DUF4296 - PFAM28P - GREMLIN Contacts

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DUF4296 - Domain of unknown function (DUF4296)

PFAM:	PF14129	Sequences: PKNLIPEDKMVDILTDIHLAEAALSTNPLKLDSDSAKSIAYYESIFKKHGITSEQFDKSLKYYASHPEELEKIYDKVIDRLSKEKKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (85)
Sequences:	8761 (7446)
Seq/√Len:	807.6
META:	0.936

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_T	80_R	2.950	1.00
11_V	76_K	2.716	1.00
16_D	49_H	2.709	1.00
52_T	55_Q	2.028	1.00
53_S	57_D	1.981	1.00
12_D	80_R	1.886	1.00
15_T	84_E	1.836	1.00
20_A	45_I	1.824	1.00
18_H	74_Y	1.822	1.00
54_E	58_K	1.822	1.00
11_V	80_R	1.808	1.00
6_P	9_K	1.718	1.00
66_H	69_E	1.639	1.00
7_E	69_E	1.622	1.00
3_N	58_K	1.608	1.00
11_V	15_T	1.567	1.00
46_F	56_F	1.565	1.00
60_L	70_L	1.511	1.00
15_T	77_V	1.447	1.00
10_M	59_S	1.433	1.00
78_I	82_S	1.415	1.00
57_D	61_K	1.409	1.00
7_E	76_K	1.361	1.00
13_I	45_I	1.348	1.00
19_L	84_E	1.347	1.00
43_E	47_K	1.334	1.00
76_K	79_D	1.330	1.00
11_V	77_V	1.330	1.00
4_L	59_S	1.272	1.00
80_R	84_E	1.271	1.00
11_V	73_I	1.257	1.00
75_D	79_D	1.254	1.00
5_I	13_I	1.247	1.00
44_S	47_K	1.245	1.00
71_E	75_D	1.233	1.00
9_K	12_D	1.228	1.00
7_E	11_V	1.214	1.00
41_Y	44_S	1.133	1.00
44_S	48_K	1.087	1.00
46_F	51_I	1.083	1.00
22_A	26_T	1.078	1.00
13_I	51_I	1.066	1.00
7_E	72_K	1.059	1.00
5_I	51_I	1.054	1.00
79_D	83_K	1.041	1.00
12_D	49_H	1.014	1.00
58_K	61_K	1.008	1.00
80_R	83_K	1.002	1.00
76_K	80_R	0.998	1.00
51_I	55_Q	0.970	1.00
51_I	59_S	0.966	1.00
21_E	42_Y	0.963	1.00
9_K	49_H	0.953	1.00
16_D	48_K	0.946	1.00
45_I	49_H	0.944	1.00
12_D	15_T	0.940	1.00
20_A	41_Y	0.938	1.00
79_D	82_S	0.937	1.00
8_D	12_D	0.932	1.00
14_L	18_H	0.902	1.00
61_K	65_S	0.897	1.00
14_L	77_V	0.896	1.00
46_F	53_S	0.881	1.00
17_I	42_Y	0.879	1.00
3_N	59_S	0.870	1.00
18_H	22_A	0.869	1.00
69_E	72_K	0.867	1.00
70_L	73_I	0.848	1.00
38_S	42_Y	0.847	1.00
15_T	81_L	0.825	1.00
43_E	53_S	0.816	1.00
60_L	64_A	0.802	1.00
59_S	63_Y	0.801	1.00
70_L	74_Y	0.798	1.00
15_T	19_L	0.794	1.00
77_V	81_L	0.793	1.00
75_D	78_I	0.765	1.00
23_A	27_N	0.764	1.00
34_D	37_K	0.751	1.00
17_I	21_E	0.747	1.00
7_E	63_Y	0.747	1.00
40_A	43_E	0.747	1.00
15_T	18_H	0.743	1.00
40_A	44_S	0.713	1.00
12_D	16_D	0.709	1.00
59_S	62_Y	0.702	1.00
9_K	55_Q	0.693	1.00
62_Y	66_H	0.693	1.00
39_I	43_E	0.687	1.00
14_L	74_Y	0.682	1.00
68_E	72_K	0.669	1.00
27_N	30_K	0.650	1.00
28_P	31_L	0.649	1.00
74_Y	78_I	0.649	1.00
7_E	73_I	0.632	1.00
64_A	70_L	0.629	1.00
23_A	41_Y	0.625	1.00
73_I	77_V	0.623	1.00
3_N	6_P	0.622	1.00
3_N	55_Q	0.621	1.00
26_T	29_L	0.618	1.00
5_I	59_S	0.598	1.00
61_K	64_A	0.597	1.00
26_T	30_K	0.583	1.00
71_E	78_I	0.575	1.00
14_L	17_I	0.565	1.00
19_L	81_L	0.562	1.00
24_L	38_S	0.562	1.00
67_P	70_L	0.556	1.00
82_S	85_K	0.555	1.00
59_S	73_I	0.554	1.00
23_A	26_T	0.553	1.00
10_M	73_I	0.553	1.00
56_F	60_L	0.548	1.00
20_A	23_A	0.546	1.00
1_P	62_Y	0.546	1.00
74_Y	77_V	0.546	1.00
55_Q	58_K	0.545	1.00
13_I	49_H	0.543	1.00
29_L	33_S	0.537	1.00
54_E	57_D	0.536	1.00
33_S	37_K	0.531	1.00
62_Y	69_E	0.527	1.00
36_A	39_I	0.525	1.00
68_E	71_E	0.524	1.00
5_I	55_Q	0.514	1.00
21_E	24_L	0.503	1.00
29_L	32_D	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
1dq3A	1	1	11.9	0.849	Contact Map
4yn0B	1	0.931	11.7	0.85	Contact Map
3umhA	1	0.8736	11.2	0.851	Contact Map
3k66A	1	0.9655	7.4	0.863	Contact Map
3pmrA	2	0.908	6.6	0.866	Contact Map
4wjwA	2	0.5287	5.2	0.872	Contact Map
3tbgA	3	0.9425	4.3	0.877	Contact Map
3iyuX	3	0.8161	4.3	0.877	Contact Map
2dlaA	2	0.908	4.1	0.878	Contact Map
5ce7A	1	0.6322	4	0.879	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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