UBN2_3 - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

UBN2_3 - gag-polypeptide of LTR copia-type

PFAM:	PF14244	Sequences: SDNPGLVLVSVKLDGSNYLLWKRQMKIALRAKNLLGFVDGTIPKPPETDPEYEAWKRCDSMVLSWILNSLSPEILSSVLYCETAKEIWDALKERFSQSNNGARIFQLKRELATLKQGGLSVSEYFTKLKSLWQEDELANYRPLPVCTCGACC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	152 (128)
Sequences:	4846 (3786)
Seq/√Len:	334.6
META:	0.377

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_K	89_D	6.391	1.00
119_L	127_K	3.858	1.00
33_N	57_R	3.156	1.00
59_D	84_A	3.148	1.00
18_Y	92_K	3.128	1.00
30_R	60_S	2.777	1.00
63_L	87_I	2.763	1.00
70_L	78_V	2.447	1.00
135_D	138_A	1.981	1.00
14_D	71_S	1.968	1.00
120_S	123_E	1.954	1.00
52_Y	56_K	1.827	1.00
33_N	53_E	1.791	1.00
89_D	92_K	1.763	1.00
44_K	56_K	1.723	1.00
26_K	82_E	1.722	1.00
27_I	67_L	1.663	1.00
74_I	95_F	1.616	1.00
83_T	86_E	1.589	1.00
26_K	35_L	1.586	1.00
22_K	92_K	1.577	1.00
114_L	128_L	1.566	1.00
29_L	38_V	1.546	1.00
30_R	56_K	1.533	1.00
35_L	38_V	1.513	1.00
37_F	58_C	1.479	1.00
25_M	66_I	1.466	1.00
81_C	87_I	1.459	1.00
106_Q	110_E	1.457	1.00
18_Y	22_K	1.453	1.00
55_W	59_D	1.418	1.00
119_L	123_E	1.406	1.00
44_K	52_Y	1.378	1.00
24_Q	72_P	1.374	1.00
59_D	83_T	1.362	1.00
24_Q	75_L	1.360	1.00
78_V	87_I	1.357	1.00
36_G	40_G	1.346	1.00
46_P	49_D	1.342	1.00
22_K	26_K	1.314	1.00
13_L	17_N	1.285	1.00
26_K	30_R	1.280	1.00
37_F	42_I	1.264	1.00
54_A	58_C	1.262	1.00
31_A	61_M	1.239	1.00
35_L	39_D	1.197	1.00
110_E	115_K	1.195	1.00
47_E	52_Y	1.193	1.00
105_F	109_R	1.182	1.00
23_R	67_L	1.180	1.00
30_R	63_L	1.180	1.00
89_D	93_E	1.177	1.00
20_L	75_L	1.176	1.00
82_E	86_E	1.147	1.00
121_V	124_Y	1.137	1.00
110_E	114_L	1.124	1.00
36_G	42_I	1.057	1.00
81_C	86_E	1.054	1.00
42_I	58_C	1.053	1.00
110_E	127_K	1.047	1.00
90_A	94_R	1.046	1.00
77_S	94_R	1.030	1.00
111_L	131_L	1.000	1.00
25_M	65_W	0.993	1.00
11_V	72_P	0.961	1.00
108_K	112_A	0.959	1.00
22_K	96_S	0.951	1.00
23_R	82_E	0.945	1.00
128_L	132_W	0.942	1.00
67_L	87_I	0.937	1.00
107_L	131_L	0.922	1.00
20_L	79_L	0.919	1.00
30_R	35_L	0.917	1.00
33_N	54_A	0.915	1.00
20_L	76_S	0.901	1.00
120_S	124_Y	0.874	1.00
90_A	93_E	0.874	1.00
121_V	125_F	0.868	1.00
92_K	96_S	0.864	1.00
90_A	129_K	0.857	1.00
101_G	106_Q	0.846	1.00
44_K	47_E	0.843	1.00
76_S	130_S	0.841	1.00
81_C	90_A	0.837	1.00
123_E	127_K	0.835	1.00
33_N	58_C	0.828	1.00
18_Y	88_W	0.815	1.00
62_V	65_W	0.811	1.00
37_F	59_D	0.811	1.00
33_N	61_M	0.803	1.00
129_K	135_D	0.800	1.00
50_P	54_A	0.800	1.00
18_Y	91_L	0.788	1.00
66_I	87_I	0.787	1.00
23_R	27_I	0.785	1.00
67_L	75_L	0.776	1.00
66_I	70_L	0.767	1.00
63_L	81_C	0.756	1.00
44_K	55_W	0.749	0.99
124_Y	127_K	0.747	0.99
31_A	64_S	0.746	0.99
116_Q	119_L	0.744	0.99
101_G	110_E	0.740	0.99
27_I	63_L	0.737	0.99
111_L	114_L	0.735	0.99
32_K	65_W	0.731	0.99
25_M	88_W	0.720	0.99
36_G	41_T	0.718	0.99
29_L	62_V	0.718	0.99
45_P	48_T	0.708	0.99
53_E	56_K	0.706	0.99
124_Y	128_L	0.700	0.99
122_S	129_K	0.699	0.99
37_F	40_G	0.697	0.99
107_L	110_E	0.694	0.99
114_L	127_K	0.693	0.99
18_Y	21_W	0.690	0.99
109_R	112_A	0.688	0.99
27_I	79_L	0.685	0.99
102_A	106_Q	0.685	0.99
103_R	107_L	0.680	0.99
28_A	32_K	0.679	0.99
36_G	53_E	0.679	0.99
109_R	114_L	0.678	0.99
30_R	33_N	0.678	0.99
110_E	113_T	0.676	0.99
26_K	63_L	0.675	0.99
70_L	91_L	0.671	0.99
34_L	37_F	0.671	0.99
25_M	69_S	0.668	0.99
56_K	59_D	0.660	0.99
26_K	92_K	0.650	0.99
19_L	79_L	0.649	0.99
49_D	52_Y	0.647	0.99
20_L	72_P	0.644	0.98
97_Q	102_A	0.641	0.98
78_V	81_C	0.634	0.98
23_R	80_Y	0.628	0.98
29_L	37_F	0.626	0.98
38_V	84_A	0.625	0.98
48_T	52_Y	0.621	0.98
63_L	67_L	0.620	0.98
122_S	126_T	0.617	0.98
46_P	50_P	0.614	0.98
104_I	108_K	0.609	0.98
58_C	61_M	0.606	0.98
73_E	123_E	0.603	0.98
38_V	62_V	0.602	0.98
104_I	107_L	0.601	0.98
30_R	53_E	0.600	0.98
116_Q	121_V	0.598	0.98
40_G	44_K	0.595	0.97
109_R	113_T	0.588	0.97
70_L	74_I	0.585	0.97
43_P	85_K	0.583	0.97
54_A	57_R	0.581	0.97
95_F	98_S	0.579	0.97
46_P	52_Y	0.578	0.97
103_R	106_Q	0.578	0.97
74_I	94_R	0.575	0.97
107_L	111_L	0.564	0.97
108_K	115_K	0.563	0.96
58_C	62_V	0.561	0.96
36_G	39_D	0.561	0.96
25_M	38_V	0.558	0.96
45_P	49_D	0.558	0.96
111_L	132_W	0.554	0.96
119_L	124_Y	0.546	0.96
40_G	55_W	0.546	0.96
40_G	43_P	0.545	0.96
117_G	124_Y	0.544	0.96
24_Q	68_N	0.544	0.96
85_K	92_K	0.543	0.96
37_F	84_A	0.541	0.96
23_R	63_L	0.538	0.95
79_L	87_I	0.537	0.95
62_V	84_A	0.531	0.95
103_R	110_E	0.524	0.95
34_L	65_W	0.521	0.95
57_R	61_M	0.519	0.95
61_M	65_W	0.518	0.94
52_Y	120_S	0.513	0.94
36_G	57_R	0.512	0.94
24_Q	79_L	0.512	0.94
56_K	60_S	0.510	0.94
38_V	85_K	0.510	0.94
13_L	87_I	0.509	0.94
113_T	128_L	0.505	0.94
74_I	79_L	0.502	0.93
25_M	29_L	0.501	0.93
45_P	50_P	0.500	0.93
22_K	88_W	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
3cxbA	1	0.4934	6.3	0.932	Contact Map
4zcfC	1	0	5.7	0.934	Contact Map
2o2cA	2	0.4737	4.4	0.938	Contact Map
1lwuB	1	0.4539	3.1	0.942	Contact Map
2m7cA	1	0.1316	3	0.942	Contact Map
3mzoA	5	0.9408	3	0.942	Contact Map
3w92A	3	0.2039	2.9	0.943	Contact Map
1i1rB	1	0.3092	2.8	0.943	Contact Map
3a11A	4	0.4737	2.7	0.943	Contact Map
1xx7A	5	0.7829	2.6	0.944	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.

Page generated in 0.0059 seconds.