TraX - PFAM28P - GREMLIN Contacts

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TraX - TraX protein

PFAM:	PF05857	Sequences: SGFALKIIAIITMLIDHIGYLFFPGLPWLRIIGRLAFPIFAFLLAEGFAHTRNRKKYLLRLLIFALISEIPYDLAFGTLFDFLPLNVFFTLALGLLALYLLEKLKKKKKLLLLIVLLLLLLALLLFVDYGWYGVLLILLFYLFRNRKLKRLLLFAVLALLLLALFLLLFIGLIQLFALLALPLILLYNGKNGKRGKGMKYFFYIFYPAHLLILYLIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	217 (215)
Sequences:	5391 (4525)
Seq/√Len:	308.6
META:	0.744

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_L	205_F	5.857	1.00
94_G	137_I	3.962	1.00
58_L	92_A	3.364	1.00
36_A	40_F	2.716	1.00
62_L	92_A	2.704	1.00
48_F	98_L	2.652	1.00
19_G	30_R	2.406	1.00
48_F	95_L	2.386	1.00
204_I	208_A	2.311	1.00
48_F	102_E	2.282	1.00
12_T	36_A	2.266	1.00
5_L	39_I	2.217	1.00
54_R	99_Y	2.166	1.00
54_R	102_E	2.161	1.00
69_E	73_D	2.078	1.00
54_R	95_L	2.022	1.00
19_G	29_L	2.013	1.00
15_I	29_L	1.994	1.00
191_N	195_G	1.979	1.00
101_L	138_L	1.977	1.00
191_N	194_R	1.970	1.00
44_L	95_L	1.942	1.00
91_L	94_G	1.870	1.00
16_D	34_R	1.856	1.00
74_L	214_Y	1.824	1.00
48_F	54_R	1.809	1.00
12_T	32_I	1.808	1.00
58_L	99_Y	1.796	1.00
41_A	137_I	1.780	1.00
15_I	32_I	1.750	1.00
97_A	118_L	1.744	1.00
44_L	91_L	1.743	1.00
69_E	85_L	1.732	1.00
189_G	192_G	1.729	1.00
64_F	88_F	1.727	1.00
147_K	150_R	1.727	1.00
8_I	12_T	1.726	1.00
31_I	176_F	1.726	1.00
10_I	205_F	1.713	1.00
65_A	89_F	1.687	1.00
61_L	95_L	1.679	1.00
47_G	57_Y	1.645	1.00
14_L	18_I	1.634	1.00
18_I	213_L	1.579	1.00
37_F	41_A	1.565	1.00
10_I	40_F	1.565	1.00
75_A	210_L	1.553	1.00
49_A	144_R	1.553	1.00
194_R	197_G	1.540	1.00
99_Y	103_K	1.529	1.00
59_L	63_I	1.528	1.00
58_L	95_L	1.526	1.00
10_I	201_F	1.515	1.00
192_G	195_G	1.505	1.00
42_F	46_E	1.498	1.00
129_Y	133_G	1.479	1.00
16_D	30_R	1.472	1.00
73_D	85_L	1.425	1.00
3_F	7_I	1.409	1.00
55_K	59_L	1.406	1.00
37_F	133_G	1.363	1.00
20_Y	30_R	1.353	1.00
56_K	59_L	1.308	1.00
88_F	91_L	1.299	1.00
98_L	141_Y	1.284	1.00
211_L	214_Y	1.279	1.00
68_S	71_P	1.263	1.00
58_L	96_L	1.242	1.00
182_P	186_L	1.225	1.00
68_S	72_Y	1.223	1.00
197_G	201_F	1.220	1.00
190_K	193_K	1.207	1.00
123_L	130_G	1.205	1.00
41_A	94_G	1.204	1.00
123_L	131_W	1.202	1.00
97_A	138_L	1.199	1.00
158_A	162_L	1.199	1.00
11_I	15_I	1.194	1.00
55_K	99_Y	1.191	1.00
64_F	68_S	1.182	1.00
187_Y	190_K	1.171	1.00
2_G	43_L	1.169	1.00
85_L	89_F	1.166	1.00
62_L	66_L	1.164	1.00
71_P	211_L	1.134	1.00
179_L	183_L	1.122	1.00
46_E	49_A	1.102	1.00
200_Y	204_I	1.097	1.00
43_L	46_E	1.095	1.00
159_L	163_A	1.090	1.00
154_F	158_A	1.088	1.00
102_E	141_Y	1.088	1.00
179_L	182_P	1.082	1.00
161_L	165_F	1.069	1.00
95_L	99_Y	1.066	1.00
23_F	26_L	1.061	1.00
46_E	50_H	1.053	1.00
86_N	89_F	1.053	1.00
97_A	134_V	1.044	1.00
198_M	201_F	1.030	1.00
195_G	198_M	1.027	1.00
93_L	97_A	1.022	1.00
172_L	176_F	1.014	1.00
189_G	193_K	1.010	1.00
180_A	184_I	1.000	1.00
7_I	198_M	0.998	1.00
90_T	133_G	0.992	1.00
150_R	153_L	0.989	1.00
10_I	14_L	0.985	1.00
104_L	107_K	0.980	1.00
119_L	131_W	0.979	1.00
3_F	197_G	0.969	1.00
30_R	34_R	0.963	1.00
178_L	181_L	0.960	1.00
191_N	197_G	0.959	1.00
182_P	185_L	0.953	1.00
65_A	69_E	0.947	1.00
183_L	187_Y	0.938	1.00
62_L	89_F	0.936	1.00
57_Y	95_L	0.934	1.00
212_I	216_I	0.932	1.00
7_I	11_I	0.923	1.00
180_A	183_L	0.921	1.00
49_A	141_Y	0.920	1.00
47_G	51_T	0.919	1.00
190_K	195_G	0.918	1.00
46_E	144_R	0.917	1.00
3_F	196_K	0.912	1.00
201_F	205_F	0.908	1.00
59_L	62_L	0.901	1.00
37_F	87_V	0.888	1.00
64_F	200_Y	0.885	1.00
203_Y	207_P	0.884	1.00
95_L	98_L	0.883	1.00
58_L	62_L	0.882	1.00
93_L	118_L	0.877	1.00
61_L	88_F	0.877	1.00
119_L	122_A	0.871	1.00
74_L	211_L	0.868	1.00
45_A	140_F	0.866	1.00
174_Q	177_A	0.865	1.00
45_A	49_A	0.859	1.00
157_L	161_L	0.859	1.00
21_L	213_L	0.858	1.00
94_G	133_G	0.857	1.00
117_L	121_L	0.856	1.00
9_A	39_I	0.852	1.00
148_L	151_L	0.847	1.00
123_L	126_F	0.846	1.00
39_I	43_L	0.839	1.00
51_T	57_Y	0.838	1.00
54_R	58_L	0.838	1.00
53_N	56_K	0.836	1.00
13_M	17_H	0.831	1.00
35_L	38_P	0.831	1.00
23_F	27_P	0.829	1.00
158_A	161_L	0.827	1.00
101_L	142_L	0.825	1.00
214_Y	217_R	0.825	1.00
183_L	186_L	0.819	1.00
41_A	136_L	0.817	1.00
75_A	214_Y	0.814	1.00
176_F	187_Y	0.813	1.00
136_L	140_F	0.809	1.00
106_K	110_L	0.803	1.00
34_R	129_Y	0.798	1.00
205_F	213_L	0.798	1.00
151_L	155_A	0.798	1.00
150_R	161_L	0.796	1.00
12_T	35_L	0.796	1.00
71_P	74_L	0.788	1.00
174_Q	178_L	0.781	0.99
120_L	124_L	0.780	0.99
15_I	19_G	0.779	0.99
57_Y	60_R	0.776	0.99
72_Y	84_P	0.771	0.99
6_K	202_F	0.769	0.99
146_R	149_K	0.765	0.99
65_A	88_F	0.756	0.99
205_F	209_H	0.756	0.99
174_Q	180_A	0.754	0.99
70_I	74_L	0.752	0.99
109_K	112_L	0.747	0.99
137_I	141_Y	0.746	0.99
31_I	173_I	0.746	0.99
92_A	96_L	0.741	0.99
128_D	133_G	0.741	0.99
9_A	36_A	0.739	0.99
41_A	133_G	0.735	0.99
172_L	175_L	0.731	0.99
5_L	183_L	0.725	0.99
166_L	169_F	0.720	0.99
90_T	128_D	0.720	0.99
46_E	187_Y	0.719	0.99
3_F	198_M	0.719	0.99
35_L	39_I	0.717	0.99
61_L	64_F	0.716	0.99
165_F	169_F	0.714	0.99
209_H	213_L	0.712	0.99
78_T	82_F	0.711	0.99
177_A	183_L	0.711	0.99
150_R	154_F	0.711	0.99
140_F	144_R	0.710	0.99
18_I	29_L	0.703	0.99
14_L	212_I	0.703	0.99
211_L	215_L	0.702	0.99
206_Y	209_H	0.701	0.99
150_R	158_A	0.699	0.99
155_A	159_L	0.699	0.99
102_E	105_K	0.697	0.99
149_K	152_L	0.697	0.99
113_L	119_L	0.696	0.99
72_Y	76_F	0.694	0.99
42_F	187_Y	0.690	0.99
2_G	46_E	0.684	0.99
140_F	143_F	0.682	0.99
141_Y	145_N	0.681	0.99
151_L	154_F	0.678	0.99
108_K	111_L	0.677	0.99
100_L	103_K	0.675	0.99
163_A	167_L	0.674	0.99
60_R	199_K	0.671	0.98
118_L	122_A	0.670	0.98
45_A	48_F	0.667	0.98
143_F	146_R	0.667	0.98
41_A	91_L	0.664	0.98
176_F	179_L	0.661	0.98
21_L	75_A	0.657	0.98
193_K	196_K	0.657	0.98
199_K	202_F	0.656	0.98
61_L	91_L	0.655	0.98
78_T	81_D	0.651	0.98
153_L	157_L	0.639	0.98
147_K	151_L	0.639	0.98
107_K	110_L	0.639	0.98
62_L	65_A	0.638	0.98
22_F	25_G	0.637	0.98
175_L	178_L	0.637	0.98
105_K	110_L	0.636	0.98
19_G	33_G	0.631	0.98
47_G	53_N	0.630	0.98
148_L	152_L	0.628	0.98
148_L	158_A	0.628	0.98
43_L	47_G	0.628	0.98
20_Y	25_G	0.617	0.97
20_Y	23_F	0.615	0.97
156_V	160_L	0.615	0.97
98_L	137_I	0.611	0.97
69_E	86_N	0.608	0.97
73_D	82_F	0.606	0.97
36_A	43_L	0.605	0.97
100_L	104_L	0.601	0.97
73_D	77_G	0.600	0.97
63_I	67_I	0.598	0.97
149_K	153_L	0.598	0.97
20_Y	27_P	0.598	0.97
190_K	194_R	0.597	0.97
160_L	164_L	0.597	0.97
47_G	50_H	0.596	0.97
107_K	111_L	0.596	0.97
137_I	140_F	0.595	0.97
14_L	213_L	0.595	0.97
116_L	123_L	0.591	0.97
33_G	36_A	0.590	0.97
181_L	185_L	0.588	0.97
45_A	144_R	0.587	0.96
177_A	180_A	0.586	0.96
87_V	94_G	0.582	0.96
22_F	26_L	0.581	0.96
93_L	127_V	0.581	0.96
208_A	212_I	0.580	0.96
40_F	129_Y	0.579	0.96
25_G	28_W	0.575	0.96
153_L	156_V	0.573	0.96
16_D	33_G	0.573	0.96
39_I	42_F	0.570	0.96
155_A	158_A	0.568	0.96
10_I	36_A	0.565	0.96
142_L	146_R	0.562	0.96
53_N	60_R	0.559	0.95
152_L	156_V	0.559	0.95
18_I	22_F	0.556	0.95
104_L	114_I	0.556	0.95
39_I	184_I	0.554	0.95
2_G	47_G	0.551	0.95
44_L	98_L	0.549	0.95
161_L	164_L	0.545	0.95
12_T	40_F	0.544	0.95
52_R	59_L	0.542	0.95
122_A	127_V	0.542	0.95
174_Q	183_L	0.542	0.95
193_K	198_M	0.536	0.94
64_F	87_V	0.535	0.94
52_R	56_K	0.531	0.94
154_F	157_L	0.530	0.94
37_F	40_F	0.530	0.94
131_W	135_L	0.526	0.94
44_L	57_Y	0.525	0.94
162_L	165_F	0.525	0.94
7_I	197_G	0.525	0.94
130_G	133_G	0.521	0.93
126_F	130_G	0.519	0.93
23_F	29_L	0.519	0.93
139_L	143_F	0.519	0.93
12_T	15_I	0.518	0.93
81_D	85_L	0.517	0.93
37_F	69_E	0.516	0.93
79_L	82_F	0.515	0.93
99_Y	102_E	0.514	0.93
22_F	213_L	0.513	0.93
26_L	29_L	0.512	0.93
20_Y	24_P	0.512	0.93
196_K	199_K	0.512	0.93
41_A	87_V	0.507	0.92
64_F	71_P	0.506	0.92
101_L	141_Y	0.505	0.92
43_L	50_H	0.503	0.92
17_H	34_R	0.502	0.92
91_L	95_L	0.501	0.92
3_F	195_G	0.501	0.92
164_L	168_L	0.501	0.92
122_A	126_F	0.500	0.92

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
3j01B	1	0.5115	9	0.942	Contact Map
3wajA	1	0.9585	3.6	0.952	Contact Map
3qmlC	1	0.1613	1.2	0.963	Contact Map
4cxfB	1	0	1.1	0.964	Contact Map
1sbxA	1	0.1659	0.9	0.966	Contact Map
4qncA	2	0.3502	0.9	0.967	Contact Map
2xesA	1	0.2535	0.8	0.967	Contact Map
3rceA	1	0.9171	0.8	0.967	Contact Map
1kf6C	1	0.5346	0.7	0.969	Contact Map
3t97B	1	0.0783	0.6	0.969	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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