DUF4355 - PFAM28P - GREMLIN Contacts

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DUF4355 - Domain of unknown function (DUF4355)

PFAM:	PF14265	Sequences: EKTFTQEEVDKIVQKRLAREKKKLEKELEEELKEEAEKLAKMSEEEKAKYELEKLEKELEELEAELARRELKAEARKILAEKGLPVELADFLVGEDAEETKANIEALEKLFNKAVEKAVEERLKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	125 (122)
Sequences:	2239 (1918)
Seq/√Len:	173.7
META:	0.767

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_D	99_E	2.814	1.00
58_E	63_E	2.744	1.00
53_E	57_K	2.646	1.00
9_V	12_I	2.639	1.00
56_E	60_E	2.271	1.00
57_K	61_E	2.268	1.00
82_K	108_E	2.253	1.00
25_E	29_E	2.109	1.00
108_E	112_N	2.064	1.00
61_E	65_E	2.049	1.00
116_E	120_E	2.046	1.00
20_E	24_L	1.798	1.00
118_A	121_E	1.750	1.00
6_Q	10_D	1.677	1.00
7_E	10_D	1.590	1.00
74_E	97_A	1.565	1.00
111_F	115_V	1.559	1.00
51_E	56_E	1.559	1.00
111_F	114_A	1.542	1.00
24_L	27_E	1.514	1.00
45_E	49_K	1.474	1.00
16_R	19_R	1.465	1.00
72_K	90_D	1.428	1.00
75_A	100_T	1.404	1.00
42_M	50_Y	1.398	1.00
121_E	124_K	1.396	1.00
8_E	11_K	1.374	1.00
50_Y	54_K	1.371	1.00
62_L	66_L	1.360	1.00
21_K	25_E	1.358	1.00
24_L	28_L	1.354	1.00
23_K	27_E	1.354	1.00
60_E	64_A	1.348	1.00
17_L	20_E	1.340	1.00
20_E	23_K	1.331	1.00
28_L	31_E	1.322	1.00
29_E	32_L	1.317	1.00
93_V	100_T	1.316	1.00
15_K	19_R	1.261	1.00
43_S	46_E	1.253	1.00
59_L	62_L	1.211	1.00
15_K	18_A	1.204	1.00
53_E	56_E	1.198	1.00
55_L	59_L	1.197	1.00
91_F	103_N	1.194	1.00
64_A	68_R	1.189	1.00
49_K	53_E	1.173	1.00
90_D	106_A	1.159	1.00
94_G	99_E	1.159	1.00
18_A	21_K	1.155	1.00
57_K	60_E	1.151	1.00
26_K	30_E	1.151	1.00
5_T	8_E	1.151	1.00
102_A	105_E	1.146	1.00
52_L	56_E	1.126	1.00
12_I	16_R	1.121	1.00
68_R	72_K	1.121	1.00
18_A	22_K	1.112	1.00
5_T	9_V	1.095	1.00
55_L	58_E	1.088	1.00
4_F	8_E	1.086	1.00
44_E	48_A	1.083	1.00
87_E	106_A	1.079	1.00
82_K	105_E	1.062	1.00
94_G	103_N	1.049	1.00
78_I	81_E	1.042	0.99
109_K	113_K	1.029	0.99
34_E	37_E	1.027	0.99
101_K	105_E	1.025	0.99
119_V	122_R	1.018	0.99
54_K	58_E	1.002	0.99
28_L	32_L	0.993	0.99
38_K	50_Y	0.970	0.99
16_R	20_E	0.958	0.99
46_E	49_K	0.957	0.99
35_E	39_L	0.948	0.99
105_E	109_K	0.946	0.99
35_E	38_K	0.941	0.99
34_E	38_K	0.912	0.99
95_E	99_E	0.909	0.99
27_E	31_E	0.902	0.98
50_Y	53_E	0.900	0.98
69_R	73_A	0.899	0.98
38_K	42_M	0.898	0.98
11_K	15_K	0.895	0.98
99_E	103_N	0.882	0.98
66_L	69_R	0.882	0.98
6_Q	9_V	0.880	0.98
11_K	14_Q	0.874	0.98
45_E	48_A	0.868	0.98
62_L	65_E	0.864	0.98
115_V	119_V	0.863	0.98
78_I	82_K	0.863	0.98
113_K	116_E	0.860	0.98
3_T	6_Q	0.859	0.98
10_D	14_Q	0.853	0.98
21_K	24_L	0.851	0.98
9_V	13_V	0.839	0.98
78_I	101_K	0.838	0.98
74_E	77_K	0.836	0.98
92_L	107_L	0.833	0.97
52_L	55_L	0.833	0.97
26_K	29_E	0.830	0.97
63_E	67_A	0.825	0.97
14_Q	18_A	0.819	0.97
117_K	121_E	0.808	0.97
79_L	92_L	0.807	0.97
66_L	70_E	0.804	0.97
62_L	69_R	0.799	0.97
65_E	70_E	0.797	0.97
79_L	104_I	0.791	0.97
37_E	41_K	0.788	0.96
27_E	30_E	0.788	0.96
44_E	47_K	0.784	0.96
22_K	25_E	0.783	0.96
33_K	37_E	0.778	0.96
114_A	118_A	0.777	0.96
118_A	122_R	0.769	0.96
100_T	103_N	0.761	0.96
37_E	40_A	0.752	0.95
81_E	101_K	0.738	0.95
8_E	12_I	0.734	0.95
117_K	120_E	0.734	0.95
80_A	86_V	0.732	0.95
13_V	16_R	0.726	0.94
65_E	69_R	0.724	0.94
55_L	66_L	0.724	0.94
13_V	17_L	0.720	0.94
78_I	104_I	0.713	0.94
61_E	64_A	0.710	0.94
48_A	52_L	0.710	0.94
76_R	86_V	0.707	0.94
72_K	76_R	0.706	0.94
38_K	41_K	0.691	0.93
39_L	47_K	0.677	0.92
115_V	118_A	0.671	0.92
63_E	66_L	0.670	0.92
51_E	54_K	0.667	0.92
58_E	62_L	0.665	0.91
62_L	73_A	0.657	0.91
104_I	108_E	0.656	0.91
58_E	61_E	0.655	0.91
71_L	94_G	0.649	0.90
39_L	43_S	0.647	0.90
97_A	101_K	0.637	0.90
23_K	26_K	0.634	0.89
24_L	31_E	0.633	0.89
5_T	12_I	0.632	0.89
19_R	23_K	0.632	0.89
114_A	117_K	0.625	0.89
85_P	88_L	0.620	0.88
6_Q	16_R	0.611	0.88
7_E	11_K	0.603	0.87
48_A	51_E	0.597	0.86
54_K	57_K	0.593	0.86
39_L	97_A	0.583	0.85
102_A	106_A	0.582	0.85
25_E	31_E	0.582	0.85
91_F	107_L	0.572	0.84
64_A	95_E	0.569	0.84
71_L	97_A	0.568	0.84
67_A	95_E	0.566	0.83
62_L	70_E	0.566	0.83
12_I	17_L	0.565	0.83
5_T	13_V	0.563	0.83
64_A	67_A	0.562	0.83
49_K	52_L	0.561	0.83
10_D	19_R	0.556	0.82
73_A	76_R	0.551	0.82
4_F	9_V	0.546	0.81
92_L	104_I	0.546	0.81
87_E	113_K	0.542	0.81
3_T	7_E	0.540	0.80
51_E	55_L	0.540	0.80
100_T	107_L	0.538	0.80
36_A	39_L	0.530	0.79
22_K	26_K	0.528	0.79
120_E	124_K	0.526	0.79
99_E	102_A	0.524	0.78
113_K	117_K	0.520	0.78
76_R	80_A	0.513	0.77
31_E	37_E	0.504	0.76
82_K	101_K	0.500	0.75

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
3dmqA	1	0.576	9.2	0.886	Contact Map
3jywX	1	0.568	5.4	0.898	Contact Map
4ujrU	1	0.568	4.8	0.9	Contact Map
1u7lA	1	0.832	3.6	0.906	Contact Map
3j39h	1	0.6	3.1	0.909	Contact Map
2bnxA	2	0.184	3.1	0.909	Contact Map
1u2mA	3	0.864	2.8	0.911	Contact Map
4w20h	1	0.592	2.7	0.912	Contact Map
4uaeA	1	0.344	2.4	0.914	Contact Map
2ll2A	1	0.072	2.3	0.915	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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