YibE_F - PFAM28P - GREMLIN Contacts

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YibE_F - YibE/F-like protein

PFAM:	PF07907	Sequences: LLLLAALFALLLILVGGWKGLRALLGLAFTFLVIFKFLLPAILAGYNPLLVALVGSALITFVTLYLVHGFNKKTLAAILGTLLGLLLTGLLALLFVKLAHLTGLGSEEAEFLLYLGQGGIDLRGLLLAGIIIGALGALMDVAISQASAVWELKEANPDLSRKELFRSGMNVGRDHIGTMVNTLVLAYAGASLPLLLLFSAYGTPLGQILNSELIAEEIVRTLVGSIGLVLAVPITTLIAAW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	241 (239)
Sequences:	5482 (3964)
Seq/√Len:	256.4
META:	0.738

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_Y	75_L	4.865	1.00
38_L	55_G	3.867	1.00
148_A	171_V	3.702	1.00
9_A	24_L	3.696	1.00
47_N	50_L	3.057	1.00
80_G	235_T	3.019	1.00
41_A	46_Y	2.992	1.00
88_T	227_G	2.868	1.00
52_A	128_A	2.810	1.00
162_K	166_R	2.603	1.00
13_I	21_L	2.599	1.00
41_A	51_V	2.554	1.00
2_L	6_A	2.546	1.00
160_S	163_E	2.473	1.00
149_V	168_G	2.472	1.00
32_L	36_K	2.380	1.00
83_L	234_I	2.348	1.00
151_E	170_N	2.315	1.00
147_S	174_D	2.302	1.00
146_A	235_T	2.139	1.00
64_L	74_T	2.131	1.00
150_W	154_E	2.084	1.00
61_F	78_I	2.019	1.00
33_V	55_G	1.978	1.00
163_E	167_S	1.954	1.00
142_A	231_A	1.939	1.00
47_N	124_G	1.935	1.00
29_F	62_V	1.934	1.00
18_W	22_R	1.934	1.00
156_N	159_L	1.912	1.00
76_A	238_I	1.867	1.00
99_A	219_V	1.854	1.00
79_L	238_I	1.827	1.00
205_L	209_L	1.799	1.00
90_L	94_L	1.793	1.00
11_L	226_I	1.783	1.00
19_K	22_R	1.770	1.00
176_I	232_V	1.764	1.00
6_A	10_L	1.756	1.00
76_A	239_A	1.725	1.00
153_K	159_L	1.701	1.00
76_A	146_A	1.695	1.00
60_T	78_I	1.694	1.00
87_L	230_L	1.664	1.00
53_L	89_G	1.653	1.00
149_V	239_A	1.645	1.00
46_Y	51_V	1.637	1.00
151_E	167_S	1.626	1.00
57_A	82_L	1.623	1.00
104_L	122_L	1.620	1.00
217_E	220_R	1.612	1.00
94_L	98_L	1.611	1.00
121_D	124_G	1.576	1.00
161_R	240_A	1.562	1.00
156_N	163_E	1.561	1.00
165_F	237_L	1.511	1.00
68_H	143_I	1.506	1.00
161_R	165_F	1.469	1.00
3_L	7_L	1.466	1.00
68_H	74_T	1.459	1.00
188_A	195_L	1.416	1.00
84_G	231_A	1.401	1.00
5_A	222_L	1.400	1.00
93_L	97_K	1.391	1.00
133_G	220_R	1.391	1.00
91_L	223_V	1.379	1.00
133_G	187_Y	1.376	1.00
155_A	159_L	1.345	1.00
165_F	240_A	1.339	1.00
73_K	150_W	1.338	1.00
152_L	155_A	1.330	1.00
145_Q	236_T	1.326	1.00
97_K	100_H	1.315	1.00
26_G	67_V	1.310	1.00
33_V	37_F	1.274	1.00
39_L	195_L	1.268	1.00
161_R	237_L	1.255	1.00
70_F	75_L	1.255	1.00
155_A	163_E	1.248	1.00
204_P	207_Q	1.233	1.00
41_A	44_A	1.233	1.00
168_G	236_T	1.229	1.00
159_L	163_E	1.229	1.00
37_F	41_A	1.221	1.00
155_A	167_S	1.217	1.00
65_Y	78_I	1.214	1.00
39_L	199_S	1.211	1.00
55_G	59_I	1.205	1.00
34_I	188_A	1.164	1.00
65_Y	70_F	1.160	1.00
9_A	13_I	1.157	1.00
73_K	174_D	1.150	1.00
170_N	173_R	1.145	1.00
203_T	207_Q	1.145	1.00
12_L	180_V	1.144	1.00
97_K	123_R	1.136	1.00
10_L	14_L	1.134	1.00
2_L	205_L	1.123	1.00
37_F	55_G	1.122	1.00
152_L	168_G	1.122	1.00
84_G	88_T	1.114	1.00
81_T	142_A	1.107	1.00
184_V	221_T	1.105	1.00
71_N	74_T	1.096	1.00
83_L	238_I	1.077	1.00
37_F	51_V	1.073	1.00
152_L	171_V	1.073	1.00
4_L	95_F	1.061	1.00
92_A	130_I	1.061	1.00
237_L	240_A	1.059	1.00
77_A	142_A	1.051	1.00
75_L	78_I	1.037	1.00
139_M	181_N	1.036	1.00
143_I	178_T	1.032	1.00
165_F	236_T	1.028	1.00
149_V	236_T	1.025	1.00
50_L	54_V	1.024	1.00
163_E	166_R	1.023	1.00
7_L	95_F	1.022	1.00
149_V	159_L	1.013	1.00
102_T	212_E	1.011	1.00
12_L	24_L	1.008	1.00
133_G	186_A	1.008	1.00
190_A	193_P	0.992	1.00
105_G	216_E	0.988	1.00
17_G	173_R	0.970	1.00
4_L	219_V	0.970	1.00
137_A	177_G	0.968	1.00
80_G	84_G	0.957	1.00
168_G	240_A	0.941	1.00
56_S	60_T	0.939	1.00
62_V	66_L	0.937	1.00
54_V	58_L	0.935	1.00
126_L	130_I	0.924	1.00
145_Q	175_H	0.923	1.00
101_L	126_L	0.920	1.00
8_F	225_S	0.916	1.00
96_V	127_L	0.914	1.00
165_F	169_M	0.910	1.00
223_V	227_G	0.886	1.00
20_G	23_A	0.884	1.00
74_T	78_I	0.883	1.00
57_A	61_F	0.880	1.00
59_I	63_T	0.874	1.00
60_T	64_L	0.869	1.00
38_L	51_V	0.866	1.00
37_F	54_V	0.860	1.00
153_K	157_P	0.857	0.99
64_L	143_I	0.849	0.99
86_L	90_L	0.848	0.99
29_F	66_L	0.847	0.99
2_L	5_A	0.841	0.99
141_V	179_M	0.839	0.99
13_I	24_L	0.827	0.99
95_F	99_A	0.827	0.99
202_G	206_G	0.826	0.99
17_G	21_L	0.822	0.99
61_F	65_Y	0.821	0.99
15_V	169_M	0.817	0.99
139_M	178_T	0.817	0.99
167_S	170_N	0.816	0.99
209_L	218_I	0.814	0.99
226_I	230_L	0.814	0.99
101_L	216_E	0.811	0.99
4_L	222_L	0.809	0.99
12_L	229_V	0.808	0.99
16_G	23_A	0.808	0.99
89_G	131_I	0.806	0.99
83_L	87_L	0.805	0.99
146_A	150_W	0.803	0.99
38_L	132_I	0.802	0.99
30_T	185_L	0.801	0.99
3_L	6_A	0.798	0.99
33_V	58_L	0.795	0.99
150_W	153_K	0.793	0.99
108_E	112_L	0.789	0.99
64_L	81_T	0.784	0.99
56_S	135_L	0.782	0.99
152_L	167_S	0.780	0.99
154_E	157_P	0.776	0.99
124_G	224_G	0.771	0.99
127_L	224_G	0.769	0.99
187_Y	224_G	0.762	0.99
166_R	170_N	0.759	0.99
218_I	222_L	0.753	0.99
154_E	166_R	0.751	0.99
141_V	175_H	0.747	0.99
148_A	152_L	0.746	0.99
106_S	109_A	0.744	0.99
38_L	42_I	0.742	0.99
127_L	133_G	0.739	0.98
64_L	78_I	0.735	0.98
153_K	164_L	0.733	0.98
7_L	10_L	0.733	0.98
38_L	128_A	0.733	0.98
225_S	229_V	0.730	0.98
39_L	196_L	0.722	0.98
56_S	131_I	0.717	0.98
38_L	52_A	0.717	0.98
80_G	146_A	0.715	0.98
94_L	97_K	0.710	0.98
184_V	225_S	0.710	0.98
33_V	59_I	0.709	0.98
207_Q	211_S	0.706	0.98
60_T	81_T	0.702	0.98
7_L	11_L	0.701	0.98
221_T	225_S	0.700	0.98
37_F	46_Y	0.697	0.98
22_R	25_L	0.695	0.98
53_L	56_S	0.693	0.98
129_G	133_G	0.690	0.98
26_G	66_L	0.689	0.98
51_V	59_I	0.684	0.98
49_L	93_L	0.682	0.97
53_L	131_I	0.678	0.97
63_T	181_N	0.677	0.97
17_G	22_R	0.677	0.97
92_A	127_L	0.675	0.97
16_G	177_G	0.674	0.97
149_V	164_L	0.674	0.97
73_K	147_S	0.672	0.97
90_L	93_L	0.671	0.97
164_L	168_G	0.669	0.97
78_I	82_L	0.668	0.97
172_G	232_V	0.667	0.97
190_A	220_R	0.666	0.97
88_T	92_A	0.664	0.97
18_W	21_L	0.664	0.97
197_L	208_I	0.661	0.97
31_F	188_A	0.658	0.97
75_L	79_L	0.658	0.97
25_L	66_L	0.657	0.97
15_V	176_I	0.655	0.97
169_M	236_T	0.653	0.97
105_G	212_E	0.652	0.97
147_S	150_W	0.648	0.97
208_I	214_I	0.646	0.97
21_L	25_L	0.645	0.96
79_L	83_L	0.641	0.96
144_S	148_A	0.641	0.96
129_G	220_R	0.637	0.96
185_L	188_A	0.637	0.96
111_F	197_L	0.636	0.96
68_H	178_T	0.634	0.96
68_H	71_N	0.629	0.96
27_L	195_L	0.625	0.96
65_Y	74_T	0.624	0.96
203_T	211_S	0.623	0.96
128_A	171_V	0.623	0.96
96_V	130_I	0.621	0.96
143_I	174_D	0.619	0.96
134_A	185_L	0.618	0.96
152_L	164_L	0.615	0.95
141_V	144_S	0.615	0.95
188_A	191_S	0.612	0.95
8_F	222_L	0.611	0.95
193_P	208_I	0.610	0.95
188_A	228_L	0.609	0.95
68_H	174_D	0.609	0.95
149_V	171_V	0.604	0.95
124_G	128_A	0.602	0.95
7_L	91_L	0.602	0.95
90_L	97_K	0.601	0.95
135_L	174_D	0.601	0.95
216_E	228_L	0.600	0.95
76_A	150_W	0.599	0.95
30_T	176_I	0.598	0.95
215_A	218_I	0.597	0.95
83_L	86_L	0.597	0.95
153_K	156_N	0.594	0.94
154_E	167_S	0.594	0.94
105_G	109_A	0.588	0.94
144_S	179_M	0.587	0.94
107_E	111_F	0.586	0.94
11_L	14_L	0.586	0.94
84_G	234_I	0.582	0.94
101_L	212_E	0.579	0.94
117_Q	120_I	0.578	0.94
77_A	143_I	0.576	0.94
104_L	116_G	0.575	0.93
30_T	34_I	0.573	0.93
137_A	179_M	0.571	0.93
148_A	168_G	0.568	0.93
122_L	125_L	0.567	0.93
46_Y	50_L	0.566	0.93
174_D	185_L	0.566	0.93
121_D	187_Y	0.565	0.93
34_I	39_L	0.564	0.93
127_L	130_I	0.563	0.93
154_E	170_N	0.562	0.93
143_I	179_M	0.562	0.93
43_L	196_L	0.561	0.93
159_L	167_S	0.561	0.93
40_P	45_G	0.560	0.93
23_A	180_V	0.560	0.93
109_A	122_L	0.559	0.92
47_N	51_V	0.554	0.92
4_L	221_T	0.553	0.92
77_A	146_A	0.553	0.92
3_L	98_L	0.552	0.92
29_F	32_L	0.552	0.92
72_K	76_A	0.551	0.92
186_A	224_G	0.547	0.92
159_L	164_L	0.547	0.92
168_G	172_G	0.546	0.92
60_T	82_L	0.546	0.92
32_L	35_F	0.546	0.92
110_E	114_Y	0.545	0.92
174_D	179_M	0.544	0.91
4_L	91_L	0.541	0.91
49_L	127_L	0.541	0.91
56_S	132_I	0.539	0.91
198_F	208_I	0.538	0.91
30_T	59_I	0.538	0.91
49_L	131_I	0.538	0.91
38_L	50_L	0.534	0.91
76_A	80_G	0.534	0.91
56_S	59_I	0.534	0.91
45_G	48_P	0.533	0.91
203_T	208_I	0.533	0.91
183_L	187_Y	0.530	0.90
175_H	178_T	0.530	0.90
119_G	123_R	0.530	0.90
19_K	173_R	0.530	0.90
51_V	54_V	0.528	0.90
175_H	236_T	0.525	0.90
63_T	151_E	0.524	0.90
83_L	90_L	0.523	0.90
87_L	234_I	0.523	0.90
183_L	224_G	0.522	0.90
141_V	232_V	0.518	0.89
91_L	226_I	0.518	0.89
115_L	200_A	0.516	0.89
106_S	110_E	0.516	0.89
60_T	139_M	0.516	0.89
230_L	234_I	0.515	0.89
152_L	159_L	0.515	0.89
130_I	219_V	0.514	0.89
134_A	137_A	0.514	0.89
8_F	232_V	0.512	0.89
3_L	10_L	0.511	0.89
72_K	75_L	0.510	0.89
48_P	52_A	0.510	0.89
153_K	161_R	0.510	0.89
144_S	175_H	0.507	0.88
133_G	193_P	0.507	0.88
151_E	155_A	0.506	0.88
81_T	141_V	0.506	0.88
8_F	24_L	0.505	0.88
102_T	105_G	0.505	0.88
236_T	240_A	0.505	0.88
198_F	214_I	0.504	0.88
64_L	139_M	0.504	0.88
59_I	135_L	0.504	0.88
104_L	109_A	0.503	0.88
53_L	57_A	0.502	0.88
157_P	160_S	0.502	0.88
15_V	165_F	0.500	0.88

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
3aqpA	1	0.7635	14.4	0.95	Contact Map
4mt1A	3	0.7676	13	0.951	Contact Map
3w9iA	3	0.7801	11.9	0.952	Contact Map
4k0jA	3	0.7178	8.2	0.956	Contact Map
4dx5A	3	0.7801	7	0.957	Contact Map
3ne5A	3	0.7676	6.2	0.958	Contact Map
3d31C	2	0.2822	3.8	0.962	Contact Map
3tuiA	2	0.2905	2.8	0.964	Contact Map
2onkC	2	0.2905	2.5	0.966	Contact Map
3qe7A	2	0.9087	2.4	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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