DUF4845 - PFAM28P - GREMLIN Contacts

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DUF4845 - Domain of unknown function (DUF4845)

PFAM:	PF16137	Sequences: KLVPAYLEYYTVKKALESVAAEPGAAGASVAEIRRAFDKRADIDDIDSIKGKDLEITKEGGGVVISVAYEVRVPLFGNVSLLVDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (85)
Sequences:	9547 (6588)
Seq/√Len:	714.5
META:	0.947

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_S	84_D	2.344	1.00
3_V	7_L	2.292	1.00
35_R	39_K	2.284	1.00
38_D	51_G	2.012	1.00
70_E	84_D	1.999	1.00
13_K	17_E	1.991	1.00
30_V	34_R	1.963	1.00
75_L	81_L	1.928	1.00
72_R	82_L	1.914	1.00
9_Y	13_K	1.870	1.00
79_V	83_V	1.865	1.00
41_A	46_I	1.831	1.00
72_R	80_S	1.787	1.00
50_K	53_D	1.780	1.00
18_S	40_R	1.721	1.00
5_A	83_V	1.697	1.00
29_S	32_E	1.605	1.00
2_L	83_V	1.594	1.00
59_E	64_V	1.581	1.00
72_R	84_D	1.580	1.00
32_E	35_R	1.579	1.00
31_A	35_R	1.527	1.00
5_A	85_F	1.522	1.00
10_Y	14_K	1.468	1.00
5_A	73_V	1.466	1.00
37_F	41_A	1.424	1.00
39_K	42_D	1.399	1.00
28_A	36_A	1.334	1.00
25_A	28_A	1.299	1.00
15_A	44_D	1.262	1.00
28_A	32_E	1.252	1.00
35_R	38_D	1.225	1.00
70_E	82_L	1.200	1.00
48_S	71_V	1.184	1.00
38_D	42_D	1.159	1.00
55_E	66_S	1.151	1.00
36_A	40_R	1.151	1.00
57_T	66_S	1.136	1.00
5_A	71_V	1.091	1.00
57_T	64_V	1.090	1.00
42_D	45_D	1.071	1.00
73_V	81_L	1.067	1.00
19_V	65_I	1.049	1.00
7_L	10_Y	1.018	1.00
8_E	48_S	1.016	1.00
41_A	54_L	1.006	1.00
6_Y	10_Y	1.000	1.00
11_T	44_D	0.975	1.00
68_A	84_D	0.946	1.00
49_I	53_D	0.945	1.00
12_V	16_L	0.930	1.00
31_A	34_R	0.917	1.00
22_E	25_A	0.912	1.00
74_P	80_S	0.911	1.00
16_L	67_V	0.905	1.00
10_Y	13_K	0.896	1.00
3_V	10_Y	0.888	1.00
14_K	18_S	0.886	1.00
17_E	21_A	0.876	1.00
15_A	40_R	0.872	1.00
19_V	37_F	0.867	1.00
7_L	11_T	0.864	1.00
33_I	65_I	0.862	1.00
39_K	43_I	0.854	1.00
37_F	54_L	0.847	1.00
49_I	67_V	0.844	1.00
22_E	40_R	0.815	1.00
33_I	56_I	0.809	1.00
19_V	36_A	0.807	1.00
58_K	63_V	0.795	1.00
74_P	84_D	0.794	1.00
36_A	39_K	0.774	1.00
14_K	44_D	0.772	1.00
15_A	18_S	0.769	1.00
59_E	62_G	0.764	1.00
5_A	9_Y	0.753	1.00
38_D	50_K	0.753	1.00
54_L	67_V	0.751	1.00
2_L	79_V	0.735	1.00
30_V	56_I	0.735	1.00
2_L	81_L	0.721	1.00
19_V	25_A	0.715	1.00
30_V	63_V	0.714	1.00
73_V	83_V	0.708	1.00
12_V	67_V	0.702	1.00
2_L	5_A	0.700	1.00
32_E	36_A	0.699	1.00
15_A	37_F	0.698	1.00
16_L	65_I	0.696	1.00
8_E	11_T	0.690	1.00
40_R	44_D	0.687	1.00
24_G	27_G	0.680	1.00
22_E	36_A	0.676	1.00
23_P	26_A	0.666	1.00
20_A	23_P	0.659	1.00
11_T	45_D	0.650	1.00
14_K	17_E	0.650	1.00
2_L	6_Y	0.648	1.00
70_E	80_S	0.642	1.00
38_D	52_K	0.642	1.00
34_R	51_G	0.637	1.00
21_A	24_G	0.637	1.00
22_E	26_A	0.617	1.00
16_L	54_L	0.616	1.00
40_R	43_I	0.615	1.00
30_V	58_K	0.613	1.00
42_D	47_D	0.600	1.00
1_K	73_V	0.596	1.00
20_A	24_G	0.593	1.00
12_V	46_I	0.589	1.00
33_I	63_V	0.581	1.00
8_E	71_V	0.574	1.00
1_K	74_P	0.564	1.00
6_Y	83_V	0.563	1.00
16_L	66_S	0.553	1.00
1_K	9_Y	0.553	1.00
12_V	41_A	0.546	1.00
74_P	83_V	0.532	1.00
13_K	16_L	0.532	1.00
37_F	46_I	0.531	1.00
11_T	14_K	0.523	1.00
41_A	44_D	0.520	1.00
18_S	21_A	0.518	1.00
74_P	77_G	0.517	1.00
15_A	46_I	0.517	1.00
19_V	33_I	0.514	1.00
3_V	6_Y	0.502	0.99
8_E	45_D	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
2pftA	1	0.5176	12.2	0.869	Contact Map
3l6iA	2	0.8353	10.7	0.873	Contact Map
2b1eA	1	0.4706	9.2	0.876	Contact Map
1q1vA	1	0.7529	7.7	0.88	Contact Map
4ye0A	2	0.6824	5.7	0.887	Contact Map
1q7hA	2	0.6706	5.7	0.887	Contact Map
3aabA	2	0.8588	5.7	0.887	Contact Map
1txlA	1	0.9647	5.5	0.888	Contact Map
1vqqA	1	0.9529	4.9	0.89	Contact Map
3woaA	1	0.4588	4.4	0.893	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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