TnpV - PFAM28P - GREMLIN Contacts

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TnpV - Transposon-encoded protein TnpV

PFAM:	PF14198	Sequences: TYTLVGDYYIPNLTLPEEEEERPIGKYGRMRLRYLKEHRPVLYTNLLLSGKLNEHLAEIDEQAEERFERLVKQMAEAEGVTEQLKAEDQMEWVGRMNNIRNRAEEIVLNELI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	112 (111)
Sequences:	4361 (2584)
Seq/√Len:	245.3
META:	0.937

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_E	95_R	3.491	1.00
4_L	9_Y	3.385	1.00
3_T	12_N	3.206	1.00
78_E	102_R	2.836	1.00
31_R	55_H	2.779	1.00
41_V	45_N	2.611	1.00
26_K	30_M	2.400	1.00
88_D	91_E	2.379	1.00
83_Q	87_E	2.359	1.00
46_L	51_K	2.292	1.00
25_G	60_D	2.111	1.00
33_R	37_E	1.920	1.00
5_V	10_I	1.892	1.00
69_R	73_Q	1.809	1.00
91_E	94_G	1.789	1.00
98_N	102_R	1.775	1.00
4_L	7_D	1.692	1.00
1_T	12_N	1.616	1.00
44_T	48_L	1.586	1.00
27_Y	30_M	1.518	1.00
22_R	61_E	1.509	1.00
60_D	64_E	1.494	1.00
89_Q	93_V	1.424	1.00
108_L	112_I	1.415	1.00
104_E	108_L	1.394	1.00
45_N	48_L	1.394	1.00
35_L	42_L	1.357	1.00
28_G	60_D	1.334	1.00
22_R	57_A	1.311	1.00
26_K	104_E	1.309	1.00
100_R	104_E	1.267	1.00
24_I	28_G	1.265	1.00
66_R	110_E	1.232	1.00
90_M	93_V	1.231	1.00
16_P	50_G	1.229	1.00
66_R	69_R	1.225	1.00
30_M	108_L	1.210	1.00
75_A	96_M	1.180	1.00
1_T	9_Y	1.178	1.00
29_R	32_L	1.175	1.00
61_E	65_E	1.174	1.00
39_R	42_L	1.161	1.00
103_A	107_V	1.146	1.00
67_F	71_V	1.122	1.00
42_L	45_N	1.120	1.00
41_V	48_L	1.113	1.00
55_H	59_I	1.083	1.00
6_G	10_I	1.069	1.00
43_Y	47_L	1.067	1.00
78_E	99_I	1.059	1.00
1_T	4_L	1.055	1.00
31_R	34_Y	1.054	1.00
27_Y	108_L	1.048	1.00
58_E	62_Q	1.039	1.00
95_R	99_I	1.031	1.00
67_F	104_E	1.029	1.00
72_K	75_A	1.023	1.00
80_V	99_I	1.013	1.00
53_N	57_A	1.011	1.00
67_F	100_R	0.996	1.00
72_K	76_E	0.994	1.00
92_W	96_M	0.993	1.00
68_E	71_V	0.970	1.00
51_K	54_E	0.967	1.00
64_E	67_F	0.962	1.00
66_R	111_L	0.951	1.00
73_Q	77_A	0.950	1.00
74_M	99_I	0.945	1.00
66_R	70_L	0.941	1.00
40_P	44_T	0.940	1.00
32_L	43_Y	0.934	1.00
99_I	102_R	0.930	1.00
24_I	56_L	0.928	1.00
62_Q	66_R	0.925	1.00
32_L	44_T	0.919	1.00
57_A	61_E	0.911	1.00
45_N	49_S	0.902	1.00
24_I	57_A	0.899	1.00
32_L	35_L	0.856	0.99
31_R	35_L	0.850	0.99
78_E	95_R	0.843	0.99
63_A	107_V	0.840	0.99
42_L	46_L	0.818	0.99
33_R	36_K	0.816	0.99
32_L	36_K	0.806	0.99
27_Y	67_F	0.806	0.99
73_Q	76_E	0.800	0.99
1_T	5_V	0.796	0.99
74_M	102_R	0.765	0.99
29_R	33_R	0.756	0.98
93_V	97_N	0.755	0.98
15_L	18_E	0.752	0.98
89_Q	92_W	0.747	0.98
80_V	95_R	0.743	0.98
31_R	56_L	0.737	0.98
80_V	84_L	0.732	0.98
75_A	81_T	0.718	0.98
85_K	92_W	0.713	0.98
34_Y	38_H	0.705	0.98
65_E	69_R	0.705	0.98
82_E	85_K	0.704	0.98
70_L	106_I	0.697	0.97
5_V	12_N	0.696	0.97
74_M	103_A	0.685	0.97
17_E	20_E	0.674	0.97
34_Y	42_L	0.668	0.97
22_R	53_N	0.662	0.97
81_T	84_L	0.661	0.97
55_H	58_E	0.659	0.96
57_A	60_D	0.651	0.96
67_F	107_V	0.651	0.96
27_Y	104_E	0.643	0.96
18_E	54_E	0.642	0.96
71_V	96_M	0.640	0.96
17_E	21_E	0.636	0.96
50_G	54_E	0.635	0.96
64_E	68_E	0.633	0.96
71_V	100_R	0.632	0.96
101_N	104_E	0.627	0.95
3_T	10_I	0.626	0.95
75_A	79_G	0.625	0.95
98_N	101_N	0.616	0.95
70_L	74_M	0.610	0.95
18_E	21_E	0.608	0.94
62_Q	69_R	0.606	0.94
67_F	103_A	0.606	0.94
35_L	55_H	0.605	0.94
26_K	29_R	0.603	0.94
9_Y	12_N	0.602	0.94
62_Q	111_L	0.599	0.94
5_V	9_Y	0.597	0.94
71_V	75_A	0.596	0.94
3_T	14_T	0.595	0.94
70_L	73_Q	0.594	0.94
41_V	44_T	0.593	0.94
87_E	91_E	0.586	0.93
94_G	98_N	0.586	0.93
71_V	99_I	0.585	0.93
84_L	91_E	0.582	0.93
32_L	47_L	0.579	0.93
59_I	111_L	0.575	0.93
14_T	17_E	0.559	0.92
102_R	105_E	0.559	0.92
24_I	53_N	0.559	0.92
22_R	60_D	0.559	0.92
36_K	43_Y	0.559	0.92
101_N	110_E	0.558	0.92
24_I	60_D	0.556	0.91
75_A	80_V	0.552	0.91
40_P	48_L	0.543	0.90
74_M	106_I	0.542	0.90
107_V	111_L	0.539	0.90
74_M	77_A	0.536	0.90
71_V	103_A	0.533	0.90
3_T	9_Y	0.528	0.89
97_N	100_R	0.527	0.89
11_P	16_P	0.527	0.89
93_V	96_M	0.521	0.89
70_L	103_A	0.515	0.88
90_M	94_G	0.513	0.88
5_V	16_P	0.512	0.88
31_R	42_L	0.512	0.88
95_R	102_R	0.505	0.87
34_Y	39_R	0.504	0.87
94_G	97_N	0.500	0.86
1_T	16_P	0.500	0.86

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
4cr2Z	1	0.9554	11.6	0.903	Contact Map
2aplA	1	0.625	11.1	0.904	Contact Map
2rawB	1	0.3929	5.9	0.915	Contact Map
2qfaB	1	0.5268	5.5	0.916	Contact Map
1urjA	1	0.7054	3.2	0.925	Contact Map
4um2A	1	0.4911	3.2	0.925	Contact Map
3j21O	1	0.6071	3	0.926	Contact Map
4rndA	2	0.9018	2.5	0.929	Contact Map
2lseA	1	0.6518	1.8	0.934	Contact Map
2hy6A	3	0.1518	1.6	0.936	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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