ThylakoidFormat - PFAM28P - GREMLIN Contacts

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ThylakoidFormat - Thylakoid formation protein

PFAM:	PF11264	Sequences: TVSDTKRAFYEAFPRPINSLYRRVVDELLVELHLLSVNADFKYDPLFALGLVTTFDRFMKGYRPEKDLDSIFEALCSAVGFDPKEYREDAQKLQAEAKGKSSEDLLKWLSEKGEGAGDGDLAAILKAIASNSKFKYSRLFAIGLYTLLENADDEKVKDESERNKALEDIAEALGLSADKAEKDLDLYRSNLEKMAQAKELMEELLIAEKKKREERQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	216 (215)
Sequences:	670 (359)
Seq/√Len:	24.5
META:	0.721

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_D	87_R	4.244	1.00
43_Y	89_D	3.792	1.00
91_Q	95_A	3.588	1.00
43_Y	48_A	3.553	1.00
32_L	47_F	3.462	1.00
2_V	25_V	3.348	1.00
8_A	12_A	3.013	1.00
202_E	206_I	3.007	1.00
23_R	26_D	2.596	0.99
81_F	86_Y	2.536	0.99
211_K	214_E	2.535	0.99
98_K	150_N	2.489	0.99
52_V	72_F	2.425	0.98
77_S	83_P	2.373	0.98
208_E	211_K	2.337	0.98
47_F	86_Y	2.116	0.96
46_L	140_F	2.101	0.96
53_T	57_R	2.087	0.96
10_Y	14_P	2.065	0.95
201_M	204_L	2.060	0.95
134_F	140_F	2.019	0.95
93_L	147_L	2.003	0.95
148_L	209_K	1.994	0.95
148_L	151_A	1.991	0.94
47_F	205_L	1.987	0.94
69_D	99_G	1.924	0.93
170_A	180_A	1.827	0.91
200_L	203_E	1.757	0.90
46_L	147_L	1.740	0.89
47_F	51_L	1.696	0.88
208_E	214_E	1.691	0.88
187_Y	193_K	1.649	0.86
31_E	35_L	1.630	0.86
10_Y	13_F	1.621	0.86
164_K	167_E	1.599	0.85
201_M	208_E	1.590	0.84
126_K	174_G	1.551	0.83
82_D	85_E	1.542	0.82
1_T	9_F	1.530	0.82
194_M	202_E	1.526	0.82
44_D	140_F	1.516	0.81
118_D	122_A	1.511	0.81
1_T	5_T	1.506	0.81
8_A	80_G	1.501	0.81
100_K	104_D	1.490	0.80
5_T	16_P	1.490	0.80
12_A	54_T	1.474	0.79
96_E	108_W	1.461	0.79
134_F	203_E	1.442	0.78
1_T	4_D	1.439	0.78
209_K	213_E	1.439	0.78
103_E	106_L	1.435	0.78
72_F	76_C	1.419	0.77
5_T	26_D	1.419	0.77
99_G	151_A	1.418	0.77
27_E	30_V	1.400	0.76
206_I	213_E	1.395	0.76
161_E	164_K	1.394	0.75
152_D	161_E	1.372	0.74
195_A	199_E	1.362	0.74
207_A	213_E	1.333	0.72
28_L	54_T	1.325	0.72
13_F	18_N	1.319	0.71
192_E	199_E	1.316	0.71
102_S	151_A	1.315	0.71
98_K	144_L	1.315	0.71
187_Y	191_L	1.302	0.70
65_E	68_L	1.255	0.67
66_K	69_D	1.246	0.67
198_K	202_E	1.239	0.66
109_L	169_I	1.219	0.65
94_Q	98_K	1.208	0.64
22_R	41_F	1.206	0.64
209_K	212_R	1.198	0.64
14_P	29_L	1.195	0.63
72_F	83_P	1.186	0.63
48_A	89_D	1.183	0.63
190_N	196_Q	1.178	0.62
149_E	215_R	1.175	0.62
67_D	210_K	1.171	0.62
90_A	215_R	1.170	0.62
198_K	215_R	1.138	0.60
103_E	150_N	1.129	0.59
35_L	76_C	1.125	0.59
91_Q	109_L	1.103	0.57
43_Y	85_E	1.097	0.57
81_F	85_E	1.092	0.56
156_V	160_S	1.091	0.56
182_K	186_L	1.087	0.56
111_E	114_E	1.083	0.56
5_T	10_Y	1.083	0.56
6_K	30_V	1.060	0.54
41_F	47_F	1.055	0.54
91_Q	121_L	1.049	0.53
107_K	158_D	1.046	0.53
69_D	84_K	1.045	0.53
110_S	172_A	1.027	0.52
38_N	52_V	1.025	0.52
161_E	206_I	1.019	0.51
185_D	188_R	1.007	0.50
24_V	59_M	0.995	0.49
154_E	157_K	0.991	0.49
49_L	187_Y	0.985	0.49
72_F	196_Q	0.985	0.49
91_Q	94_Q	0.971	0.48
57_R	149_E	0.969	0.48
107_K	205_L	0.961	0.47
203_E	207_A	0.960	0.47
204_L	214_E	0.952	0.46
169_I	174_G	0.951	0.46
90_A	166_L	0.949	0.46
195_A	208_E	0.946	0.46
84_K	91_Q	0.943	0.46
7_R	23_R	0.941	0.46
182_K	207_A	0.930	0.45
106_L	113_G	0.927	0.45
167_E	177_A	0.927	0.45
44_D	137_S	0.925	0.44
92_K	120_D	0.923	0.44
47_F	81_F	0.916	0.44
19_S	168_D	0.913	0.44
169_I	194_M	0.913	0.44
82_D	95_A	0.911	0.43
149_E	194_M	0.898	0.43
55_F	59_M	0.894	0.42
126_K	195_A	0.885	0.42
36_S	46_L	0.883	0.42
39_A	144_L	0.882	0.41
4_D	7_R	0.881	0.41
54_T	194_M	0.877	0.41
74_A	99_G	0.876	0.41
6_K	9_F	0.876	0.41
170_A	177_A	0.866	0.40
141_A	180_A	0.860	0.40
200_L	204_L	0.859	0.40
59_M	71_I	0.857	0.40
13_F	47_F	0.855	0.40
44_D	134_F	0.854	0.40
31_E	75_L	0.852	0.39
82_D	88_E	0.852	0.39
140_F	173_L	0.849	0.39
62_Y	137_S	0.847	0.39
136_Y	141_A	0.841	0.39
77_S	92_K	0.841	0.39
31_E	64_P	0.839	0.38
45_P	168_D	0.832	0.38
16_P	37_V	0.832	0.38
10_Y	15_R	0.829	0.38
35_L	139_L	0.826	0.38
13_F	26_D	0.825	0.38
95_A	150_N	0.824	0.37
29_L	215_R	0.822	0.37
198_K	203_E	0.816	0.37
94_Q	147_L	0.815	0.37
20_L	46_L	0.813	0.37
10_Y	16_P	0.811	0.37
110_S	171_E	0.809	0.36
156_V	159_E	0.808	0.36
23_R	31_E	0.808	0.36
179_K	185_D	0.807	0.36
183_D	187_Y	0.807	0.36
63_R	80_G	0.807	0.36
198_K	206_I	0.797	0.36
109_L	124_I	0.797	0.36
97_A	148_L	0.796	0.36
41_F	44_D	0.796	0.36
16_P	38_N	0.794	0.35
43_Y	78_A	0.792	0.35
35_L	64_P	0.791	0.35
71_I	185_D	0.789	0.35
20_L	140_F	0.780	0.35
173_L	211_K	0.776	0.34
4_D	10_Y	0.775	0.34
125_L	128_I	0.775	0.34
2_V	9_F	0.774	0.34
6_K	17_I	0.769	0.34
22_R	35_L	0.768	0.34
23_R	35_L	0.763	0.33
85_E	120_D	0.762	0.33
52_V	87_R	0.759	0.33
117_G	122_A	0.759	0.33
73_E	111_E	0.756	0.33
125_L	144_L	0.755	0.33
207_A	212_R	0.753	0.33
22_R	27_E	0.746	0.32
17_I	104_D	0.743	0.32
106_L	147_L	0.740	0.32
95_A	98_K	0.737	0.32
74_A	78_A	0.731	0.31
115_G	206_I	0.729	0.31
4_D	142_I	0.729	0.31
83_P	89_D	0.728	0.31
21_Y	28_L	0.723	0.31
36_S	160_S	0.720	0.31
5_T	8_A	0.719	0.31
104_D	114_E	0.712	0.30
79_V	150_N	0.708	0.30
69_D	144_L	0.708	0.30
99_G	169_I	0.706	0.30
58_F	190_N	0.705	0.30
13_F	71_I	0.698	0.29
77_S	82_D	0.697	0.29
16_P	19_S	0.697	0.29
59_M	185_D	0.695	0.29
44_D	116_A	0.694	0.29
63_R	194_M	0.693	0.29
51_L	86_Y	0.692	0.29
111_E	151_A	0.690	0.29
121_L	130_S	0.689	0.29
76_C	179_K	0.688	0.29
87_R	167_E	0.687	0.29
124_I	129_A	0.685	0.29
99_G	104_D	0.682	0.28
104_D	132_S	0.682	0.28
54_T	63_R	0.674	0.28
13_F	70_S	0.673	0.28
92_K	126_K	0.673	0.28
68_L	78_A	0.670	0.28
5_T	14_P	0.668	0.28
2_V	5_T	0.662	0.27
26_D	30_V	0.660	0.27
200_L	208_E	0.656	0.27
30_V	148_L	0.653	0.27
55_F	202_E	0.651	0.27
187_Y	196_Q	0.648	0.27
124_I	169_I	0.647	0.26
97_A	111_E	0.647	0.26
60_K	209_K	0.646	0.26
32_L	36_S	0.646	0.26
92_K	173_L	0.643	0.26
146_T	207_A	0.643	0.26
42_K	95_A	0.642	0.26
66_K	156_V	0.642	0.26
82_D	87_R	0.640	0.26
201_M	206_I	0.637	0.26
9_F	17_I	0.634	0.26
121_L	158_D	0.634	0.26
26_D	31_E	0.631	0.26
73_E	83_P	0.630	0.26
71_I	91_Q	0.630	0.26
111_E	171_E	0.629	0.26
32_L	86_Y	0.625	0.25
43_Y	166_L	0.622	0.25
114_E	118_D	0.619	0.25
126_K	200_L	0.617	0.25
5_T	51_L	0.615	0.25
8_A	79_V	0.613	0.25
115_G	118_D	0.612	0.25
88_E	92_K	0.612	0.25
34_L	58_F	0.611	0.25
49_L	90_A	0.611	0.25
5_T	29_L	0.611	0.25
15_R	70_S	0.609	0.24
26_D	32_L	0.608	0.24
73_E	160_S	0.608	0.24
92_K	96_E	0.603	0.24
81_F	147_L	0.594	0.24
82_D	132_S	0.594	0.24
4_D	9_F	0.592	0.24
141_A	205_L	0.591	0.23
99_G	116_A	0.591	0.23
48_A	70_S	0.590	0.23
29_L	199_E	0.589	0.23
8_A	19_S	0.588	0.23
69_D	78_A	0.583	0.23
96_E	204_L	0.581	0.23
34_L	138_R	0.581	0.23
52_V	211_K	0.581	0.23
148_L	169_I	0.580	0.23
84_K	208_E	0.579	0.23
116_A	174_G	0.577	0.23
49_L	52_V	0.574	0.23
95_A	215_R	0.574	0.23
156_V	202_E	0.573	0.23
30_V	35_L	0.573	0.23
112_K	115_G	0.568	0.22
171_E	177_A	0.568	0.22
167_E	208_E	0.566	0.22
60_K	102_S	0.565	0.22
13_F	67_D	0.564	0.22
66_K	91_Q	0.564	0.22
106_L	152_D	0.563	0.22
117_G	120_D	0.563	0.22
128_I	140_F	0.558	0.22
88_E	99_G	0.557	0.22
69_D	103_E	0.555	0.22
69_D	73_E	0.555	0.22
171_E	206_I	0.555	0.22
94_Q	161_E	0.555	0.22
31_E	139_L	0.554	0.22
24_V	215_R	0.549	0.21
8_A	62_Y	0.549	0.21
62_Y	138_R	0.548	0.21
170_A	192_E	0.548	0.21
206_I	209_K	0.548	0.21
76_C	83_P	0.547	0.21
42_K	164_K	0.541	0.21
40_D	60_K	0.540	0.21
181_E	211_K	0.540	0.21
66_K	130_S	0.538	0.21
35_L	135_K	0.538	0.21
164_K	168_D	0.536	0.21
51_L	76_C	0.536	0.21
15_R	23_R	0.534	0.21
84_K	174_G	0.534	0.21
111_E	189_S	0.533	0.21
121_L	137_S	0.532	0.21
5_T	12_A	0.529	0.20
85_E	157_K	0.528	0.20
160_S	164_K	0.522	0.20
22_R	192_E	0.522	0.20
3_S	6_K	0.517	0.20
102_S	176_S	0.514	0.20
8_A	11_E	0.513	0.20
145_Y	206_I	0.511	0.20
34_L	37_V	0.511	0.20
52_V	86_Y	0.510	0.20
31_E	138_R	0.509	0.20
1_T	6_K	0.505	0.19
100_K	105_L	0.504	0.19
106_L	170_A	0.503	0.19
94_Q	107_K	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
3hoaA	2	0.5185	40.5	0.957	Contact Map
3kw6A	1	0.3472	36.1	0.958	Contact Map
4g3aA	1	0.9028	27.5	0.961	Contact Map
3w3wA	1	0.838	20.7	0.963	Contact Map
2i6xA	1	0.5694	18.6	0.964	Contact Map
2h5nA	5	0.5972	17.1	0.964	Contact Map
2yd0A	1	0.8333	17	0.964	Contact Map
4pj6A	2	0.8148	16.7	0.965	Contact Map
2dznB	1	0.3241	16.5	0.965	Contact Map
2ou3A	2	0.6759	14.4	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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