
63_D	71_A	0.733	0.99
113_L	130_V	0.729	0.99
95_R	99_R	0.726	0.99
57_P	67_R	0.724	0.99
113_L	132_L	0.723	0.99
112_Q	115_D	0.721	0.99
26_L	33_L	0.719	0.99
59_V	75_A	0.715	0.99
85_L	88_A	0.709	0.99
64_G	67_R	0.704	0.99
11_E	15_R	0.704	0.99
92_V	97_D	0.697	0.99
85_L	101_L	0.696	0.99
5_K	8_Y	0.692	0.99
140_M	144_G	0.689	0.99
55_F	117_V	0.688	0.99
81_V	110_A	0.686	0.99
63_D	67_R	0.684	0.99
48_Y	52_D	0.683	0.99
146_I	150_L	0.677	0.99
66_P	70_E	0.675	0.99
46_Q	133_P	0.674	0.99
3_R	6_R	0.673	0.99
138_V	141_Y	0.667	0.99
128_V	131_W	0.666	0.99
32_L	39_K	0.665	0.99
123_L	128_V	0.664	0.99
89_F	101_L	0.663	0.99
71_A	75_A	0.655	0.98
60_L	67_R	0.651	0.98
73_A	114_R	0.650	0.98
82_R	95_R	0.650	0.98
28_F	31_F	0.643	0.98
67_R	71_A	0.641	0.98
134_A	142_L	0.637	0.98
71_A	74_T	0.636	0.98
64_G	71_A	0.634	0.98
87_A	127_T	0.632	0.98
6_R	9_A	0.629	0.98
60_L	75_A	0.625	0.98
141_Y	147_D	0.625	0.98
6_R	10_A	0.623	0.98
29_L	55_F	0.622	0.98
28_F	35_S	0.620	0.98
107_S	135_S	0.620	0.98
94_G	99_R	0.618	0.98
47_T	138_V	0.617	0.98
63_D	68_D	0.616	0.98
18_G	22_I	0.614	0.98
72_L	75_A	0.612	0.98
55_F	132_L	0.607	0.97
136_D	140_M	0.607	0.97
107_S	136_D	0.606	0.97
135_S	140_M	0.594	0.97
60_L	80_L	0.592	0.97
81_V	113_L	0.584	0.97
70_E	74_T	0.584	0.97
92_V	98_K	0.581	0.97
69_P	124_I	0.581	0.97
33_L	36_I	0.580	0.97
59_V	80_L	0.578	0.97
94_G	98_K	0.575	0.96
8_Y	14_F	0.571	0.96
20_A	27_L	0.565	0.96
51_L	132_L	0.565	0.96
53_V	130_V	0.564	0.96
60_L	71_A	0.561	0.96
3_R	33_L	0.560	0.96
16_A	23_A	0.558	0.96
49_I	105_V	0.556	0.96
141_Y	150_L	0.556	0.96
21_A	25_A	0.555	0.96
113_L	116_M	0.555	0.96
5_K	12_R	0.550	0.95
42_S	145_R	0.545	0.95
109_A	132_L	0.541	0.95
93_T	96_R	0.540	0.95
22_I	32_L	0.540	0.95
79_G	82_R	0.536	0.95
141_Y	146_I	0.533	0.95
72_L	118_L	0.531	0.95
52_D	88_A	0.529	0.94
69_P	72_L	0.521	0.94
132_L	135_S	0.520	0.94
61_D	71_A	0.520	0.94
112_Q	132_L	0.509	0.93
66_P	72_L	0.507	0.93
9_A	12_R	0.506	0.93
135_S	138_V	0.506	0.93
31_F	34_G	0.506	0.93
93_T	98_K	0.504	0.93
8_Y	11_E	0.503	0.93
121_P	124_I	0.501	0.93
89_F	105_V	0.500	0.93

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
2m8rA	1	0.2566	11.7	0.941	Contact Map
2w3zA	1	0.4868	7.7	0.945	Contact Map
4ud4A	1	0.5	6.8	0.946	Contact Map
3j00Z	1	0.6382	5.9	0.948	Contact Map
2kogA	1	0.2632	5.6	0.949	Contact Map
3owqA	1	0.3684	4.4	0.951	Contact Map
2adlA	2	0.4737	4	0.952	Contact Map
1p3qQ	2	0.3553	4	0.952	Contact Map
3k6qA	2	0.5461	3.7	0.953	Contact Map
3hd7A	1	0.2632	3.6	0.953	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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