DUF3307 - PFAM28P - GREMLIN Contacts

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DUF3307 - Protein of unknown function (DUF3307)

PFAM:	PF11750	Sequences: LLLLLLLAHLLADFVLQTDWMAKNKGKKGHKSPGLLLHALIHALLTLLLLLLLGFDLPSAWLLALLIFVSHFLIDWLKLRLKKKKNFWLLFLLDQLLHLLTLLLIALWLLTINWQSVLSQWQLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (106)
Sequences:	7874 (6379)
Seq/√Len:	619.5
META:	0.887

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_A	72_F	3.972	1.00
43_A	68_F	3.759	1.00
74_I	97_L	3.734	1.00
70_S	101_T	3.649	1.00
19_D	23_K	2.953	1.00
14_F	91_F	2.546	1.00
18_T	21_M	2.531	1.00
12_A	42_H	2.431	1.00
12_A	45_L	2.269	1.00
6_L	99_L	2.245	1.00
88_W	92_L	2.182	1.00
63_L	67_I	1.866	1.00
36_L	72_F	1.848	1.00
10_L	15_V	1.649	1.00
11_L	16_L	1.613	1.00
11_L	15_V	1.564	1.00
76_W	80_R	1.547	1.00
89_L	92_L	1.480	1.00
35_L	39_A	1.463	1.00
20_W	24_N	1.457	1.00
42_H	46_T	1.437	1.00
39_A	68_F	1.434	1.00
21_M	41_I	1.426	1.00
74_I	101_T	1.372	1.00
30_H	76_W	1.354	1.00
8_A	12_A	1.348	1.00
28_K	31_K	1.341	1.00
50_L	54_G	1.339	1.00
8_A	46_T	1.318	1.00
43_A	64_A	1.318	1.00
24_N	34_G	1.297	1.00
20_W	37_L	1.259	1.00
102_L	105_I	1.239	1.00
12_A	41_I	1.203	1.00
87_F	92_L	1.152	1.00
66_L	70_S	1.144	1.00
88_W	91_F	1.135	1.00
51_L	54_G	1.132	1.00
24_N	31_K	1.130	1.00
24_N	28_K	1.121	1.00
22_A	25_K	1.112	1.00
66_L	105_I	1.079	1.00
77_L	81_L	1.073	1.00
99_L	102_L	1.066	1.00
101_T	105_I	1.049	1.00
16_L	41_I	1.012	1.00
49_L	53_L	1.011	1.00
77_L	97_L	1.003	1.00
19_D	22_A	1.002	1.00
85_K	89_L	0.989	1.00
7_L	96_L	0.977	1.00
59_S	62_L	0.973	1.00
35_L	72_F	0.969	1.00
13_D	94_D	0.966	1.00
47_L	64_A	0.955	1.00
17_Q	25_K	0.937	1.00
29_G	76_W	0.936	1.00
2_L	103_L	0.934	1.00
21_M	24_N	0.933	1.00
48_L	52_L	0.917	1.00
67_I	105_I	0.911	1.00
35_L	76_W	0.907	1.00
64_A	67_I	0.899	1.00
92_L	96_L	0.896	1.00
21_M	37_L	0.891	1.00
24_N	27_K	0.879	1.00
67_I	102_L	0.876	1.00
42_H	45_L	0.854	1.00
67_I	101_T	0.852	1.00
75_D	94_D	0.845	1.00
51_L	55_F	0.841	1.00
70_S	74_I	0.834	1.00
93_L	97_L	0.831	1.00
77_L	80_R	0.824	1.00
86_N	89_L	0.824	1.00
2_L	106_A	0.823	1.00
30_H	34_G	0.812	1.00
28_K	73_L	0.804	1.00
4_L	8_A	0.801	1.00
81_L	90_L	0.798	1.00
29_G	80_R	0.793	1.00
83_K	87_F	0.790	1.00
87_F	90_L	0.789	1.00
49_L	52_L	0.788	1.00
99_L	103_L	0.771	1.00
20_W	31_K	0.766	1.00
61_W	65_L	0.760	1.00
72_F	76_W	0.760	1.00
8_A	45_L	0.759	1.00
56_D	59_S	0.751	1.00
64_A	68_F	0.738	1.00
61_W	64_A	0.734	1.00
60_A	64_A	0.734	1.00
73_L	77_L	0.731	1.00
36_L	39_A	0.730	1.00
63_L	105_I	0.726	1.00
62_L	65_L	0.723	1.00
3_L	6_L	0.723	1.00
82_K	86_N	0.720	1.00
20_W	23_K	0.714	1.00
24_N	30_H	0.710	1.00
48_L	53_L	0.699	1.00
9_H	13_D	0.686	1.00
17_Q	94_D	0.678	1.00
69_V	73_L	0.677	1.00
49_L	54_G	0.677	1.00
84_K	87_F	0.669	1.00
53_L	56_D	0.664	1.00
60_A	63_L	0.663	1.00
82_K	85_K	0.661	1.00
66_L	101_T	0.658	1.00
83_K	86_N	0.651	1.00
18_T	22_A	0.649	1.00
10_L	99_L	0.643	1.00
23_K	27_K	0.641	1.00
22_A	79_L	0.636	1.00
71_H	75_D	0.635	1.00
10_L	14_F	0.633	1.00
42_H	67_I	0.632	1.00
101_T	104_L	0.631	1.00
83_K	88_W	0.630	1.00
89_L	93_L	0.624	1.00
12_A	15_V	0.623	1.00
87_F	91_F	0.620	1.00
43_A	46_T	0.619	1.00
20_W	34_G	0.618	1.00
26_G	79_L	0.604	1.00
10_L	93_L	0.602	1.00
39_A	43_A	0.590	1.00
73_L	76_W	0.583	1.00
50_L	53_L	0.583	1.00
2_L	6_L	0.581	1.00
93_L	96_L	0.576	1.00
25_K	79_L	0.576	1.00
40_L	44_L	0.573	1.00
12_A	16_L	0.573	1.00
39_A	42_H	0.566	1.00
85_K	91_F	0.558	1.00
85_K	88_W	0.556	1.00
21_M	25_K	0.549	1.00
63_L	66_L	0.546	0.99
14_F	95_Q	0.538	0.99
82_K	90_L	0.536	0.99
86_N	90_L	0.536	0.99
5_L	102_L	0.534	0.99
62_L	66_L	0.531	0.99
6_L	10_L	0.530	0.99
85_K	90_L	0.527	0.99
14_F	92_L	0.515	0.99
5_L	46_T	0.512	0.99
37_L	40_L	0.512	0.99
83_K	90_L	0.510	0.99
82_K	87_F	0.509	0.99
104_L	108_W	0.506	0.99
75_D	78_K	0.503	0.99
6_L	96_L	0.502	0.99
42_H	50_L	0.500	0.99
78_K	94_D	0.500	0.99
21_M	31_K	0.500	0.99

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
3tx3A	2	0.6371	31.1	0.87	Contact Map
1vsy5	1	0.8548	1.8	0.928	Contact Map
2ls4A	1	0.1613	1.7	0.929	Contact Map
1emzA	1	0.1694	0.7	0.945	Contact Map
3wu2L	1	0.1371	0.5	0.949	Contact Map
3nd0A	2	0.2177	0.5	0.95	Contact Map
3vbcA	1	0.3468	0.5	0.95	Contact Map
3wmiB	1	0.1048	0.4	0.953	Contact Map
3ar4A	1	0.6774	0.4	0.954	Contact Map
1v54M	1	0.3387	0.4	0.954	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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