DUF1772 - PFAM28P - GREMLIN Contacts

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DUF1772 - Domain of unknown function (DUF1772)

PFAM:	PF08592	Sequences: GAFFAFSVVVMPALLRLPDRAGILLPQFQPSYRRGAAMFPPLALGSLLAGLLLALRWWGPGAAWLLLAAAALLLLGVVPVTLLVNVPLNNRLAAADPASAAADAAAAEARALLERWGRLHAVRTVLSLAAFALLLWA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	137 (129)
Sequences:	13554 (10559)
Seq/√Len:	929.7
META:	0.826

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_V	90_N	3.449	1.00
84_V	119_L	2.653	1.00
17_L	21_A	2.488	1.00
109_A	112_L	2.438	1.00
4_F	8_V	2.361	1.00
25_L	29_Q	2.095	1.00
18_P	21_A	2.006	1.00
88_L	115_R	1.963	1.00
5_A	9_V	1.952	1.00
37_A	41_P	1.935	1.00
36_A	39_F	1.912	1.00
42_L	45_G	1.901	1.00
63_A	66_L	1.788	1.00
7_S	121_A	1.763	1.00
28_F	32_Y	1.747	1.00
105_A	109_A	1.736	1.00
25_L	28_F	1.724	1.00
77_V	127_S	1.697	1.00
36_A	40_P	1.669	1.00
24_L	29_Q	1.668	1.00
43_A	46_S	1.664	1.00
105_A	108_E	1.641	1.00
4_F	124_T	1.640	1.00
108_E	112_L	1.609	1.00
2_A	5_A	1.579	1.00
30_P	33_R	1.566	1.00
80_V	85_N	1.563	1.00
80_V	122_V	1.560	1.00
108_E	111_A	1.556	1.00
131_F	135_L	1.548	1.00
95_A	109_A	1.520	1.00
109_A	113_L	1.508	1.00
115_R	118_R	1.506	1.00
2_A	9_V	1.503	1.00
85_N	119_L	1.491	1.00
29_Q	32_Y	1.476	1.00
42_L	46_S	1.475	1.00
24_L	28_F	1.437	1.00
79_P	83_L	1.414	1.00
26_P	30_P	1.413	1.00
107_A	110_R	1.398	1.00
26_P	29_Q	1.368	1.00
106_A	109_A	1.354	1.00
60_P	63_A	1.266	1.00
110_R	113_L	1.242	1.00
76_G	126_L	1.241	1.00
6_F	9_V	1.229	1.00
82_L	86_V	1.229	1.00
32_Y	35_G	1.223	1.00
10_V	14_L	1.209	1.00
33_R	93_A	1.186	1.00
91_R	108_E	1.172	1.00
110_R	114_E	1.163	1.00
27_Q	31_S	1.146	1.00
5_A	10_V	1.144	1.00
42_L	47_L	1.138	1.00
103_D	106_A	1.130	1.00
46_S	50_G	1.125	1.00
42_L	50_G	1.123	1.00
107_A	111_A	1.099	1.00
37_A	40_P	1.091	1.00
73_L	76_G	1.083	1.00
43_A	50_G	1.075	1.00
132_A	136_W	1.071	1.00
29_Q	33_R	1.065	1.00
19_D	110_R	1.055	1.00
84_V	88_L	1.054	1.00
28_F	31_S	1.030	1.00
36_A	41_P	1.001	1.00
61_G	64_W	0.999	1.00
105_A	112_L	0.995	1.00
92_L	95_A	0.993	1.00
62_A	65_L	0.979	1.00
60_P	65_L	0.978	1.00
24_L	27_Q	0.970	1.00
57_W	61_G	0.964	1.00
47_L	50_G	0.962	1.00
111_A	114_E	0.954	1.00
43_A	47_L	0.952	1.00
46_S	49_A	0.947	1.00
91_R	112_L	0.943	1.00
78_V	82_L	0.943	1.00
105_A	110_R	0.929	1.00
89_N	116_W	0.928	1.00
42_L	49_A	0.925	1.00
42_L	48_L	0.923	1.00
77_V	126_L	0.921	1.00
25_L	32_Y	0.912	1.00
45_G	50_G	0.909	1.00
81_T	85_N	0.894	1.00
117_G	121_A	0.885	1.00
59_G	62_A	0.879	1.00
118_R	121_A	0.870	1.00
47_L	75_L	0.864	1.00
90_N	93_A	0.859	1.00
7_S	124_T	0.851	1.00
106_A	110_R	0.850	1.00
43_A	49_A	0.838	1.00
38_M	41_P	0.833	1.00
33_R	36_A	0.833	1.00
59_G	63_A	0.813	1.00
121_A	125_V	0.792	1.00
12_P	16_R	0.791	1.00
27_Q	32_Y	0.789	1.00
44_L	48_L	0.784	1.00
81_T	123_R	0.783	1.00
77_V	80_V	0.781	1.00
41_P	45_G	0.779	1.00
115_R	119_L	0.770	1.00
105_A	113_L	0.770	1.00
44_L	50_G	0.767	1.00
58_W	62_A	0.764	1.00
57_W	60_P	0.763	1.00
69_A	72_L	0.758	1.00
29_Q	35_G	0.756	1.00
81_T	86_V	0.752	1.00
31_S	35_G	0.750	1.00
126_L	130_A	0.744	1.00
50_G	134_L	0.740	1.00
24_L	32_Y	0.735	1.00
91_R	94_A	0.734	1.00
15_L	117_G	0.731	1.00
112_L	115_R	0.726	1.00
57_W	66_L	0.726	1.00
120_H	124_T	0.725	1.00
80_V	126_L	0.721	1.00
43_A	48_L	0.721	1.00
27_Q	30_P	0.721	1.00
28_F	35_G	0.718	1.00
25_L	31_S	0.714	1.00
11_M	15_L	0.711	1.00
11_M	14_L	0.708	1.00
24_L	35_G	0.703	1.00
80_V	119_L	0.695	1.00
118_R	122_V	0.693	1.00
114_E	118_R	0.688	1.00
80_V	84_V	0.685	1.00
90_N	94_A	0.661	1.00
30_P	34_R	0.660	1.00
38_M	42_L	0.657	1.00
85_N	88_L	0.655	1.00
61_G	65_L	0.646	1.00
12_P	15_L	0.639	1.00
55_L	59_G	0.636	1.00
11_M	117_G	0.631	1.00
103_D	109_A	0.631	1.00
60_P	64_W	0.630	1.00
47_L	51_L	0.626	1.00
40_P	43_A	0.620	1.00
120_H	131_F	0.619	1.00
58_W	61_G	0.617	1.00
20_R	26_P	0.615	1.00
36_A	43_A	0.601	1.00
3_F	77_V	0.599	1.00
9_V	12_P	0.596	1.00
73_L	129_A	0.594	1.00
55_L	58_W	0.590	1.00
40_P	46_S	0.590	1.00
34_R	37_A	0.589	1.00
128_L	132_A	0.587	1.00
69_A	133_L	0.585	1.00
5_A	8_V	0.579	1.00
58_W	64_W	0.578	1.00
19_D	107_A	0.577	1.00
75_L	79_P	0.574	1.00
104_A	108_E	0.572	1.00
14_L	31_S	0.568	1.00
44_L	47_L	0.568	1.00
56_R	60_P	0.567	1.00
71_A	75_L	0.556	1.00
55_L	64_W	0.555	1.00
73_L	130_A	0.554	1.00
58_W	66_L	0.550	1.00
88_L	119_L	0.550	1.00
6_F	120_H	0.546	1.00
127_S	131_F	0.545	1.00
2_A	8_V	0.543	1.00
38_M	45_G	0.540	1.00
39_F	42_L	0.538	1.00
69_A	73_L	0.538	1.00
65_L	69_A	0.538	1.00
57_W	62_A	0.538	1.00
108_E	113_L	0.532	1.00
76_G	80_V	0.521	1.00
129_A	133_L	0.519	1.00
95_A	106_A	0.518	1.00
59_G	66_L	0.514	1.00
45_G	49_A	0.512	1.00
56_R	61_G	0.511	1.00
24_L	31_S	0.511	1.00
74_L	130_A	0.507	1.00
25_L	35_G	0.502	1.00
48_L	53_L	0.501	1.00
6_F	10_V	0.500	1.00

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	0.6569	6.6	0.897	Contact Map
3ne5A	3	0.9124	6.3	0.899	Contact Map
4k0jA	3	0.8248	5.7	0.9	Contact Map
4pd6A	3	0.8905	5.1	0.902	Contact Map
4oh3A	2	0.6715	4.8	0.904	Contact Map
3qnqA	2	0.7007	4.4	0.905	Contact Map
4tphA	2	0.5693	4.3	0.906	Contact Map
4dx5A	3	0.708	4	0.907	Contact Map
3w9iA	3	0.6788	3.3	0.911	Contact Map
3o7qA	1	0.9124	3.3	0.911	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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