DUF123 - PFAM28P - GREMLIN Contacts

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DUF123 - Domain of unknown function DUF123

PFAM:	PF01986	Sequences: IDFPAGYYVYVGSALGPGGLEARIARHLRRSKGKDKKLHWHIDYLLAHAEVEIVWVIYSPERLECELARALAAGAPVPGFGSSDCRCPSHLFY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	93 (86)
Sequences:	5995 (4859)
Seq/√Len:	523.9
META:	0.933

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_C	85_C	4.006	1.00
65_C	87_C	3.875	1.00
68_A	92_F	2.747	1.00
11_V	68_A	2.618	1.00
38_L	47_A	2.449	1.00
15_L	62_R	2.273	1.00
45_L	91_L	2.191	1.00
76_P	89_S	2.164	1.00
16_G	19_G	2.147	1.00
59_S	63_L	2.144	1.00
15_L	59_S	1.910	1.00
22_A	25_A	1.865	1.00
80_F	91_L	1.751	1.00
78_P	88_P	1.660	1.00
30_R	36_K	1.648	1.00
11_V	71_L	1.613	1.00
63_L	66_E	1.597	1.00
11_V	92_F	1.588	1.00
87_C	90_H	1.563	1.00
49_A	53_I	1.530	1.00
27_H	36_K	1.471	1.00
20_L	24_I	1.460	1.00
53_I	56_V	1.423	1.00
19_G	22_A	1.417	1.00
26_R	38_L	1.383	1.00
41_H	83_S	1.359	1.00
38_L	44_Y	1.316	1.00
15_L	61_E	1.291	1.00
21_E	25_A	1.234	1.00
46_L	51_V	1.222	1.00
15_L	63_L	1.088	1.00
28_L	31_S	1.080	1.00
13_S	16_G	1.060	1.00
25_A	29_R	1.047	1.00
30_R	46_L	1.045	1.00
82_S	89_S	1.031	1.00
9_V	71_L	1.023	1.00
45_L	80_F	1.013	1.00
25_A	28_L	1.007	1.00
71_L	92_F	1.000	1.00
4_P	76_P	0.998	1.00
7_Y	54_V	0.989	1.00
3_F	8_Y	0.939	1.00
11_V	67_L	0.939	1.00
36_K	46_L	0.934	1.00
32_K	36_K	0.927	1.00
41_H	44_Y	0.917	1.00
3_F	45_L	0.909	1.00
59_S	62_R	0.909	1.00
28_L	53_I	0.887	1.00
57_I	67_L	0.880	1.00
16_G	22_A	0.875	1.00
62_R	67_L	0.864	1.00
49_A	55_W	0.863	1.00
65_C	90_H	0.862	1.00
51_V	54_V	0.853	1.00
28_L	56_V	0.853	1.00
14_A	19_G	0.821	1.00
13_S	61_E	0.818	1.00
42_I	47_A	0.818	1.00
85_C	90_H	0.814	1.00
27_H	46_L	0.811	1.00
3_F	44_Y	0.807	1.00
68_A	90_H	0.805	1.00
23_R	40_W	0.798	1.00
26_R	32_K	0.794	1.00
28_L	51_V	0.781	1.00
55_W	58_Y	0.779	1.00
46_L	49_A	0.766	1.00
32_K	46_L	0.759	1.00
45_L	49_A	0.759	1.00
3_F	77_V	0.750	1.00
82_S	85_C	0.746	1.00
14_A	20_L	0.739	1.00
71_L	75_A	0.738	1.00
24_I	56_V	0.736	1.00
82_S	92_F	0.733	1.00
29_R	36_K	0.732	1.00
20_L	58_Y	0.730	1.00
66_E	69_R	0.727	1.00
63_L	67_L	0.717	1.00
29_R	32_K	0.714	1.00
48_H	51_V	0.706	1.00
77_V	89_S	0.699	1.00
57_I	63_L	0.690	1.00
52_E	56_V	0.673	1.00
26_R	36_K	0.666	1.00
6_G	10_Y	0.660	1.00
13_S	62_R	0.656	1.00
69_R	88_P	0.648	1.00
8_Y	77_V	0.639	1.00
79_G	82_S	0.633	1.00
49_A	52_E	0.627	1.00
31_S	38_L	0.625	1.00
53_I	58_Y	0.625	1.00
3_F	80_F	0.624	1.00
27_H	30_R	0.619	1.00
42_I	46_L	0.616	1.00
89_S	92_F	0.603	1.00
59_S	67_L	0.586	0.99
36_K	47_A	0.581	0.99
23_R	27_H	0.580	0.99
30_R	51_V	0.575	0.99
72_A	75_A	0.574	0.99
65_C	68_A	0.572	0.99
50_E	53_I	0.562	0.99
76_P	82_S	0.561	0.99
54_V	57_I	0.557	0.99
46_L	53_I	0.552	0.99
77_V	80_F	0.550	0.99
16_G	20_L	0.546	0.99
24_I	54_V	0.545	0.99
24_I	42_I	0.528	0.99
79_G	88_P	0.525	0.99
26_R	37_K	0.525	0.99
47_A	50_E	0.525	0.99
3_F	65_C	0.523	0.99
68_A	85_C	0.522	0.99
42_I	45_L	0.519	0.99
41_H	91_L	0.518	0.99
3_F	90_H	0.514	0.99
38_L	46_L	0.513	0.99
81_G	84_D	0.512	0.98
16_G	63_L	0.510	0.98
27_H	31_S	0.509	0.98
15_L	19_G	0.507	0.98
2_D	5_A	0.504	0.98
21_E	24_I	0.503	0.98
28_L	54_V	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
1yd0A	1	0.6882	59.6	0.886	Contact Map
2wshA	4	0.7957	49.9	0.892	Contact Map
1yd6A	5	0.7742	45.6	0.895	Contact Map
1mk0A	1	0.8172	41.3	0.897	Contact Map
3mx1A	2	0.9032	9.5	0.924	Contact Map
2wnwA	2	0.6344	9.1	0.925	Contact Map
4b0hA	3	0.828	6.6	0.93	Contact Map
4egcB	1	0.4301	5	0.933	Contact Map
3clwA	1	0.3333	4.8	0.934	Contact Map
1ufiA	3	0.2258	4.8	0.934	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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