DUF1018 - PFAM28P - GREMLIN Contacts

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DUF1018 - Protein of unknown function (DUF1018)

PFAM:	PF06252	Sequences: LDDDTYRALLERVTGKRSAKDLTDAQLEAVLDHLKRLGFKPKPKKKKRRRPPGAMATPAQLRKIRALWIELGWLGAVRDRSAALDAFVKRQTGVDRLRWLTDAQASKVIEALKAWAKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	118 (118)
Sequences:	4130 (3509)
Seq/√Len:	323.0
META:	0.805

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_D	5_T	3.616	1.00
89_K	95_D	2.975	1.00
11_E	17_R	2.941	1.00
3_D	7_R	2.748	1.00
110_E	113_K	2.689	1.00
16_K	26_Q	2.571	1.00
6_Y	10_L	2.344	1.00
27_L	31_L	2.278	1.00
33_H	37_L	2.269	1.00
33_H	36_R	2.256	1.00
63_K	66_A	2.018	1.00
6_Y	19_A	1.966	1.00
23_T	26_Q	1.948	1.00
12_R	33_H	1.910	1.00
14_T	30_V	1.882	1.00
28_E	32_D	1.812	1.00
17_R	21_D	1.808	1.00
94_V	104_Q	1.755	1.00
8_A	17_R	1.680	1.00
85_D	96_R	1.644	1.00
101_T	104_Q	1.630	1.00
85_D	97_L	1.585	1.00
1_L	9_L	1.584	1.00
13_V	33_H	1.512	1.00
14_T	26_Q	1.443	1.00
5_T	8_A	1.433	1.00
95_D	99_W	1.422	1.00
24_D	27_L	1.384	1.00
60_Q	109_I	1.378	1.00
10_L	22_L	1.334	1.00
9_L	34_L	1.330	1.00
70_E	116_A	1.312	1.00
96_R	99_W	1.310	1.00
11_E	15_G	1.303	1.00
68_W	84_L	1.303	1.00
64_I	108_V	1.302	1.00
88_V	108_V	1.300	1.00
87_F	111_A	1.291	1.00
32_D	35_K	1.290	1.00
83_A	86_A	1.282	1.00
10_L	19_A	1.233	1.00
100_L	105_A	1.218	1.00
9_L	33_H	1.213	1.00
71_L	116_A	1.211	1.00
83_A	87_F	1.189	1.00
19_A	22_L	1.173	1.00
22_L	27_L	1.169	1.00
110_E	114_A	1.161	1.00
24_D	28_E	1.159	1.00
10_L	30_V	1.146	1.00
34_L	39_F	1.122	1.00
87_F	91_Q	1.120	1.00
94_V	99_W	1.115	1.00
19_A	27_L	1.098	1.00
87_F	108_V	1.089	1.00
68_W	83_A	1.084	1.00
14_T	22_L	1.063	1.00
71_L	76_A	1.056	1.00
35_K	41_P	1.056	1.00
59_A	62_R	1.044	1.00
30_V	34_L	1.034	1.00
14_T	29_A	1.010	1.00
64_I	105_A	1.006	1.00
16_K	21_D	1.002	1.00
72_G	77_V	1.002	1.00
71_L	115_W	0.980	1.00
13_V	29_A	0.977	1.00
8_A	12_R	0.965	1.00
100_L	108_V	0.962	1.00
67_L	109_I	0.956	1.00
16_K	22_L	0.954	1.00
62_R	65_R	0.933	1.00
91_Q	111_A	0.931	1.00
87_F	115_W	0.930	1.00
61_L	65_R	0.927	1.00
108_V	111_A	0.923	1.00
67_L	116_A	0.893	1.00
102_D	106_S	0.886	1.00
60_Q	106_S	0.874	1.00
65_R	69_I	0.874	1.00
63_K	67_L	0.871	1.00
88_V	92_T	0.865	1.00
9_L	13_V	0.863	1.00
6_Y	34_L	0.848	1.00
70_E	73_W	0.846	1.00
88_V	91_Q	0.838	1.00
58_P	61_L	0.834	1.00
69_I	73_W	0.828	1.00
56_A	61_L	0.826	1.00
22_L	30_V	0.816	1.00
39_F	42_K	0.811	1.00
72_G	80_R	0.811	1.00
114_A	117_K	0.795	1.00
66_A	69_I	0.778	1.00
113_K	116_A	0.765	1.00
66_A	70_E	0.760	0.99
51_P	54_A	0.759	0.99
92_T	107_K	0.753	0.99
58_P	62_R	0.743	0.99
26_Q	29_A	0.736	0.99
86_A	89_K	0.735	0.99
35_K	38_G	0.727	0.99
10_L	14_T	0.725	0.99
25_A	28_E	0.711	0.99
47_K	50_R	0.709	0.99
13_V	30_V	0.702	0.99
63_K	109_I	0.698	0.99
115_W	118_R	0.696	0.99
31_L	39_F	0.695	0.99
63_K	70_E	0.692	0.99
12_R	37_L	0.687	0.99
11_E	14_T	0.685	0.99
84_L	88_V	0.683	0.99
107_K	114_A	0.681	0.99
34_L	38_G	0.679	0.99
57_T	60_Q	0.675	0.99
73_W	80_R	0.673	0.99
104_Q	107_K	0.673	0.99
50_R	53_G	0.668	0.99
106_S	110_E	0.668	0.99
60_Q	105_A	0.666	0.99
92_T	100_L	0.663	0.99
63_K	113_K	0.659	0.99
60_Q	67_L	0.659	0.99
97_L	100_L	0.644	0.98
103_A	107_K	0.642	0.98
90_R	111_A	0.634	0.98
82_A	86_A	0.632	0.98
46_K	50_R	0.626	0.98
23_T	27_L	0.626	0.98
1_L	34_L	0.623	0.98
111_A	114_A	0.623	0.98
48_R	51_P	0.620	0.98
63_K	116_A	0.617	0.98
113_K	117_K	0.598	0.97
27_L	35_K	0.595	0.97
92_T	108_V	0.589	0.97
56_A	60_Q	0.589	0.97
57_T	102_D	0.587	0.97
8_A	11_E	0.584	0.97
9_L	30_V	0.581	0.97
7_R	10_L	0.579	0.97
87_F	92_T	0.578	0.97
62_R	66_A	0.576	0.97
86_A	90_R	0.571	0.96
68_W	73_W	0.568	0.96
22_L	26_Q	0.564	0.96
29_A	32_D	0.563	0.96
110_E	118_R	0.563	0.96
84_L	87_F	0.561	0.96
47_K	52_P	0.559	0.96
68_W	72_G	0.554	0.96
105_A	109_I	0.554	0.96
83_A	115_W	0.551	0.96
76_A	116_A	0.551	0.96
71_L	74_L	0.545	0.95
85_D	98_R	0.539	0.95
43_P	46_K	0.539	0.95
31_L	34_L	0.531	0.95
3_D	6_Y	0.531	0.95
38_G	42_K	0.528	0.94
113_K	118_R	0.526	0.94
92_T	111_A	0.526	0.94
107_K	111_A	0.524	0.94
101_T	105_A	0.524	0.94
68_W	87_F	0.522	0.94
50_R	54_A	0.520	0.94
77_V	80_R	0.520	0.94
69_I	72_G	0.519	0.94
9_L	12_R	0.518	0.94
35_K	40_K	0.516	0.94
9_L	37_L	0.516	0.94
85_D	92_T	0.514	0.94
60_Q	63_K	0.504	0.93
1_L	5_T	0.504	0.93
10_L	16_K	0.501	0.93
72_G	83_A	0.500	0.93

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
3deuA	2	0.7797	25	0.875	Contact Map
3nqoA	2	0.8475	22.9	0.878	Contact Map
1z91A	2	0.8305	20.9	0.88	Contact Map
2rdpA	2	0.822	20.2	0.881	Contact Map
2nyxA	2	0.8475	19.1	0.882	Contact Map
2nnnA	2	0.8305	18.8	0.883	Contact Map
4trbA	2	0.4831	18.1	0.883	Contact Map
3boqA	2	0.7881	17.9	0.884	Contact Map
2a61A	2	0.8475	17.4	0.884	Contact Map
1s3jA	2	0.8475	17.3	0.885	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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