Plant_tran - PFAM28P - GREMLIN Contacts

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Plant_tran - Plant transposon protein

PFAM:	PF04827	Sequences: CEYLRRPTPEDLQRILKFEEKRGFPGCIGAIDGTHIPIKNCPTAWSGQYYRNRKGYPSIVLQAVCDADLRFWHVFVGWPGSVNDANVLRNSPLFKDLENGEAPPVKYLLNGREYNLPYYLGDGAYPLWPWLMKPYRNPQTEKEKLFNYRLSRARKVVERAFGILKARFRILKRPIRLWDPEKIPKIILACCILHNMIIEDERDGY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	205 (182)
Sequences:	3034 (2380)
Seq/√Len:	176.4
META:	0.474

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_C	157_V	5.272	1.00
69_L	163_I	3.973	1.00
63_A	161_F	3.863	1.00
64_V	93_L	3.468	1.00
66_D	70_R	3.307	1.00
37_P	56_Y	3.039	1.00
71_F	160_A	2.857	1.00
63_A	71_F	2.822	1.00
74_V	191_C	2.763	1.00
52_N	58_S	2.755	1.00
69_L	159_R	2.575	1.00
60_V	87_V	2.475	1.00
62_Q	125_Y	2.417	1.00
132_M	146_F	2.377	1.00
34_T	165_K	2.352	1.00
70_R	199_E	2.178	1.00
155_K	159_R	2.168	1.00
171_L	190_C	2.152	1.00
45_W	48_Q	2.075	1.00
134_P	147_N	2.044	1.00
146_F	150_L	2.041	1.00
158_E	162_G	1.863	1.00
62_Q	73_H	1.862	1.00
164_L	190_C	1.752	1.00
167_R	197_I	1.701	1.00
121_G	131_L	1.690	1.00
64_V	119_Y	1.611	1.00
22_R	153_A	1.598	1.00
52_N	56_Y	1.510	1.00
179_D	182_K	1.509	1.00
31_I	64_V	1.498	1.00
89_R	94_F	1.493	1.00
140_T	143_E	1.479	1.00
35_H	58_S	1.476	1.00
88_L	130_W	1.462	1.00
156_V	159_R	1.407	1.00
103_P	106_K	1.406	1.00
50_Y	57_P	1.400	1.00
88_L	94_F	1.353	1.00
24_F	150_L	1.334	1.00
69_L	156_V	1.327	1.00
84_D	158_E	1.326	1.00
75_F	78_W	1.321	1.00
145_L	149_R	1.297	1.00
44_A	48_Q	1.263	1.00
127_L	132_M	1.256	1.00
30_A	156_V	1.254	1.00
78_W	87_V	1.254	1.00
110_N	113_E	1.253	1.00
123_G	133_K	1.245	1.00
154_R	162_G	1.225	1.00
31_I	121_G	1.225	1.00
108_L	111_G	1.222	1.00
188_L	191_C	1.212	1.00
30_A	120_L	1.201	1.00
122_D	125_Y	1.198	1.00
44_A	47_G	1.197	1.00
164_L	191_C	1.176	1.00
35_H	60_V	1.168	1.00
65_C	160_A	1.163	1.00
46_S	50_Y	1.155	1.00
182_K	186_I	1.154	1.00
102_A	105_V	1.153	1.00
38_I	41_C	1.138	1.00
47_G	50_Y	1.137	1.00
78_W	82_V	1.136	1.00
160_A	164_L	1.123	1.00
45_W	50_Y	1.117	1.00
166_A	169_R	1.090	1.00
128_W	131_L	1.076	1.00
96_D	101_E	1.069	1.00
189_A	192_I	1.065	1.00
63_A	157_V	1.059	1.00
180_P	183_I	1.054	1.00
157_V	161_F	1.054	1.00
66_D	72_W	1.046	1.00
136_R	139_Q	1.040	1.00
110_N	114_Y	1.038	0.99
27_C	120_L	1.034	0.99
78_W	90_N	1.022	0.99
127_L	133_K	1.022	0.99
83_N	86_N	1.019	0.99
126_P	131_L	1.018	0.99
46_S	49_Y	1.006	0.99
149_R	152_R	0.996	0.99
32_D	84_D	0.987	0.99
175_I	183_I	0.985	0.99
148_Y	151_S	0.983	0.99
29_G	64_V	0.981	0.99
120_L	150_L	0.974	0.99
184_P	187_I	0.974	0.99
174_P	177_L	0.958	0.99
170_I	186_I	0.957	0.99
111_G	114_Y	0.944	0.99
169_R	172_K	0.944	0.99
178_W	182_K	0.940	0.99
121_G	124_A	0.936	0.99
173_R	176_R	0.929	0.99
107_Y	111_G	0.925	0.99
19_E	22_R	0.924	0.99
139_Q	143_E	0.922	0.99
132_M	135_Y	0.918	0.99
34_T	61_L	0.909	0.99
24_F	27_C	0.908	0.99
63_A	160_A	0.906	0.99
39_K	172_K	0.895	0.98
184_P	191_C	0.893	0.98
145_L	148_Y	0.877	0.98
48_Q	52_N	0.875	0.98
185_K	188_L	0.875	0.98
148_Y	152_R	0.867	0.98
94_F	97_L	0.866	0.98
97_L	130_W	0.864	0.98
112_R	115_N	0.863	0.98
18_F	22_R	0.862	0.98
83_N	158_E	0.860	0.98
144_K	148_Y	0.857	0.98
17_K	20_E	0.857	0.98
170_I	175_I	0.849	0.98
41_C	45_W	0.847	0.98
184_P	188_L	0.844	0.98
74_V	188_L	0.843	0.98
41_C	48_Q	0.842	0.98
94_F	128_W	0.841	0.98
41_C	44_A	0.840	0.98
187_I	190_C	0.837	0.98
180_P	184_P	0.833	0.98
42_P	45_W	0.830	0.98
78_W	86_N	0.826	0.97
43_T	46_S	0.825	0.97
151_S	155_K	0.821	0.97
35_H	52_N	0.815	0.97
177_L	186_I	0.811	0.97
76_V	188_L	0.809	0.97
52_N	57_P	0.808	0.97
33_G	62_Q	0.805	0.97
100_G	129_P	0.804	0.97
115_N	118_Y	0.801	0.97
79_P	168_F	0.798	0.97
98_E	128_W	0.797	0.97
42_P	49_Y	0.797	0.97
37_P	55_G	0.789	0.97
79_P	82_V	0.788	0.97
109_L	112_R	0.777	0.96
108_L	113_E	0.773	0.96
84_D	154_R	0.772	0.96
53_R	60_V	0.772	0.96
66_D	69_L	0.767	0.96
46_S	57_P	0.766	0.96
82_V	86_N	0.765	0.96
83_N	155_K	0.762	0.96
102_A	107_Y	0.761	0.96
124_A	133_K	0.754	0.96
61_L	77_G	0.754	0.96
94_F	98_E	0.750	0.96
118_Y	122_D	0.750	0.96
73_H	93_L	0.749	0.96
85_A	124_A	0.747	0.95
26_G	107_Y	0.742	0.95
71_F	74_V	0.742	0.95
149_R	153_A	0.739	0.95
98_E	130_W	0.739	0.95
179_D	185_K	0.738	0.95
133_K	136_R	0.738	0.95
159_R	197_I	0.733	0.95
33_G	158_E	0.732	0.95
89_R	126_P	0.725	0.95
65_C	71_F	0.724	0.95
62_Q	91_S	0.723	0.95
124_A	127_L	0.722	0.95
32_D	158_E	0.718	0.94
61_L	191_C	0.714	0.94
34_T	161_F	0.713	0.94
115_N	119_Y	0.713	0.94
109_L	113_E	0.712	0.94
17_K	68_D	0.711	0.94
183_I	186_I	0.709	0.94
109_L	114_Y	0.709	0.94
125_Y	131_L	0.706	0.94
180_P	187_I	0.704	0.94
52_N	55_G	0.703	0.94
57_P	62_Q	0.703	0.94
69_L	160_A	0.702	0.94
131_L	134_P	0.697	0.93
75_F	92_P	0.696	0.93
177_L	182_K	0.692	0.93
114_Y	120_L	0.690	0.93
101_E	104_P	0.684	0.93
39_K	176_R	0.680	0.93
106_K	109_L	0.676	0.92
26_G	118_Y	0.671	0.92
36_I	187_I	0.666	0.92
175_I	178_W	0.662	0.92
85_A	126_P	0.660	0.91
41_C	50_Y	0.660	0.91
147_N	151_S	0.659	0.91
108_L	112_R	0.658	0.91
17_K	21_K	0.658	0.91
94_F	130_W	0.657	0.91
103_P	107_Y	0.656	0.91
63_A	191_C	0.652	0.91
182_K	185_K	0.652	0.91
111_G	115_N	0.649	0.91
73_H	91_S	0.645	0.91
73_H	79_P	0.639	0.90
33_G	87_V	0.637	0.90
153_A	168_F	0.632	0.90
116_L	119_Y	0.630	0.89
37_P	174_P	0.630	0.89
105_V	108_L	0.629	0.89
88_L	128_W	0.626	0.89
32_D	154_R	0.625	0.89
148_Y	155_K	0.620	0.89
125_Y	132_M	0.614	0.88
82_V	168_F	0.608	0.88
32_D	162_G	0.603	0.87
159_R	163_I	0.602	0.87
50_Y	54_K	0.602	0.87
181_E	188_L	0.602	0.87
125_Y	128_W	0.591	0.86
100_G	103_P	0.590	0.86
127_L	130_W	0.586	0.86
38_I	183_I	0.586	0.86
140_T	144_K	0.585	0.86
62_Q	65_C	0.581	0.85
84_D	162_G	0.580	0.85
178_W	183_I	0.577	0.85
58_S	62_Q	0.576	0.85
78_W	81_S	0.576	0.85
121_G	133_K	0.575	0.85
110_N	121_G	0.574	0.85
86_N	90_N	0.572	0.84
91_S	94_F	0.569	0.84
85_A	89_R	0.567	0.84
169_R	176_R	0.563	0.84
121_G	127_L	0.563	0.84
183_I	187_I	0.562	0.83
179_D	183_I	0.560	0.83
33_G	161_F	0.560	0.83
27_C	153_A	0.559	0.83
122_D	134_P	0.559	0.83
113_E	116_L	0.559	0.83
167_R	194_H	0.558	0.83
107_Y	110_N	0.556	0.83
38_I	57_P	0.556	0.83
21_K	67_A	0.550	0.82
167_R	198_I	0.549	0.82
168_F	197_I	0.549	0.82
123_G	128_W	0.549	0.82
17_K	67_A	0.548	0.82
122_D	132_M	0.548	0.82
40_N	44_A	0.547	0.82
116_L	129_P	0.538	0.81
164_L	171_L	0.535	0.80
40_N	57_P	0.530	0.80
88_L	91_S	0.529	0.80
18_F	21_K	0.528	0.80
53_R	58_S	0.528	0.80
63_A	74_V	0.522	0.79
54_K	57_P	0.522	0.79
103_P	108_L	0.522	0.79
82_V	90_N	0.521	0.79
21_K	153_A	0.518	0.78
119_Y	122_D	0.518	0.78
96_D	99_N	0.517	0.78
125_Y	130_W	0.513	0.78
62_Q	66_D	0.512	0.77
71_F	161_F	0.507	0.77
104_P	107_Y	0.505	0.76
147_N	150_L	0.503	0.76
171_L	187_I	0.502	0.76
182_K	188_L	0.500	0.76
61_L	187_I	0.500	0.76

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
4mq3A	1	0.6244	13.1	0.958	Contact Map
3kksA	2	0.6585	9.9	0.96	Contact Map
1c6vA	4	0.6244	8	0.962	Contact Map
3l3uA	2	0.6634	6.8	0.963	Contact Map
1bcoA	1	0.8049	6.3	0.964	Contact Map
2pc1A	1	0.2195	6.2	0.964	Contact Map
4hqeA	2	0.2732	5.7	0.965	Contact Map
1cxqA	2	0.678	5.2	0.965	Contact Map
1ex4A	5	0.6585	4.9	0.966	Contact Map
5afua	1	0.2341	4.7	0.966	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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