DUF4168 - PFAM28P - GREMLIN Contacts

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DUF4168 - Domain of unknown function (DUF4168)

PFAM:	PF13767	Sequences: SDQELDAFAAAYLEVEEIRQEYQQRLKQAAEDPSVPEIVCNEPESEEAQRIQQEANAEMVKAVEDQGLSVEEYNQILQAAQNDPELRQRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	90 (77)
Sequences:	2888 (2145)
Seq/√Len:	244.4
META:	0.845

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_E	72_E	5.559	1.00
80_A	90_I	3.499	1.00
69_S	72_E	2.889	1.00
8_F	77_L	2.806	1.00
2_D	89_R	2.024	1.00
14_E	66_Q	1.977	1.00
60_V	64_E	1.756	1.00
54_E	58_E	1.714	1.00
63_V	70_V	1.655	1.00
22_Y	51_I	1.646	1.00
47_E	50_R	1.604	1.00
53_Q	57_A	1.573	1.00
18_I	62_A	1.527	1.00
25_R	54_E	1.500	1.00
14_E	62_A	1.423	1.00
79_A	86_L	1.362	1.00
32_D	46_E	1.314	1.00
11_A	68_L	1.283	1.00
49_Q	53_Q	1.281	1.00
11_A	66_Q	1.251	1.00
32_D	47_E	1.240	1.00
80_A	86_L	1.230	1.00
7_A	68_L	1.222	1.00
9_A	12_Y	1.212	1.00
79_A	83_D	1.208	1.00
49_Q	52_Q	1.207	1.00
16_E	20_Q	1.204	1.00
72_E	75_Q	1.184	1.00
22_Y	26_L	1.167	1.00
10_A	66_Q	1.156	1.00
19_R	23_Q	1.153	1.00
33_P	48_A	1.091	1.00
46_E	49_Q	1.091	1.00
61_K	65_D	1.057	1.00
26_L	48_A	1.052	1.00
8_F	76_I	1.051	1.00
3_Q	7_A	1.024	1.00
18_I	55_A	1.021	1.00
4_E	76_I	1.019	1.00
21_E	25_R	1.018	1.00
22_Y	25_R	1.013	1.00
7_A	67_G	1.009	1.00
55_A	59_M	1.006	1.00
26_L	52_Q	1.006	1.00
6_D	9_A	1.001	1.00
48_A	52_Q	0.981	1.00
70_V	74_N	0.974	1.00
17_E	20_Q	0.973	1.00
4_E	7_A	0.968	1.00
84_P	87_R	0.936	1.00
52_Q	56_N	0.906	1.00
16_E	56_N	0.890	1.00
85_E	88_Q	0.881	1.00
1_S	4_E	0.858	0.99
5_L	80_A	0.856	0.99
16_E	19_R	0.852	0.99
50_R	54_E	0.844	0.99
12_Y	80_A	0.838	0.99
11_A	62_A	0.834	0.99
76_I	86_L	0.826	0.99
26_L	51_I	0.812	0.99
7_A	66_Q	0.811	0.99
33_P	46_E	0.792	0.99
77_L	80_A	0.783	0.99
25_R	51_I	0.750	0.98
22_Y	58_E	0.739	0.98
78_Q	81_Q	0.737	0.98
59_M	63_V	0.728	0.98
56_N	59_M	0.719	0.98
21_E	58_E	0.715	0.98
71_E	75_Q	0.709	0.98
29_A	75_Q	0.708	0.98
31_E	47_E	0.698	0.97
22_Y	54_E	0.689	0.97
15_V	59_M	0.688	0.97
30_A	47_E	0.687	0.97
14_E	17_E	0.673	0.97
3_Q	6_D	0.673	0.97
18_I	22_Y	0.672	0.97
13_L	17_E	0.669	0.97
74_N	77_L	0.667	0.97
30_A	33_P	0.665	0.97
81_Q	84_P	0.663	0.97
24_Q	28_Q	0.659	0.96
56_N	60_V	0.657	0.96
59_M	70_V	0.641	0.96
30_A	48_A	0.634	0.96
79_A	82_N	0.631	0.95
75_Q	79_A	0.625	0.95
18_I	80_A	0.616	0.95
46_E	57_A	0.615	0.95
19_R	59_M	0.599	0.94
47_E	51_I	0.599	0.94
29_A	32_D	0.591	0.94
2_D	6_D	0.584	0.93
61_K	64_E	0.581	0.93
12_Y	77_L	0.575	0.93
59_M	62_A	0.574	0.93
80_A	87_R	0.569	0.92
8_F	52_Q	0.568	0.92
32_D	48_A	0.567	0.92
24_Q	29_A	0.562	0.92
19_R	24_Q	0.561	0.92
79_A	84_P	0.560	0.92
14_E	18_I	0.556	0.91
9_A	76_I	0.555	0.91
30_A	58_E	0.552	0.91
9_A	90_I	0.536	0.90
21_E	24_Q	0.524	0.89
11_A	15_V	0.523	0.89
83_D	86_L	0.518	0.88
23_Q	28_Q	0.509	0.87
76_I	90_I	0.508	0.87
12_Y	81_Q	0.503	0.87
56_N	74_N	0.503	0.87
5_L	89_R	0.500	0.86

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
3viuA	1	0.3556	28	0.831	Contact Map
1zymA	2	0.9333	11.7	0.858	Contact Map
4xlgB	1	0.2667	10.3	0.861	Contact Map
4ynhA	2	0.4556	8.3	0.867	Contact Map
2wqdA	2	0.9333	7.3	0.87	Contact Map
3fh3A	2	0.9333	7.1	0.871	Contact Map
3b34A	1	0.7667	6.4	0.874	Contact Map
4qhpA	1	0.7667	6.3	0.874	Contact Map
4ka7A	1	0.9333	6.2	0.874	Contact Map
1jk0B	1	0.8556	6.1	0.874	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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