YIF1 - PFAM28P - GREMLIN Contacts

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YIF1 - YIF1

PFAM:	PF03878	Sequences: DPTAQMAMQYGQSALGAGQEYVQKNFGRYVSVSALKYYFAVSNSYVLNKLKLLLFPFRHKPWSRKYERDEPYLPPRDDINAPDLYIPLMAFVTYILLAGLVLGLQGRFSPELLGITASSALAVVILEVLLLKLGLYLLNISLPLLDLVAYSGYKFVGIIVTLLAGLLFGSGTGYYLVLLYTSLANAFFLLRSLKYVLLPEASQTVSRSQRSRRRQFLFLYAAVLQPLLMWW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	231 (228)
Sequences:	505 (361)
Seq/√Len:	23.9
META:	0.17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_N	51_K	4.718	1.00
37_Y	81_A	3.786	1.00
216_F	221_A	3.657	1.00
214_R	222_A	3.626	1.00
64_R	78_D	3.379	1.00
86_I	156_V	3.036	1.00
164_A	177_V	2.839	0.99
52_L	55_F	2.824	0.99
45_Y	49_K	2.821	0.99
214_R	221_A	2.549	0.99
163_L	167_L	2.438	0.98
45_Y	86_I	2.367	0.98
12_Q	65_K	2.348	0.98
168_F	173_G	2.249	0.97
54_L	181_T	2.194	0.97
81_A	109_S	2.182	0.96
75_P	78_D	2.131	0.96
64_R	75_P	2.096	0.96
124_V	155_F	2.048	0.95
21_Y	25_N	2.022	0.95
90_A	156_V	2.007	0.94
75_P	81_A	1.980	0.94
118_S	122_A	1.968	0.94
10_Y	14_A	1.931	0.93
210_R	218_F	1.919	0.93
49_K	86_I	1.903	0.93
100_L	150_Y	1.892	0.92
22_V	130_L	1.813	0.91
157_G	161_T	1.811	0.91
20_E	24_K	1.797	0.90
64_R	72_Y	1.766	0.89
125_I	129_L	1.766	0.89
40_A	81_A	1.702	0.88
210_R	214_R	1.680	0.87
23_Q	28_R	1.680	0.87
120_A	191_R	1.678	0.87
45_Y	83_D	1.635	0.85
175_Y	180_Y	1.618	0.85
22_V	26_F	1.560	0.82
23_Q	127_E	1.543	0.82
194_K	198_L	1.531	0.81
134_G	137_L	1.502	0.80
39_F	56_P	1.500	0.80
216_F	220_Y	1.494	0.80
74_P	78_D	1.467	0.78
118_S	136_Y	1.462	0.78
214_R	220_Y	1.411	0.75
161_T	181_T	1.408	0.75
67_E	77_D	1.373	0.73
133_L	137_L	1.366	0.73
57_F	70_E	1.361	0.73
59_H	80_N	1.361	0.73
99_G	113_L	1.355	0.72
43_N	154_K	1.343	0.72
75_P	80_N	1.317	0.70
99_G	103_G	1.317	0.70
216_F	222_A	1.300	0.69
134_G	218_F	1.294	0.69
218_F	222_A	1.290	0.69
92_V	113_L	1.279	0.68
77_D	184_A	1.279	0.68
193_L	198_L	1.273	0.68
6_M	12_Q	1.271	0.67
51_K	223_V	1.266	0.67
114_G	148_V	1.261	0.67
134_G	216_F	1.261	0.67
101_V	104_L	1.260	0.67
62_W	81_A	1.255	0.66
103_G	113_L	1.248	0.66
146_D	193_L	1.241	0.65
52_L	59_H	1.239	0.65
78_D	81_A	1.235	0.65
50_L	227_L	1.233	0.65
84_L	105_Q	1.219	0.64
86_I	150_Y	1.209	0.63
82_P	150_Y	1.205	0.63
9_Q	17_A	1.198	0.63
45_Y	94_Y	1.194	0.62
18_G	25_N	1.188	0.62
157_G	229_M	1.178	0.61
91_F	146_D	1.165	0.60
64_R	80_N	1.160	0.60
13_S	29_Y	1.143	0.59
126_L	162_L	1.138	0.59
137_L	210_R	1.133	0.58
99_G	182_S	1.123	0.58
136_Y	154_K	1.121	0.57
189_L	194_K	1.118	0.57
65_K	140_I	1.118	0.57
160_V	181_T	1.117	0.57
51_K	167_L	1.111	0.57
60_K	115_I	1.107	0.56
93_T	99_G	1.105	0.56
6_M	23_Q	1.103	0.56
215_Q	218_F	1.096	0.56
129_L	176_L	1.085	0.55
62_W	75_P	1.073	0.54
14_A	19_Q	1.064	0.53
88_L	100_L	1.058	0.53
86_I	90_A	1.056	0.53
119_S	228_L	1.055	0.53
23_Q	29_Y	1.051	0.53
27_G	228_L	1.050	0.52
21_Y	54_L	1.041	0.52
62_W	80_N	1.038	0.52
98_A	152_G	1.038	0.52
82_P	96_L	1.036	0.51
213_R	220_Y	1.032	0.51
127_E	154_K	1.031	0.51
210_R	217_L	1.027	0.51
46_V	225_Q	1.017	0.50
72_Y	119_S	1.011	0.50
57_F	230_W	1.003	0.49
197_L	213_R	1.003	0.49
111_E	220_Y	0.993	0.48
55_F	90_A	0.983	0.48
111_E	115_I	0.983	0.48
124_V	152_G	0.983	0.48
82_P	108_F	0.976	0.47
44_S	88_L	0.973	0.47
50_L	86_I	0.971	0.47
43_N	95_I	0.955	0.46
27_G	131_L	0.953	0.46
104_L	111_E	0.953	0.46
81_A	91_F	0.950	0.45
205_V	208_S	0.949	0.45
180_Y	184_A	0.946	0.45
213_R	222_A	0.945	0.45
98_A	104_L	0.944	0.45
183_L	201_A	0.943	0.45
179_L	219_L	0.943	0.45
133_L	141_S	0.940	0.45
218_F	221_A	0.935	0.44
9_Q	26_F	0.933	0.44
37_Y	42_S	0.931	0.44
59_H	76_R	0.927	0.44
140_I	191_R	0.925	0.44
165_G	186_A	0.922	0.43
120_A	127_E	0.922	0.43
53_L	157_G	0.917	0.43
107_R	170_S	0.916	0.43
13_S	17_A	0.916	0.43
57_F	184_A	0.913	0.43
11_G	109_S	0.911	0.43
131_L	228_L	0.906	0.42
84_L	99_G	0.899	0.42
83_D	86_I	0.897	0.42
49_K	110_P	0.896	0.42
38_Y	145_L	0.889	0.41
120_A	149_A	0.884	0.41
223_V	230_W	0.882	0.41
50_L	156_V	0.878	0.40
50_L	203_Q	0.876	0.40
157_G	177_V	0.874	0.40
41_V	56_P	0.869	0.40
70_E	125_I	0.865	0.40
131_L	201_A	0.864	0.39
160_V	168_F	0.860	0.39
118_S	159_I	0.859	0.39
98_A	102_L	0.855	0.39
18_G	41_V	0.854	0.39
53_L	169_G	0.851	0.39
27_G	30_V	0.851	0.39
53_L	122_A	0.850	0.39
89_M	153_Y	0.850	0.39
110_P	155_F	0.850	0.39
171_G	186_A	0.850	0.39
62_W	78_D	0.849	0.38
86_I	94_Y	0.839	0.38
104_L	148_V	0.835	0.38
16_G	177_V	0.833	0.37
112_L	151_S	0.832	0.37
18_G	34_A	0.831	0.37
35_L	105_Q	0.828	0.37
82_P	110_P	0.825	0.37
133_L	224_L	0.821	0.37
5_Q	185_N	0.819	0.36
94_Y	153_Y	0.817	0.36
10_Y	160_V	0.811	0.36
96_L	150_Y	0.811	0.36
96_L	155_F	0.810	0.36
94_Y	150_Y	0.810	0.36
3_T	74_P	0.809	0.36
47_L	79_I	0.807	0.36
159_I	192_S	0.803	0.35
145_L	181_T	0.795	0.35
131_L	170_S	0.792	0.35
51_K	130_L	0.791	0.35
84_L	149_A	0.791	0.35
54_L	160_V	0.791	0.35
81_A	97_L	0.787	0.34
53_L	230_W	0.777	0.34
26_F	149_A	0.775	0.34
84_L	131_L	0.770	0.33
131_L	181_T	0.769	0.33
103_G	108_F	0.768	0.33
5_Q	135_L	0.768	0.33
78_D	83_D	0.767	0.33
43_N	67_E	0.755	0.32
88_L	104_L	0.750	0.32
97_L	104_L	0.750	0.32
199_P	217_L	0.750	0.32
31_S	170_S	0.744	0.32
87_P	153_Y	0.739	0.31
24_K	95_I	0.733	0.31
122_A	167_L	0.730	0.31
27_G	38_Y	0.728	0.31
28_R	200_E	0.727	0.31
96_L	217_L	0.723	0.30
41_V	78_D	0.723	0.30
42_S	86_I	0.722	0.30
144_L	167_L	0.716	0.30
41_V	46_V	0.716	0.30
4_A	194_K	0.715	0.30
88_L	165_G	0.707	0.29
129_L	148_V	0.707	0.29
131_L	190_L	0.707	0.29
138_L	142_L	0.703	0.29
195_Y	227_L	0.701	0.29
92_V	96_L	0.700	0.29
53_L	177_V	0.699	0.29
107_R	144_L	0.698	0.29
205_V	219_L	0.691	0.29
36_K	127_E	0.688	0.28
95_I	191_R	0.685	0.28
18_G	33_S	0.683	0.28
114_G	193_L	0.681	0.28
203_Q	206_S	0.680	0.28
117_A	121_L	0.678	0.28
186_A	223_V	0.672	0.27
86_I	192_S	0.672	0.27
124_V	151_S	0.671	0.27
96_L	108_F	0.670	0.27
189_L	213_R	0.668	0.27
167_L	223_V	0.665	0.27
92_V	154_K	0.662	0.27
180_Y	190_L	0.661	0.27
125_I	143_P	0.660	0.27
15_L	36_K	0.659	0.27
80_N	146_D	0.655	0.26
49_K	146_D	0.654	0.26
32_V	208_S	0.653	0.26
118_S	170_S	0.652	0.26
98_A	184_A	0.651	0.26
189_L	217_L	0.649	0.26
131_L	220_Y	0.647	0.26
7_A	17_A	0.646	0.26
104_L	165_G	0.645	0.26
50_L	68_R	0.642	0.26
91_F	108_F	0.641	0.26
12_Q	16_G	0.641	0.26
13_S	16_G	0.640	0.26
8_M	187_F	0.639	0.26
101_V	180_Y	0.637	0.25
178_L	216_F	0.637	0.25
103_G	128_V	0.636	0.25
124_V	192_S	0.635	0.25
48_N	174_Y	0.634	0.25
217_L	220_Y	0.634	0.25
124_V	202_S	0.633	0.25
15_L	186_A	0.632	0.25
190_L	229_M	0.631	0.25
160_V	223_V	0.630	0.25
90_A	101_V	0.629	0.25
9_Q	12_Q	0.622	0.25
45_Y	53_L	0.617	0.24
165_G	223_V	0.615	0.24
113_L	202_S	0.613	0.24
23_Q	27_G	0.612	0.24
185_N	193_L	0.612	0.24
130_L	141_S	0.612	0.24
214_R	217_L	0.611	0.24
4_A	8_M	0.610	0.24
206_S	211_S	0.608	0.24
31_S	99_G	0.602	0.24
162_L	212_R	0.601	0.24
18_G	21_Y	0.600	0.24
136_Y	152_G	0.600	0.24
29_Y	219_L	0.599	0.24
28_R	141_S	0.598	0.23
111_E	121_L	0.596	0.23
97_L	159_I	0.596	0.23
57_F	180_Y	0.595	0.23
96_L	166_L	0.595	0.23
161_T	177_V	0.592	0.23
50_L	54_L	0.592	0.23
130_L	219_L	0.591	0.23
39_F	87_P	0.591	0.23
123_V	190_L	0.589	0.23
16_G	53_L	0.588	0.23
18_G	23_Q	0.583	0.23
121_L	137_L	0.582	0.23
46_V	81_A	0.581	0.23
66_Y	125_I	0.580	0.23
83_D	153_Y	0.578	0.22
173_G	226_P	0.577	0.22
49_K	53_L	0.573	0.22
173_G	193_L	0.571	0.22
56_P	85_Y	0.570	0.22
27_G	141_S	0.570	0.22
117_A	127_E	0.566	0.22
217_L	229_M	0.566	0.22
39_F	85_Y	0.563	0.22
133_L	166_L	0.560	0.22
36_K	114_G	0.559	0.22
16_G	33_S	0.557	0.21
71_P	125_I	0.555	0.21
103_G	154_K	0.552	0.21
211_S	227_L	0.552	0.21
94_Y	158_I	0.551	0.21
212_R	215_Q	0.551	0.21
60_K	95_I	0.549	0.21
39_F	49_K	0.549	0.21
150_Y	191_R	0.549	0.21
64_R	73_L	0.549	0.21
86_I	110_P	0.548	0.21
195_Y	214_R	0.548	0.21
94_Y	108_F	0.547	0.21
159_I	186_A	0.544	0.21
16_G	223_V	0.543	0.21
16_G	29_Y	0.541	0.21
80_N	190_L	0.537	0.20
90_A	96_L	0.536	0.20
213_R	218_F	0.529	0.20
174_Y	178_L	0.528	0.20
61_P	69_D	0.524	0.20
58_R	74_P	0.522	0.20
38_Y	72_Y	0.522	0.20
110_P	146_D	0.522	0.20
84_L	174_Y	0.519	0.20
60_K	64_R	0.517	0.20
180_Y	189_L	0.516	0.20
7_A	61_P	0.516	0.20
49_K	108_F	0.514	0.19
8_M	162_L	0.512	0.19
214_R	218_F	0.509	0.19
50_L	231_W	0.508	0.19
82_P	91_F	0.506	0.19
132_K	209_Q	0.506	0.19
133_L	160_V	0.503	0.19
26_F	36_K	0.501	0.19
72_Y	102_L	0.500	0.19

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
2ar1A	1	0.2987	5.3	0.967	Contact Map
1zceA	1	0.316	4.9	0.968	Contact Map
2gbsA	1	0.3117	2.9	0.971	Contact Map
4xtrG	1	0.0823	2.8	0.972	Contact Map
2eveA	1	0.2857	2.3	0.973	Contact Map
4n7wA	2	0.8182	2.3	0.973	Contact Map
1w8xP	1	0.0996	1.9	0.974	Contact Map
3hqiA	2	0.2554	1.6	0.975	Contact Map
3eopA	1	0.2944	1.6	0.975	Contact Map
2hgaA	1	0.3593	1.5	0.975	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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