DUF3429 - PFAM28P - GREMLIN Contacts

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DUF3429 - Protein of unknown function (DUF3429)

PFAM:	PF11911	Sequences: IPRLALLLGYAGLIPFVALALLALWLLPPGLRALALYALLAYGAVILSFLGGVHWGLALRAPGPAAARLLLSVVPALLAWLALLLPPPAALLLLAAGFLALLLVDRRLARRGLLPAWYLRLRLRLTAVVVLSLLLAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (134)
Sequences:	4678 (3552)
Seq/√Len:	306.9
META:	0.802

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_G	125_L	4.108	1.00
10_Y	124_R	3.792	1.00
39_L	136_A	3.637	1.00
47_L	97_G	3.406	1.00
102_L	123_L	3.384	1.00
39_L	133_L	2.594	1.00
45_V	76_A	2.344	1.00
99_L	130_V	2.326	1.00
13_L	128_V	2.286	1.00
19_L	39_L	2.269	1.00
95_A	130_V	2.260	1.00
98_F	129_V	2.250	1.00
53_V	118_Y	2.187	1.00
78_L	97_G	2.024	1.00
20_A	132_S	1.998	1.00
43_G	133_L	1.947	1.00
17_V	132_S	1.938	1.00
17_V	128_V	1.799	1.00
101_L	105_D	1.779	1.00
6_L	10_Y	1.731	1.00
51_G	75_P	1.679	1.00
40_L	90_A	1.660	1.00
82_A	93_L	1.655	1.00
43_G	94_L	1.625	1.00
41_A	83_L	1.578	1.00
126_T	130_V	1.522	1.00
16_F	129_V	1.402	1.00
82_A	94_L	1.365	1.00
127_A	131_L	1.362	1.00
6_L	124_R	1.351	1.00
19_L	35_A	1.347	1.00
13_L	17_V	1.338	1.00
120_R	124_R	1.330	1.00
45_V	80_W	1.315	1.00
47_L	98_F	1.283	1.00
50_L	101_L	1.281	1.00
129_V	132_S	1.263	1.00
49_F	55_W	1.257	1.00
92_L	137_L	1.244	1.00
39_L	43_G	1.244	1.00
10_Y	13_L	1.238	1.00
44_A	48_S	1.228	1.00
14_I	18_A	1.220	1.00
73_V	76_A	1.187	1.00
44_A	83_L	1.183	1.00
71_L	101_L	1.176	1.00
46_I	50_L	1.167	1.00
48_S	80_W	1.166	1.00
12_G	46_I	1.124	1.00
95_A	137_L	1.105	1.00
5_A	117_W	1.097	1.00
28_P	31_L	1.097	1.00
3_R	7_L	1.066	1.00
70_L	73_V	1.058	1.00
16_F	46_I	1.057	1.00
104_V	108_L	1.056	1.00
34_L	37_Y	1.045	1.00
9_G	13_L	1.035	1.00
47_L	79_A	1.034	1.00
107_R	111_R	1.029	1.00
48_S	76_A	1.028	1.00
109_A	119_L	1.027	1.00
130_V	134_L	1.021	1.00
82_A	90_A	1.018	1.00
9_G	121_L	1.016	1.00
71_L	104_V	1.000	1.00
102_L	106_R	0.998	1.00
37_Y	41_A	0.991	1.00
78_L	93_L	0.967	1.00
57_L	114_L	0.964	1.00
13_L	125_L	0.964	1.00
59_L	118_Y	0.963	1.00
53_V	56_G	0.962	1.00
41_A	80_W	0.960	1.00
107_R	110_R	0.947	1.00
133_L	136_A	0.945	1.00
54_H	68_R	0.921	1.00
102_L	105_D	0.912	1.00
90_A	94_L	0.908	1.00
128_V	132_S	0.905	1.00
20_A	136_A	0.902	1.00
123_L	127_A	0.897	1.00
51_G	79_A	0.895	1.00
8_L	73_V	0.889	1.00
89_A	92_L	0.883	1.00
54_H	101_L	0.882	1.00
58_A	69_L	0.876	1.00
95_A	134_L	0.875	1.00
54_H	105_D	0.868	1.00
101_L	104_V	0.868	1.00
33_A	37_Y	0.859	1.00
93_L	96_A	0.857	1.00
3_R	6_L	0.852	1.00
46_I	73_V	0.840	1.00
4_L	70_L	0.838	1.00
44_A	79_A	0.833	1.00
46_I	76_A	0.830	1.00
38_A	84_L	0.817	1.00
10_Y	128_V	0.803	1.00
25_W	28_P	0.801	1.00
50_L	72_S	0.800	1.00
32_R	36_L	0.799	1.00
38_A	80_W	0.797	1.00
40_L	91_L	0.789	1.00
103_L	106_R	0.784	1.00
103_L	107_R	0.781	0.99
124_R	127_A	0.781	0.99
109_A	114_L	0.769	0.99
36_L	87_P	0.762	0.99
57_L	60_R	0.760	0.99
22_L	35_A	0.758	0.99
42_Y	77_L	0.758	0.99
54_H	118_Y	0.755	0.99
8_L	70_L	0.754	0.99
106_R	110_R	0.744	0.99
46_I	129_V	0.735	0.99
15_P	42_Y	0.733	0.99
7_L	10_Y	0.733	0.99
121_L	125_L	0.730	0.99
53_V	72_S	0.723	0.99
51_G	73_V	0.723	0.99
130_V	133_L	0.721	0.99
91_L	136_A	0.716	0.99
101_L	118_Y	0.713	0.99
30_G	34_L	0.712	0.99
61_A	64_P	0.707	0.99
125_L	129_V	0.703	0.99
102_L	126_T	0.702	0.99
54_H	102_L	0.701	0.99
89_A	93_L	0.700	0.99
42_Y	46_I	0.698	0.99
12_G	129_V	0.693	0.99
54_H	104_V	0.689	0.99
131_L	135_L	0.679	0.99
41_A	84_L	0.675	0.99
6_L	9_G	0.675	0.99
5_A	69_L	0.651	0.98
63_G	66_A	0.644	0.98
47_L	101_L	0.643	0.98
19_L	38_A	0.641	0.98
18_A	22_L	0.636	0.98
24_L	27_L	0.636	0.98
20_A	135_L	0.636	0.98
63_G	67_A	0.635	0.98
31_L	34_L	0.632	0.98
24_L	28_P	0.626	0.98
40_L	87_P	0.625	0.98
70_L	74_V	0.624	0.98
77_L	81_L	0.612	0.97
120_R	123_L	0.612	0.97
50_L	76_A	0.610	0.97
109_A	112_G	0.609	0.97
22_L	34_L	0.608	0.97
40_L	94_L	0.604	0.97
16_F	43_G	0.598	0.97
74_V	93_L	0.598	0.97
42_Y	55_W	0.598	0.97
75_P	100_A	0.597	0.97
11_A	46_I	0.596	0.97
71_L	105_D	0.596	0.97
29_P	32_R	0.594	0.97
50_L	129_V	0.593	0.97
56_G	60_R	0.587	0.96
95_A	133_L	0.583	0.96
14_I	17_V	0.581	0.96
69_L	72_S	0.580	0.96
39_L	129_V	0.578	0.96
85_L	90_A	0.576	0.96
27_L	31_L	0.575	0.96
57_L	115_P	0.575	0.96
18_A	21_L	0.573	0.96
16_F	39_L	0.569	0.96
61_A	66_A	0.568	0.96
46_I	55_W	0.566	0.96
53_V	57_L	0.564	0.96
27_L	30_G	0.564	0.96
106_R	123_L	0.563	0.95
5_A	121_L	0.563	0.95
98_F	126_T	0.561	0.95
106_R	119_L	0.558	0.95
7_L	11_A	0.550	0.95
58_A	72_S	0.549	0.95
44_A	76_A	0.547	0.95
41_A	45_V	0.546	0.95
22_L	30_G	0.544	0.95
11_A	14_I	0.543	0.95
98_F	101_L	0.539	0.94
60_R	64_P	0.537	0.94
8_L	77_L	0.537	0.94
124_R	128_V	0.535	0.94
44_A	53_V	0.531	0.94
46_I	49_F	0.529	0.94
91_L	137_L	0.529	0.94
22_L	27_L	0.527	0.94
26_L	32_R	0.525	0.94
85_L	93_L	0.518	0.93
52_G	71_L	0.510	0.93
81_L	85_L	0.507	0.92
48_S	51_G	0.503	0.92
54_H	108_L	0.500	0.92
109_A	115_P	0.500	0.92

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
4q2eA	2	0.4745	2.5	0.932	Contact Map
3lbwA	3	0.1606	1.3	0.942	Contact Map
4tphA	2	0.9416	1.2	0.943	Contact Map
2mmuA	1	0.3431	1.1	0.944	Contact Map
2mwrA	1	0.2628	0.9	0.948	Contact Map
2mgyA	1	0.3796	0.9	0.948	Contact Map
3ne5A	3	0.8467	0.9	0.948	Contact Map
3bkdA	4	0.1825	0.7	0.951	Contact Map
4wzgA	1	0.2774	0.7	0.951	Contact Map
2jp3A	1	0.2409	0.7	0.952	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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