DUF1043 - PFAM28P - GREMLIN Contacts

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DUF1043 - Protein of unknown function (DUF1043)

PFAM:	PF06295	Sequences: AIIGLLVGLIIGALLARLLSSSAKKQRELEQELDELKEELEQYQQEVTEHFAQTAELVNNLTESYRDVYQHLAEGAQRLCPELPRQDLPAASKLEESEAEAEEEEDVEPPRDYAPKASGLLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	122 (117)
Sequences:	1404 (1061)
Seq/√Len:	98.1
META:	0.691

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_Y	47_V	3.266	1.00
32_E	37_K	2.955	1.00
36_L	40_L	2.752	1.00
13_A	16_A	2.721	1.00
51_F	76_A	2.376	1.00
5_L	8_G	2.326	1.00
58_V	72_L	2.312	1.00
57_L	71_H	2.290	1.00
53_Q	56_E	2.281	1.00
5_L	11_I	2.146	1.00
58_V	68_V	2.145	1.00
8_G	12_G	2.105	1.00
69_Y	73_A	2.081	1.00
60_N	64_S	2.004	1.00
65_Y	71_H	1.897	1.00
54_T	58_V	1.876	1.00
66_R	70_Q	1.771	1.00
61_L	68_V	1.662	1.00
83_L	86_Q	1.650	1.00
54_T	65_Y	1.585	1.00
65_Y	69_Y	1.581	1.00
84_P	87_D	1.571	1.00
55_A	73_A	1.546	1.00
62_T	69_Y	1.480	1.00
71_H	75_G	1.480	1.00
85_R	88_L	1.446	1.00
34_D	38_E	1.429	1.00
10_I	14_L	1.400	0.99
108_E	111_R	1.398	0.99
64_S	69_Y	1.380	0.99
30_E	34_D	1.379	0.99
86_Q	90_A	1.378	0.99
33_L	36_L	1.355	0.99
62_T	68_V	1.343	0.99
60_N	63_E	1.338	0.99
50_H	71_H	1.297	0.99
9_L	14_L	1.273	0.99
42_Q	48_T	1.264	0.99
111_R	114_A	1.214	0.99
73_A	76_A	1.213	0.99
51_F	65_Y	1.195	0.98
83_L	87_D	1.172	0.98
82_E	85_R	1.170	0.98
55_A	69_Y	1.149	0.98
87_D	90_A	1.144	0.98
14_L	18_L	1.140	0.98
59_N	69_Y	1.108	0.97
50_H	57_L	1.096	0.97
9_L	12_G	1.075	0.97
54_T	72_L	1.053	0.96
82_E	89_P	1.043	0.96
51_F	75_G	1.042	0.96
31_Q	34_D	1.037	0.96
82_E	88_L	1.037	0.96
13_A	19_L	1.034	0.96
84_P	88_L	1.016	0.96
51_F	69_Y	1.015	0.96
42_Q	46_E	1.005	0.95
85_R	89_P	0.986	0.95
38_E	42_Q	0.983	0.95
82_E	86_Q	0.980	0.95
6_L	10_I	0.972	0.94
95_E	98_E	0.967	0.94
40_L	43_Y	0.965	0.94
64_S	68_V	0.963	0.94
91_A	95_E	0.949	0.94
29_L	36_L	0.948	0.94
43_Y	79_L	0.946	0.94
28_E	32_E	0.927	0.93
42_Q	49_E	0.926	0.93
58_V	65_Y	0.922	0.93
31_Q	35_E	0.919	0.93
47_V	75_G	0.909	0.92
11_I	17_R	0.906	0.92
44_Q	76_A	0.901	0.92
72_L	75_G	0.896	0.92
84_P	89_P	0.883	0.91
51_F	73_A	0.879	0.91
17_R	33_L	0.875	0.91
36_L	39_E	0.863	0.90
107_V	114_A	0.861	0.90
94_L	97_S	0.859	0.90
51_F	55_A	0.855	0.90
57_L	68_V	0.848	0.89
60_N	67_D	0.845	0.89
69_Y	72_L	0.844	0.89
55_A	66_R	0.839	0.89
55_A	71_H	0.834	0.88
83_L	89_P	0.828	0.88
54_T	71_H	0.826	0.88
55_A	62_T	0.824	0.88
81_P	84_P	0.820	0.88
100_E	103_E	0.816	0.87
62_T	75_G	0.810	0.87
38_E	41_E	0.803	0.86
83_L	90_A	0.802	0.86
35_E	39_E	0.796	0.86
11_I	14_L	0.796	0.86
98_E	102_E	0.794	0.86
59_N	62_T	0.787	0.85
49_E	53_Q	0.781	0.85
35_E	38_E	0.775	0.84
6_L	9_L	0.761	0.83
40_L	68_V	0.760	0.83
86_Q	94_L	0.757	0.83
8_G	16_A	0.753	0.83
90_A	94_L	0.751	0.83
17_R	20_S	0.750	0.82
66_R	69_Y	0.746	0.82
9_L	15_L	0.733	0.81
35_E	41_E	0.732	0.81
43_Y	48_T	0.724	0.80
99_A	102_E	0.719	0.80
15_L	82_E	0.716	0.79
82_E	87_D	0.715	0.79
85_R	91_A	0.714	0.79
99_A	103_E	0.711	0.79
3_I	7_V	0.708	0.79
57_L	65_Y	0.704	0.78
10_I	19_L	0.704	0.78
80_C	88_L	0.693	0.77
16_A	20_S	0.681	0.76
44_Q	80_C	0.675	0.75
32_E	35_E	0.671	0.75
86_Q	92_S	0.667	0.75
61_L	69_Y	0.654	0.73
97_S	100_E	0.653	0.73
63_E	70_Q	0.650	0.73
97_S	101_A	0.643	0.72
113_Y	118_S	0.640	0.71
100_E	104_E	0.634	0.71
70_Q	74_E	0.633	0.71
47_V	50_H	0.630	0.70
29_L	33_L	0.630	0.70
82_E	90_A	0.626	0.70
50_H	65_Y	0.625	0.70
74_E	77_Q	0.625	0.70
16_A	44_Q	0.620	0.69
53_Q	57_L	0.618	0.69
91_A	97_S	0.607	0.67
85_R	90_A	0.601	0.67
65_Y	68_V	0.600	0.67
36_L	75_G	0.597	0.66
66_R	111_R	0.595	0.66
4_G	7_V	0.588	0.65
54_T	62_T	0.585	0.65
114_A	118_S	0.584	0.64
63_E	83_L	0.584	0.64
86_Q	89_P	0.582	0.64
26_Q	32_E	0.577	0.64
7_V	45_Q	0.575	0.63
46_E	78_R	0.572	0.63
44_Q	62_T	0.571	0.63
51_F	62_T	0.570	0.63
58_V	70_Q	0.565	0.62
62_T	72_L	0.565	0.62
94_L	102_E	0.565	0.62
55_A	65_Y	0.562	0.62
48_T	52_A	0.562	0.62
47_V	68_V	0.558	0.61
65_Y	76_A	0.553	0.60
85_R	92_S	0.553	0.60
43_Y	65_Y	0.542	0.59
47_V	65_Y	0.540	0.58
50_H	54_T	0.537	0.58
97_S	106_D	0.536	0.58
82_E	94_L	0.524	0.56
50_H	75_G	0.520	0.56
58_V	69_Y	0.520	0.56
85_R	99_A	0.520	0.56
96_E	99_A	0.519	0.56
14_L	28_E	0.517	0.55
62_T	65_Y	0.511	0.54
109_P	115_P	0.505	0.54
93_K	100_E	0.502	0.53
55_A	80_C	0.500	0.53

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
2f95B	2	0.0984	82.8	0.838	Contact Map
4f23A	3	0.9672	82.5	0.839	Contact Map
4lvhA	3	0.1148	72.1	0.853	Contact Map
4mc5A	3	0.9672	69.4	0.856	Contact Map
4wsrA	5	0.9672	69.4	0.856	Contact Map
4cq4A	4	0.6148	68.4	0.857	Contact Map
2kluA	1	0.4672	66.8	0.858	Contact Map
2wr1A	3	0.9672	63.4	0.861	Contact Map
3qnqA	2	0.3197	63.3	0.861	Contact Map
2yp5A	3	0.9672	56.4	0.867	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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