DUF4399 - PFAM28P - GREMLIN Contacts

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DUF4399 - Domain of unknown function (DUF4399)

PFAM:	PF14347	Sequences: VRFGLEGMGVAPAGVDKPNTGHHHLLIDTDLPPPLGQPIPADDNHLHFGKGQTETTLTLPPGKHTLQLLLGDGNHVPHDPPVMSKKI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (85)
Sequences:	8034 (4634)
Seq/√Len:	502.6
META:	0.942

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_D	45_H	3.431	1.00
28_D	64_H	2.944	1.00
5_L	8_M	2.853	1.00
26_L	29_T	2.769	1.00
16_D	73_G	2.532	1.00
24_H	75_H	2.505	1.00
39_I	45_H	2.173	1.00
11_A	20_T	1.910	1.00
34_P	37_Q	1.795	1.00
72_D	76_V	1.741	1.00
10_V	51_G	1.731	1.00
2_R	54_E	1.646	1.00
11_A	17_K	1.640	1.00
29_T	45_H	1.590	1.00
29_T	44_N	1.578	1.00
3_F	48_F	1.568	1.00
30_D	86_K	1.548	1.00
9_G	20_T	1.539	1.00
43_D	46_L	1.495	1.00
23_H	68_L	1.487	1.00
67_Q	86_K	1.456	1.00
48_F	55_T	1.357	1.00
69_L	83_M	1.345	1.00
29_T	32_P	1.337	1.00
17_K	20_T	1.335	1.00
60_P	64_H	1.272	1.00
60_P	63_K	1.265	1.00
27_I	57_L	1.256	1.00
46_L	55_T	1.238	1.00
65_T	86_K	1.218	1.00
78_H	81_P	1.184	1.00
38_P	76_V	1.158	1.00
8_M	70_L	1.147	1.00
26_L	69_L	1.145	1.00
27_I	46_L	1.130	1.00
8_M	82_V	1.126	1.00
26_L	32_P	1.121	1.00
11_A	15_V	1.116	1.00
32_P	69_L	1.085	1.00
31_L	67_Q	1.040	1.00
5_L	9_G	1.040	1.00
30_D	65_T	1.040	1.00
3_F	68_L	1.006	1.00
35_L	81_P	0.978	1.00
79_D	82_V	0.976	1.00
9_G	17_K	0.969	1.00
31_L	83_M	0.954	1.00
26_L	39_I	0.953	1.00
5_L	10_V	0.949	1.00
2_R	6_E	0.938	1.00
28_D	60_P	0.934	1.00
48_F	68_L	0.930	1.00
12_P	15_V	0.928	1.00
69_L	78_H	0.917	1.00
41_A	46_L	0.912	1.00
16_D	74_N	0.912	1.00
29_T	42_D	0.912	1.00
27_I	66_L	0.907	1.00
27_I	59_L	0.906	1.00
22_H	75_H	0.905	1.00
23_H	70_L	0.892	1.00
83_M	86_K	0.853	1.00
17_K	50_K	0.828	1.00
49_G	75_H	0.824	1.00
5_L	70_L	0.820	1.00
35_L	69_L	0.811	1.00
47_H	75_H	0.806	1.00
78_H	82_V	0.804	1.00
39_I	42_D	0.786	1.00
69_L	77_P	0.780	1.00
49_G	52_Q	0.778	1.00
43_D	58_T	0.773	1.00
35_L	83_M	0.759	1.00
22_H	68_L	0.752	1.00
15_V	73_G	0.733	1.00
71_G	75_H	0.728	1.00
26_L	31_L	0.726	1.00
16_D	20_T	0.726	1.00
26_L	45_H	0.719	1.00
10_V	23_H	0.714	1.00
38_P	41_A	0.690	1.00
4_G	23_H	0.689	1.00
24_H	49_G	0.687	1.00
25_L	66_L	0.678	1.00
21_G	70_L	0.673	1.00
10_V	53_T	0.673	1.00
17_K	73_G	0.672	1.00
72_D	78_H	0.669	1.00
48_F	52_Q	0.668	1.00
24_H	71_G	0.666	1.00
39_I	69_L	0.661	1.00
41_A	50_K	0.660	1.00
9_G	15_V	0.658	1.00
52_Q	55_T	0.653	1.00
31_L	39_I	0.646	1.00
21_G	72_D	0.638	1.00
23_H	53_T	0.632	1.00
3_F	25_L	0.625	1.00
46_L	57_L	0.621	1.00
55_T	58_T	0.611	1.00
3_F	11_A	0.611	1.00
15_V	18_P	0.609	0.99
47_H	51_G	0.608	0.99
76_V	79_D	0.607	0.99
31_L	80_P	0.584	0.99
28_D	44_N	0.575	0.99
79_D	85_K	0.574	0.99
16_D	72_D	0.573	0.99
36_G	79_D	0.569	0.99
6_E	9_G	0.569	0.99
55_T	68_L	0.566	0.99
12_P	50_K	0.565	0.99
11_A	19_N	0.555	0.99
4_G	9_G	0.555	0.99
43_D	60_P	0.541	0.99
39_I	71_G	0.539	0.99
9_G	12_P	0.539	0.99
9_G	19_N	0.536	0.99
79_D	86_K	0.528	0.99
80_P	83_M	0.526	0.99
5_L	23_H	0.525	0.99
32_P	45_H	0.523	0.98
15_V	19_N	0.520	0.98
24_H	47_H	0.519	0.98
10_V	13_A	0.518	0.98
2_R	56_T	0.508	0.98
37_Q	74_N	0.504	0.98
11_A	16_D	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
4crrA	1	0.8736	46.3	0.845	Contact Map
4xvhA	1	0.8851	40.3	0.85	Contact Map
3ottA	2	0.977	39	0.851	Contact Map
3nqhA	2	0.8966	35.5	0.854	Contact Map
1uxzA	1	0.8966	34	0.856	Contact Map
2waoA	1	0.8851	33.6	0.856	Contact Map
2waaA	1	0.8966	32.3	0.858	Contact Map
3c7fA	1	0.8736	30.8	0.859	Contact Map
4e9lA	1	0.977	30.4	0.859	Contact Map
1cwvA	1	0.908	30.1	0.86	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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