DUF4342 - PFAM28P - GREMLIN Contacts

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DUF4342 - Domain of unknown function (DUF4342)

PFAM:	PF14242	Sequences: KKTRTEEFKVSGEELVDKVKELIHEGNVRRIIIKNDGKTLLEIPLTVGVVGGGVAAVLAPVLAAVGAIAALVTECTIEVER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (75)
Sequences:	7574 (4631)
Seq/√Len:	534.7
META:	0.943

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_K	21_E	5.278	1.00
34_K	78_E	3.681	1.00
27_N	46_T	2.734	1.00
13_E	17_D	2.514	1.00
39_T	42_E	2.453	1.00
35_N	38_K	2.344	1.00
30_R	42_E	2.132	1.00
29_R	45_L	2.061	1.00
11_S	14_E	2.007	1.00
24_H	28_V	1.973	1.00
32_I	42_E	1.843	1.00
32_I	78_E	1.836	1.00
40_L	75_C	1.708	1.00
14_E	17_D	1.457	1.00
4_R	8_F	1.430	1.00
21_E	25_E	1.425	1.00
26_G	46_T	1.412	1.00
69_A	73_T	1.347	1.00
25_E	29_R	1.337	1.00
72_V	75_C	1.303	1.00
7_E	78_E	1.275	1.00
68_I	72_V	1.247	1.00
34_K	39_T	1.177	1.00
23_I	27_N	1.153	1.00
22_L	28_V	1.142	1.00
32_I	80_E	1.138	1.00
61_V	65_V	1.126	1.00
17_D	21_E	1.123	1.00
35_N	40_L	1.084	1.00
59_A	62_L	1.044	1.00
16_V	20_K	1.035	1.00
31_I	43_I	1.007	1.00
43_I	48_G	0.990	1.00
5_T	78_E	0.979	1.00
56_A	60_P	0.957	1.00
46_T	49_V	0.949	1.00
57_V	61_V	0.947	1.00
6_E	10_V	0.944	1.00
7_E	11_S	0.916	1.00
57_V	60_P	0.906	1.00
46_T	50_V	0.900	1.00
70_A	77_I	0.898	1.00
8_F	11_S	0.895	1.00
3_T	80_E	0.894	1.00
56_A	59_A	0.882	1.00
5_T	8_F	0.868	1.00
4_R	11_S	0.848	1.00
3_T	7_E	0.848	1.00
23_I	26_G	0.842	1.00
9_K	74_E	0.832	1.00
17_D	20_K	0.827	1.00
35_N	75_C	0.820	1.00
5_T	9_K	0.804	1.00
10_V	15_L	0.795	1.00
12_G	16_V	0.794	1.00
63_A	66_G	0.789	1.00
14_E	18_K	0.786	1.00
33_I	75_C	0.782	1.00
31_I	48_G	0.775	1.00
32_I	39_T	0.771	1.00
4_R	9_K	0.750	1.00
5_T	32_I	0.746	1.00
9_K	76_T	0.745	1.00
64_A	67_A	0.743	1.00
16_V	65_V	0.735	1.00
22_L	79_V	0.733	1.00
61_V	64_A	0.719	1.00
13_E	20_K	0.701	1.00
7_E	34_K	0.694	1.00
4_R	49_V	0.691	1.00
26_G	49_V	0.676	1.00
47_V	50_V	0.674	1.00
61_V	68_I	0.666	1.00
8_F	79_V	0.665	1.00
19_V	31_I	0.662	1.00
34_K	76_T	0.662	1.00
43_I	61_V	0.662	1.00
6_E	81_R	0.660	1.00
41_L	68_I	0.658	1.00
63_A	68_I	0.653	1.00
64_A	68_I	0.646	1.00
47_V	51_G	0.630	1.00
44_P	47_V	0.625	1.00
56_A	63_A	0.624	1.00
50_V	58_L	0.622	1.00
20_K	24_H	0.619	1.00
22_L	26_G	0.611	1.00
7_E	76_T	0.597	1.00
74_E	78_E	0.594	1.00
38_K	42_E	0.589	0.99
30_R	80_E	0.585	0.99
34_K	37_G	0.585	0.99
35_N	78_E	0.580	0.99
28_V	44_P	0.574	0.99
40_L	72_V	0.573	0.99
5_T	11_S	0.567	0.99
5_T	21_E	0.565	0.99
9_K	14_E	0.556	0.99
3_T	81_R	0.556	0.99
51_G	58_L	0.554	0.99
8_F	18_K	0.546	0.99
19_V	23_I	0.530	0.99
33_I	37_G	0.523	0.99
67_A	71_L	0.520	0.99
41_L	44_P	0.516	0.99
49_V	56_A	0.515	0.99
58_L	77_I	0.514	0.99
23_I	46_T	0.510	0.99
11_S	18_K	0.508	0.99
63_A	67_A	0.506	0.98
71_L	77_I	0.502	0.98
4_R	14_E	0.500	0.98

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
2oarA	7	0.6173	8.8	0.865	Contact Map
3zg9B	1	0	6.2	0.874	Contact Map
3bo0B	1	0.8025	5.1	0.879	Contact Map
2xyqA	1	0.4691	5	0.88	Contact Map
3k9dA	2	0.9877	4.4	0.883	Contact Map
3jz4A	4	0.9753	4.1	0.884	Contact Map
2ww9B	1	0.7284	4	0.885	Contact Map
3ek1A	5	0.9753	3.6	0.888	Contact Map
2w8nA	4	0.963	3.5	0.888	Contact Map
3my7A	2	0.9877	3.3	0.889	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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