DUF1643 - PFAM28P - GREMLIN Contacts

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DUF1643 - Protein of unknown function (DUF1643)

PFAM:	PF07799	Sequences: RYLLWRRWDPSGPRVLFIMLNPSTADEEKDDPTIRRCIGFARRWGYGGLIVVNLFAYRATDPKDLKAAADPVGPENDAAILEAAKEADLVVAAWGNLNHGALLGRGREVLALLRAAGVPLYCLGLTKDGHPRHPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	135 (133)
Sequences:	7115 (5894)
Seq/√Len:	511.1
META:	0.881

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_G	132_R	3.586	1.00
16_L	52_V	3.204	1.00
19_M	51_V	2.644	1.00
59_A	64_D	2.463	1.00
77_D	105_R	2.441	1.00
122_C	125_L	2.422	1.00
52_V	83_A	2.389	1.00
17_F	41_A	2.278	1.00
126_T	130_H	2.260	1.00
19_M	93_A	2.100	1.00
57_Y	68_A	2.078	1.00
15_V	46_Y	1.990	1.00
34_I	51_V	1.933	1.00
14_R	48_G	1.899	1.00
37_C	51_V	1.812	1.00
50_I	83_A	1.653	1.00
30_D	34_I	1.640	1.00
56_A	73_G	1.630	1.00
56_A	76_N	1.615	1.00
52_V	80_I	1.598	1.00
17_F	91_V	1.598	1.00
30_D	38_I	1.590	1.00
9_D	12_G	1.572	1.00
8_W	48_G	1.570	1.00
39_G	43_R	1.552	1.00
38_I	42_R	1.551	1.00
92_A	120_L	1.545	1.00
35_R	39_G	1.540	1.00
14_R	50_I	1.539	1.00
89_L	121_Y	1.538	1.00
16_L	83_A	1.526	1.00
36_R	39_G	1.494	1.00
16_L	87_A	1.475	1.00
30_D	35_R	1.466	1.00
37_C	49_L	1.462	1.00
7_R	48_G	1.450	1.00
126_T	132_R	1.450	1.00
75_E	79_A	1.402	1.00
106_G	130_H	1.393	1.00
81_L	112_L	1.375	1.00
13_P	47_G	1.320	1.00
40_F	44_W	1.311	1.00
38_I	49_L	1.275	1.00
15_V	91_V	1.259	1.00
50_I	86_E	1.244	1.00
32_P	35_R	1.233	1.00
98_N	128_D	1.228	1.00
3_L	79_A	1.217	1.00
3_L	83_A	1.212	1.00
16_L	90_V	1.196	1.00
24_T	58_R	1.177	1.00
84_A	90_V	1.165	1.00
59_A	62_P	1.156	1.00
15_V	41_A	1.139	1.00
25_A	31_D	1.132	1.00
66_K	102_L	1.131	1.00
3_L	50_I	1.130	1.00
36_R	40_F	1.123	1.00
18_I	52_V	1.115	1.00
17_F	37_C	1.107	1.00
46_Y	89_L	1.099	1.00
84_A	113_L	1.082	1.00
15_V	44_W	1.076	1.00
68_A	71_P	1.071	1.00
19_M	37_C	1.056	1.00
9_D	47_G	1.054	1.00
12_G	47_G	1.047	1.00
15_V	89_L	1.040	1.00
16_L	84_A	1.025	1.00
34_I	49_L	1.000	1.00
7_R	14_R	0.998	1.00
5_W	50_I	0.994	1.00
32_P	60_T	0.983	1.00
5_W	48_G	0.981	1.00
78_A	82_E	0.979	1.00
61_D	64_D	0.978	1.00
18_I	90_V	0.976	1.00
55_F	102_L	0.974	1.00
106_G	110_L	0.969	1.00
41_A	49_L	0.962	1.00
105_R	108_E	0.953	1.00
52_V	84_A	0.950	1.00
79_A	83_A	0.945	1.00
100_G	106_G	0.944	1.00
6_R	30_D	0.940	1.00
80_I	109_V	0.936	1.00
20_L	62_P	0.934	1.00
105_R	109_V	0.933	1.00
66_K	99_H	0.925	1.00
75_E	78_A	0.921	1.00
64_D	67_A	0.918	1.00
101_A	130_H	0.907	1.00
24_T	60_T	0.904	1.00
57_Y	66_K	0.885	1.00
14_R	88_D	0.877	1.00
9_D	13_P	0.870	1.00
41_A	46_Y	0.869	1.00
79_A	82_E	0.856	1.00
2_Y	73_G	0.855	1.00
26_D	58_R	0.851	1.00
2_Y	56_A	0.833	1.00
59_A	65_L	0.816	1.00
11_S	47_G	0.803	1.00
117_G	120_L	0.802	1.00
100_G	103_L	0.801	1.00
77_D	109_V	0.800	1.00
7_R	10_P	0.795	1.00
37_C	93_A	0.789	1.00
24_T	29_K	0.783	1.00
91_V	123_L	0.780	1.00
99_H	102_L	0.778	1.00
54_L	109_V	0.765	1.00
35_R	40_F	0.764	1.00
34_I	37_C	0.764	1.00
84_A	109_V	0.759	1.00
17_F	93_A	0.758	1.00
76_N	80_I	0.757	1.00
40_F	43_R	0.754	1.00
20_L	54_L	0.745	1.00
3_L	52_V	0.737	1.00
109_V	112_L	0.732	1.00
108_E	112_L	0.729	1.00
54_L	106_G	0.726	1.00
17_F	49_L	0.724	1.00
110_L	114_R	0.723	1.00
77_D	112_L	0.719	1.00
107_R	110_L	0.714	1.00
60_T	64_D	0.711	1.00
55_F	105_R	0.695	1.00
16_L	50_I	0.695	1.00
36_R	43_R	0.694	1.00
101_A	106_G	0.694	1.00
39_G	42_R	0.691	1.00
13_P	88_D	0.684	1.00
57_Y	64_D	0.681	1.00
52_V	87_A	0.680	1.00
32_P	36_R	0.679	1.00
7_R	47_G	0.678	1.00
104_G	107_R	0.672	1.00
23_S	31_D	0.671	1.00
100_G	104_G	0.664	1.00
98_N	130_H	0.663	1.00
77_D	80_I	0.662	1.00
108_E	111_A	0.660	1.00
17_F	44_W	0.659	1.00
57_Y	65_L	0.650	1.00
36_R	44_W	0.648	1.00
37_C	41_A	0.642	1.00
8_W	47_G	0.642	1.00
84_A	87_A	0.641	1.00
109_V	113_L	0.619	1.00
65_L	102_L	0.614	1.00
14_R	87_A	0.612	1.00
4_L	25_A	0.610	1.00
2_Y	74_P	0.609	1.00
99_H	103_L	0.599	0.99
113_L	120_L	0.597	0.99
103_L	106_G	0.595	0.99
81_L	116_A	0.591	0.99
85_K	116_A	0.586	0.99
6_R	49_L	0.585	0.99
17_F	123_L	0.583	0.99
8_W	42_R	0.583	0.99
92_A	113_L	0.582	0.99
98_N	126_T	0.580	0.99
56_A	72_V	0.579	0.99
104_G	108_E	0.578	0.99
66_K	71_P	0.577	0.99
90_V	118_V	0.577	0.99
72_V	77_D	0.574	0.99
102_L	106_G	0.573	0.99
56_A	75_E	0.572	0.99
55_F	66_K	0.572	0.99
27_E	30_D	0.559	0.99
107_R	111_A	0.558	0.99
23_S	60_T	0.557	0.99
55_F	73_G	0.554	0.99
26_D	29_K	0.550	0.99
54_L	100_G	0.549	0.99
14_R	86_E	0.546	0.99
77_D	108_E	0.542	0.99
72_V	105_R	0.538	0.99
90_V	120_L	0.531	0.99
19_M	49_L	0.530	0.99
35_R	38_I	0.526	0.99
56_A	71_P	0.526	0.99
7_R	12_G	0.526	0.99
6_R	38_I	0.522	0.99
92_A	110_L	0.521	0.99
117_G	121_Y	0.519	0.98
20_L	65_L	0.516	0.98
21_N	25_A	0.515	0.98
81_L	85_K	0.515	0.98
81_L	115_A	0.512	0.98
24_T	59_A	0.509	0.98
121_Y	125_L	0.507	0.98
70_D	73_G	0.505	0.98
17_F	51_V	0.504	0.98
80_I	84_A	0.501	0.98
78_A	81_L	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
2d3yA	1	0.9407	51.5	0.886	Contact Map
1ui0A	1	0.9481	29.7	0.901	Contact Map
3kv1A	2	0.6296	28.3	0.902	Contact Map
4r9nA	1	0.637	26.8	0.903	Contact Map
1vk2A	1	0.9259	25	0.904	Contact Map
1oe4A	2	0.8741	21.4	0.907	Contact Map
2gnpA	1	0.7037	16.4	0.912	Contact Map
2j8xA	1	0.8815	15.9	0.912	Contact Map
4oqpA	2	0.6815	15.5	0.913	Contact Map
2okgA	2	0.7111	15.3	0.913	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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