DUF1249 - PFAM28P - GREMLIN Contacts

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DUF1249 - Protein of unknown function (DUF1249)

PFAM:	PF06853	Sequences: RLLRLLPDLRALGGSRVSRVAGDLDLHLEVLERSRYTTTLRLTYLFEDGGWLPDPDLRVRVYHDARLAEVLSCQGRRRLQALYGYPNPAMRQLDEKWQLNRFLNKWLEYCLEQGHR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (115)
Sequences:	3658 (2348)
Seq/√Len:	219.0
META:	0.88

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_T	63_H	5.483	1.00
59_V	68_A	4.634	1.00
34_S	39_T	3.024	1.00
29_E	41_R	2.669	1.00
31_L	41_R	2.287	1.00
40_L	61_V	2.139	1.00
41_R	58_R	2.031	1.00
18_S	115_H	2.000	1.00
19_R	25_D	1.957	1.00
61_V	68_A	1.942	1.00
14_G	33_R	1.883	1.00
6_L	9_L	1.879	1.00
79_L	83_Y	1.840	1.00
33_R	38_T	1.801	1.00
39_T	71_L	1.775	1.00
1_R	108_E	1.750	1.00
8_D	11_A	1.685	1.00
87_N	90_M	1.680	1.00
92_Q	95_E	1.656	1.00
44_Y	106_W	1.613	1.00
27_H	45_L	1.598	1.00
43_T	56_D	1.587	1.00
32_E	39_T	1.572	1.00
17_V	27_H	1.499	1.00
15_S	27_H	1.487	1.00
83_Y	86_P	1.480	1.00
59_V	103_L	1.470	1.00
85_Y	90_M	1.442	1.00
79_L	82_L	1.414	1.00
3_L	7_P	1.347	1.00
39_T	60_R	1.342	1.00
76_R	91_R	1.328	1.00
79_L	85_Y	1.318	1.00
58_R	72_S	1.313	1.00
30_V	38_T	1.311	1.00
99_L	102_F	1.291	1.00
17_V	25_D	1.289	1.00
31_L	58_R	1.276	1.00
30_V	33_R	1.271	1.00
36_Y	65_A	1.243	1.00
86_P	90_M	1.236	1.00
32_E	60_R	1.193	1.00
57_L	102_F	1.189	1.00
80_Q	83_Y	1.164	1.00
73_C	76_R	1.161	1.00
37_T	64_D	1.160	1.00
94_D	98_Q	1.144	1.00
10_R	33_R	1.142	1.00
8_D	12_L	1.139	1.00
95_E	98_Q	1.134	1.00
15_S	29_E	1.130	1.00
45_L	53_P	1.120	1.00
81_A	84_G	1.079	1.00
12_L	16_R	1.044	1.00
83_Y	96_K	1.027	1.00
108_E	112_E	1.027	1.00
43_T	46_F	1.026	1.00
38_T	110_C	1.007	1.00
81_A	85_Y	0.995	1.00
28_L	42_L	0.993	1.00
82_L	85_Y	0.961	1.00
24_L	44_Y	0.958	1.00
41_R	56_D	0.955	1.00
106_W	109_Y	0.932	1.00
83_Y	87_N	0.931	1.00
101_R	104_N	0.925	0.99
44_Y	97_W	0.924	0.99
60_R	65_A	0.913	0.99
19_R	22_G	0.911	0.99
14_G	18_S	0.901	0.99
4_R	111_L	0.886	0.99
3_L	10_R	0.883	0.99
104_N	108_E	0.881	0.99
35_R	93_L	0.877	0.99
9_L	13_G	0.860	0.99
42_L	59_V	0.857	0.99
26_L	42_L	0.857	0.99
13_G	16_R	0.855	0.99
8_D	13_G	0.842	0.99
7_P	12_L	0.833	0.99
18_S	26_L	0.833	0.99
44_Y	55_P	0.832	0.99
96_K	104_N	0.830	0.99
97_W	105_K	0.824	0.99
104_N	112_E	0.812	0.99
39_T	58_R	0.809	0.99
36_Y	60_R	0.799	0.98
74_Q	79_L	0.796	0.98
46_F	54_D	0.794	0.98
4_R	10_R	0.782	0.98
23_D	113_Q	0.774	0.98
73_C	102_F	0.769	0.98
13_G	19_R	0.765	0.98
62_Y	67_L	0.765	0.98
8_D	16_R	0.764	0.98
74_Q	77_R	0.761	0.98
70_V	99_L	0.756	0.98
36_Y	64_D	0.749	0.98
41_R	45_L	0.749	0.98
81_A	87_N	0.738	0.97
31_L	39_T	0.732	0.97
97_W	106_W	0.730	0.97
65_A	93_L	0.711	0.97
97_W	101_R	0.709	0.97
63_H	110_C	0.703	0.97
109_Y	113_Q	0.701	0.97
79_L	87_N	0.697	0.96
18_S	22_G	0.681	0.96
3_L	61_V	0.679	0.96
17_V	45_L	0.673	0.96
14_G	20_V	0.662	0.95
80_Q	84_G	0.661	0.95
83_Y	91_R	0.659	0.95
91_R	94_D	0.653	0.95
99_L	110_C	0.651	0.95
30_V	40_L	0.648	0.95
44_Y	109_Y	0.644	0.94
40_L	68_A	0.637	0.94
3_L	13_G	0.636	0.94
79_L	99_L	0.635	0.94
60_R	69_E	0.630	0.94
70_V	98_Q	0.628	0.94
45_L	51_W	0.626	0.94
90_M	94_D	0.622	0.93
43_T	93_L	0.619	0.93
23_D	56_D	0.619	0.93
37_T	65_A	0.617	0.93
44_Y	105_K	0.614	0.93
95_E	105_K	0.611	0.93
6_L	12_L	0.608	0.93
96_K	110_C	0.603	0.92
55_P	106_W	0.596	0.92
10_R	13_G	0.592	0.92
14_G	21_A	0.588	0.91
34_S	70_V	0.586	0.91
69_E	96_K	0.585	0.91
103_L	106_W	0.584	0.91
56_D	93_L	0.578	0.91
27_H	46_F	0.575	0.90
57_L	73_C	0.572	0.90
20_V	23_D	0.571	0.90
92_Q	96_K	0.570	0.90
7_P	10_R	0.569	0.90
87_N	92_Q	0.566	0.90
82_L	87_N	0.564	0.90
28_L	59_V	0.560	0.89
37_T	60_R	0.557	0.89
65_A	106_W	0.553	0.89
72_S	106_W	0.550	0.88
58_R	84_G	0.550	0.88
9_L	14_G	0.549	0.88
40_L	59_V	0.545	0.88
5_L	20_V	0.545	0.88
3_L	8_D	0.544	0.88
53_P	93_L	0.539	0.87
27_H	43_T	0.537	0.87
73_C	77_R	0.535	0.87
37_T	62_Y	0.531	0.87
27_H	53_P	0.530	0.86
49_G	52_L	0.523	0.86
34_S	38_T	0.519	0.85
75_G	91_R	0.518	0.85
5_L	111_L	0.518	0.85
87_N	94_D	0.509	0.84
75_G	83_Y	0.509	0.84
42_L	73_C	0.508	0.84
73_C	91_R	0.507	0.84
60_R	71_L	0.506	0.84
42_L	60_R	0.502	0.83
46_F	97_W	0.502	0.83
84_G	87_N	0.500	0.83
26_L	56_D	0.500	0.83

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
2o5nA	2	0.9483	21	0.912	Contact Map
1svdM	3	0.3276	8.9	0.926	Contact Map
1nycA	1	0.3707	5	0.934	Contact Map
4nejA	1	0.7931	4.8	0.934	Contact Map
1elkA	1	0.7155	4	0.937	Contact Map
4hn3A	3	0.75	3.3	0.939	Contact Map
1mu5A	1	0.3448	3.3	0.939	Contact Map
2ogkA	4	0.5862	3	0.94	Contact Map
2mewA	1	0.2586	2.8	0.942	Contact Map
3r2cJ	1	0.2672	2.7	0.942	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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