DUF4123 - PFAM28P - GREMLIN Contacts

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DUF4123 - Domain of unknown function (DUF4123)

PFAM:	PF13503	Sequences: LYALLDGARDPDLLALLYESGPEHRCSPLYRGTLEAELAEVAPYLVRLEPDSPLLRWLLEGKSWGIFLVSPAPLEELRRHLRRFLTVRDPDGRRLLFRFYDPRVLRALLPTCTPEELAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	119 (115)
Sequences:	5018 (4100)
Seq/√Len:	382.3
META:	0.672

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
89_D	95_L	4.709	1.00
73_P	76_E	3.478	1.00
113_T	116_E	2.526	1.00
9_R	63_S	2.417	1.00
106_R	110_P	2.363	1.00
108_L	116_E	2.344	1.00
105_L	109_L	2.340	1.00
86_T	94_R	2.259	1.00
101_D	104_V	2.201	1.00
98_R	101_D	2.032	1.00
88_R	94_R	2.006	1.00
80_H	84_F	1.989	1.00
97_F	108_L	1.913	1.00
39_A	42_A	1.888	1.00
108_L	112_C	1.881	1.00
3_A	67_F	1.808	1.00
10_D	13_L	1.796	1.00
78_R	82_R	1.738	1.00
72_A	76_E	1.719	1.00
54_L	58_L	1.716	1.00
52_S	55_L	1.708	1.00
85_L	99_F	1.613	1.00
56_R	60_E	1.603	1.00
74_L	78_R	1.588	1.00
86_T	96_L	1.583	1.00
85_L	100_Y	1.570	1.00
31_R	78_R	1.558	1.00
23_E	47_R	1.514	1.00
111_T	116_E	1.456	1.00
63_S	103_R	1.389	1.00
114_P	117_L	1.386	1.00
17_L	46_V	1.383	1.00
72_A	77_L	1.334	1.00
30_Y	96_L	1.300	1.00
14_L	18_Y	1.259	1.00
16_L	57_W	1.239	1.00
48_L	55_L	1.220	1.00
7_G	44_Y	1.218	1.00
89_D	92_G	1.212	1.00
10_D	14_L	1.204	1.00
68_L	81_L	1.199	1.00
53_P	56_R	1.187	1.00
33_T	36_A	1.165	1.00
21_G	24_H	1.159	1.00
98_R	103_R	1.146	1.00
18_Y	21_G	1.123	1.00
107_A	110_P	1.109	1.00
45_L	74_L	1.100	1.00
30_Y	100_Y	1.080	1.00
38_L	41_V	1.075	1.00
54_L	57_W	1.069	1.00
55_L	58_L	1.064	1.00
4_L	45_L	1.063	1.00
72_A	80_H	1.062	1.00
68_L	77_L	1.057	1.00
77_L	81_L	1.055	1.00
15_A	18_Y	1.046	1.00
5_L	65_G	1.034	1.00
57_W	60_E	1.030	1.00
87_V	95_L	1.024	1.00
4_L	81_L	1.007	1.00
107_A	111_T	1.000	1.00
16_L	19_E	0.988	1.00
9_R	13_L	0.968	1.00
112_C	116_E	0.944	1.00
32_G	82_R	0.932	1.00
89_D	93_R	0.924	1.00
25_R	75_E	0.920	1.00
104_V	108_L	0.905	1.00
30_Y	86_T	0.896	1.00
62_K	65_G	0.887	1.00
26_C	44_Y	0.881	1.00
35_E	41_V	0.867	1.00
20_S	24_H	0.865	1.00
74_L	77_L	0.862	1.00
23_E	26_C	0.857	1.00
109_L	112_C	0.850	1.00
18_Y	24_H	0.846	1.00
88_R	92_G	0.841	1.00
70_S	77_L	0.824	1.00
85_L	96_L	0.823	1.00
43_P	46_V	0.823	1.00
82_R	85_L	0.820	1.00
45_L	78_R	0.815	1.00
35_E	96_L	0.814	1.00
35_E	39_A	0.812	1.00
31_R	82_R	0.807	1.00
2_Y	74_L	0.804	1.00
55_L	59_L	0.803	1.00
49_E	52_S	0.776	1.00
24_H	27_S	0.772	1.00
7_G	10_D	0.764	1.00
4_L	99_F	0.763	1.00
9_R	12_D	0.750	1.00
58_L	67_F	0.750	1.00
13_L	64_W	0.739	1.00
12_D	15_A	0.738	1.00
30_Y	43_P	0.736	1.00
39_A	44_Y	0.736	1.00
30_Y	85_L	0.730	1.00
6_D	100_Y	0.727	1.00
97_F	104_V	0.726	1.00
12_D	18_Y	0.726	1.00
108_L	111_T	0.718	1.00
53_P	60_E	0.711	1.00
4_L	66_I	0.706	1.00
30_Y	98_R	0.704	1.00
10_D	62_K	0.703	1.00
27_S	74_L	0.701	1.00
25_R	74_L	0.694	0.99
25_R	47_R	0.687	0.99
89_D	94_R	0.683	0.99
67_F	70_S	0.682	0.99
20_S	26_C	0.680	0.99
25_R	78_R	0.671	0.99
14_L	40_E	0.666	0.99
3_A	48_L	0.660	0.99
37_E	40_E	0.659	0.99
12_D	16_L	0.657	0.99
15_A	19_E	0.648	0.99
37_E	41_V	0.643	0.99
5_L	46_V	0.642	0.99
30_Y	42_A	0.638	0.99
6_D	98_R	0.637	0.99
54_L	59_L	0.629	0.99
35_E	86_T	0.621	0.99
23_E	50_P	0.620	0.99
54_L	60_E	0.620	0.99
14_L	21_G	0.618	0.99
63_S	106_R	0.618	0.99
3_A	46_V	0.618	0.99
61_G	65_G	0.617	0.99
109_L	117_L	0.614	0.99
45_L	77_L	0.613	0.99
73_P	77_L	0.609	0.99
36_A	39_A	0.601	0.98
27_S	78_R	0.591	0.98
97_F	100_Y	0.591	0.98
62_K	66_I	0.587	0.98
6_D	101_D	0.582	0.98
7_G	14_L	0.578	0.98
21_G	49_E	0.575	0.98
81_L	84_F	0.571	0.98
17_L	21_G	0.565	0.98
112_C	117_L	0.564	0.98
51_D	58_L	0.561	0.98
14_L	24_H	0.554	0.97
31_R	34_L	0.551	0.97
14_L	20_S	0.551	0.97
22_P	25_R	0.545	0.97
50_P	75_E	0.540	0.97
7_G	13_L	0.538	0.97
51_D	54_L	0.534	0.97
10_D	15_A	0.532	0.97
8_A	26_C	0.527	0.97
9_R	42_A	0.517	0.96
3_A	10_D	0.517	0.96
51_D	71_P	0.515	0.96
63_S	66_I	0.515	0.96
19_E	22_P	0.513	0.96
88_R	93_R	0.512	0.96
40_E	70_S	0.511	0.96
75_E	115_E	0.510	0.96
8_A	41_V	0.508	0.96
8_A	61_G	0.507	0.96
96_L	99_F	0.505	0.96
53_P	59_L	0.505	0.96
5_L	10_D	0.505	0.96
70_S	73_P	0.502	0.95
16_L	20_S	0.502	0.95
13_L	17_L	0.501	0.95
100_Y	106_R	0.500	0.95

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
4v194	1	0.3277	26.1	0.867	Contact Map
4fhrB	1	0.3782	5.1	0.904	Contact Map
4bmaA	1	0.2941	3.8	0.91	Contact Map
1pnuU	1	0.2437	2.4	0.918	Contact Map
4euwA	1	0.4202	2.3	0.919	Contact Map
3ogzA	1	0.3277	2	0.922	Contact Map
2h9aA	1	0.6807	1.8	0.924	Contact Map
3ujmA	2	0.3697	1.8	0.924	Contact Map
4zuzA	1	0.9244	1.7	0.925	Contact Map
4p6zM	1	0.3277	1.7	0.925	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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