DUF1499 - PFAM28P - GREMLIN Contacts

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DUF1499 - Protein of unknown function (DUF1499)

PFAM:	PF07386	Sequences: DLTTDPDSPNCVSSQAAAAAYPDIAPLRLAGPPAEAFARALAAARAMGWEIPVDPEDGYIEATATTRLFGFVDDVEIRVDPDGGSRIDVRSASRVGRSDLGVNAKRIEAFRAAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	114 (113)
Sequences:	15031 (11036)
Seq/√Len:	1038.2
META:	0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_T	72_V	3.377	1.00
89_V	107_I	2.531	1.00
41_L	45_R	2.477	1.00
74_D	94_R	2.463	1.00
41_L	55_P	2.313	1.00
59_Y	76_E	2.204	1.00
64_A	75_V	1.928	1.00
32_P	35_E	1.928	1.00
5_D	11_C	1.921	1.00
79_V	85_S	1.920	1.00
31_G	36_A	1.817	1.00
43_A	47_M	1.808	1.00
47_M	113_A	1.804	1.00
65_T	72_V	1.774	1.00
37_F	79_V	1.759	1.00
37_F	41_L	1.750	1.00
80_D	88_D	1.732	1.00
27_L	111_R	1.723	1.00
102_V	105_K	1.681	1.00
15_Q	18_A	1.672	1.00
44_A	49_W	1.647	1.00
26_P	86_R	1.532	1.00
13_S	16_A	1.513	1.00
31_G	35_E	1.502	1.00
19_A	22_P	1.446	1.00
44_A	62_A	1.436	1.00
31_G	39_R	1.398	1.00
66_T	102_V	1.390	1.00
80_D	83_G	1.377	1.00
23_D	108_E	1.366	1.00
15_Q	78_R	1.353	1.00
8_S	97_R	1.344	1.00
54_D	57_D	1.343	1.00
47_M	109_A	1.335	1.00
28_R	86_R	1.321	1.00
73_D	106_R	1.298	1.00
40_A	110_F	1.279	1.00
29_L	36_A	1.269	1.00
61_E	76_E	1.262	1.00
66_T	69_F	1.246	1.00
40_A	77_I	1.231	1.00
14_S	18_A	1.211	1.00
62_A	75_V	1.179	1.00
35_E	39_R	1.176	1.00
46_A	113_A	1.169	1.00
24_I	107_I	1.164	1.00
36_A	87_I	1.164	1.00
78_R	88_D	1.151	1.00
47_M	64_A	1.149	1.00
89_V	111_R	1.145	1.00
77_I	89_V	1.136	1.00
33_P	81_P	1.118	1.00
38_A	55_P	1.112	1.00
73_D	102_V	1.109	1.00
104_A	108_E	1.078	1.00
28_R	82_D	1.078	1.00
109_A	113_A	1.077	1.00
65_T	70_G	1.075	1.00
20_A	23_D	1.074	1.00
38_A	42_A	1.052	1.00
75_V	110_F	1.044	1.00
36_A	79_V	1.043	1.00
41_L	60_I	1.032	1.00
37_F	58_G	1.008	1.00
33_P	37_F	1.002	1.00
64_A	106_R	0.994	1.00
33_P	79_V	0.994	1.00
38_A	41_L	0.988	1.00
101_G	105_K	0.978	1.00
8_S	80_D	0.958	1.00
29_L	114_L	0.952	1.00
91_S	106_R	0.949	1.00
37_F	60_I	0.945	1.00
15_Q	88_D	0.934	1.00
24_I	89_V	0.933	1.00
8_S	11_C	0.930	1.00
91_S	103_N	0.906	1.00
49_W	110_F	0.902	1.00
35_E	38_A	0.895	1.00
13_S	17_A	0.886	1.00
80_D	86_R	0.885	1.00
3_T	10_N	0.880	1.00
3_T	6_P	0.875	1.00
14_S	17_A	0.870	1.00
44_A	110_F	0.861	1.00
39_R	43_A	0.857	1.00
92_A	97_R	0.845	1.00
42_A	45_R	0.839	1.00
40_A	79_V	0.838	1.00
82_D	86_R	0.837	1.00
42_A	46_A	0.833	1.00
60_I	77_I	0.830	1.00
102_V	106_R	0.818	1.00
49_W	75_V	0.814	1.00
51_I	62_A	0.799	1.00
43_A	110_F	0.776	1.00
76_E	90_R	0.770	1.00
36_A	85_S	0.768	1.00
47_M	110_F	0.759	1.00
58_G	78_R	0.757	1.00
43_A	113_A	0.755	1.00
72_V	95_V	0.751	1.00
24_I	108_E	0.750	1.00
44_A	51_I	0.741	1.00
33_P	36_A	0.737	1.00
12_V	15_Q	0.733	1.00
66_T	71_F	0.720	1.00
36_A	114_L	0.718	1.00
108_E	111_R	0.718	1.00
50_E	63_T	0.711	1.00
25_A	28_R	0.703	1.00
58_G	81_P	0.701	1.00
54_D	61_E	0.696	1.00
32_P	36_A	0.695	1.00
11_C	14_S	0.691	1.00
61_E	74_D	0.689	1.00
95_V	98_S	0.680	1.00
44_A	77_I	0.678	1.00
10_N	92_A	0.667	1.00
83_G	86_R	0.667	1.00
98_S	101_G	0.665	1.00
34_A	38_A	0.663	1.00
24_I	104_A	0.662	1.00
98_S	105_K	0.658	1.00
6_P	10_N	0.657	1.00
29_L	79_V	0.656	1.00
50_E	65_T	0.652	1.00
33_P	58_G	0.643	1.00
66_T	73_D	0.643	1.00
81_P	84_G	0.642	1.00
6_P	11_C	0.642	1.00
9_P	97_R	0.641	1.00
4_T	16_A	0.638	1.00
50_E	72_V	0.634	1.00
40_A	44_A	0.622	1.00
37_F	55_P	0.621	1.00
75_V	93_S	0.611	1.00
93_S	103_N	0.610	1.00
21_Y	104_A	0.603	1.00
80_D	84_G	0.600	1.00
39_R	42_A	0.591	1.00
77_I	87_I	0.589	1.00
41_L	53_V	0.588	1.00
12_V	16_A	0.583	1.00
2_L	15_Q	0.582	1.00
26_P	88_D	0.578	1.00
73_D	103_N	0.576	1.00
44_A	64_A	0.571	1.00
33_P	85_S	0.569	1.00
44_A	60_I	0.562	1.00
66_T	70_G	0.558	1.00
13_S	57_D	0.549	1.00
75_V	107_I	0.549	1.00
105_K	109_A	0.549	1.00
37_F	53_V	0.548	1.00
71_F	96_G	0.544	1.00
49_W	64_A	0.543	1.00
30_A	36_A	0.535	1.00
64_A	102_V	0.533	1.00
40_A	43_A	0.530	1.00
37_F	57_D	0.526	1.00
66_T	96_G	0.525	1.00
9_P	12_V	0.524	1.00
11_C	16_A	0.520	1.00
59_Y	78_R	0.513	1.00
93_S	102_V	0.512	1.00
17_A	20_A	0.512	1.00
73_D	91_S	0.507	1.00
89_V	110_F	0.502	1.00
83_G	88_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
4ywtA	1	0.7982	22.1	0.894	Contact Map
3odnA	1	0.7193	20.7	0.896	Contact Map
1eswA	1	0.3333	19.3	0.898	Contact Map
2yh5A	1	0.9035	18.6	0.898	Contact Map
3tgoC	2	0	13.4	0.904	Contact Map
2inbA	2	0.5526	8.6	0.912	Contact Map
1tz7A	4	0.3333	7.6	0.914	Contact Map
2zq5A	1	0.3246	6.2	0.918	Contact Map
3aqtA	2	0.7719	5.7	0.919	Contact Map
1x1nA	2	0.5088	4.3	0.924	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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