Ycf34 - PFAM28P - GREMLIN Contacts

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Ycf34 - Hypothetical chloroplast protein Ycf34

PFAM:	PF10718	Sequences: MCICVNCHWVDRCITYHAVETQHGVPHLTETPDFEPKEPTIHVNIRDLDKNGDIEMEWDVVGCESFLEEPGKWSKLRP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	78 (77)
Sequences:	559 (227)
Seq/√Len:	25.9
META:	0.78

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_E	75_K	5.152	1.00
12_R	33_D	4.007	1.00
38_E	64_E	3.249	1.00
27_H	32_P	2.185	0.97
37_K	65_S	2.180	0.97
69_E	72_K	2.120	0.97
42_H	61_V	1.802	0.92
37_K	64_E	1.785	0.92
1_M	4_C	1.769	0.91
44_N	62_G	1.725	0.90
24_G	42_H	1.669	0.89
4_C	7_C	1.647	0.88
28_L	32_P	1.518	0.83
20_E	32_P	1.475	0.81
3_I	7_C	1.463	0.81
31_T	77_R	1.451	0.80
43_V	58_W	1.441	0.80
19_V	57_E	1.396	0.78
6_N	71_G	1.384	0.77
6_N	68_E	1.279	0.71
72_K	78_P	1.234	0.68
20_E	27_H	1.231	0.68
32_P	39_P	1.218	0.67
7_C	13_C	1.211	0.67
21_T	24_G	1.174	0.64
50_K	53_D	1.171	0.64
45_I	56_M	1.166	0.64
44_N	65_S	1.166	0.64
15_T	36_P	1.096	0.59
13_C	16_Y	1.066	0.57
64_E	75_K	1.064	0.57
57_E	60_V	1.042	0.55
19_V	39_P	1.034	0.54
66_F	71_G	1.030	0.54
25_V	32_P	1.029	0.54
23_H	39_P	1.007	0.52
18_A	22_Q	0.970	0.50
4_C	13_C	0.965	0.49
31_T	67_L	0.960	0.49
45_I	50_K	0.959	0.49
49_D	55_E	0.956	0.49
44_N	61_V	0.945	0.48
22_Q	58_W	0.945	0.48
37_K	67_L	0.943	0.48
73_W	78_P	0.942	0.48
63_C	66_F	0.931	0.47
2_C	7_C	0.921	0.46
9_W	12_R	0.918	0.46
71_G	78_P	0.915	0.46
46_R	54_I	0.894	0.44
6_N	70_P	0.892	0.44
18_A	28_L	0.891	0.44
44_N	54_I	0.872	0.43
17_H	20_E	0.862	0.42
3_I	13_C	0.852	0.41
14_I	36_P	0.850	0.41
27_H	39_P	0.850	0.41
58_W	65_S	0.838	0.40
68_E	74_S	0.835	0.40
26_P	37_K	0.831	0.40
17_H	32_P	0.830	0.40
65_S	77_R	0.812	0.38
3_I	6_N	0.783	0.36
18_A	29_T	0.767	0.35
39_P	60_V	0.761	0.35
25_V	61_V	0.758	0.35
9_W	61_V	0.754	0.34
7_C	16_Y	0.754	0.34
30_E	75_K	0.744	0.34
11_D	32_P	0.742	0.34
9_W	62_G	0.734	0.33
41_I	66_F	0.732	0.33
8_H	67_L	0.731	0.33
34_F	44_N	0.703	0.31
64_E	77_R	0.703	0.31
5_V	8_H	0.690	0.30
68_E	73_W	0.676	0.29
10_V	15_T	0.674	0.29
38_E	74_S	0.664	0.29
68_E	77_R	0.659	0.28
40_T	51_N	0.654	0.28
12_R	28_L	0.653	0.28
63_C	73_W	0.650	0.28
9_W	60_V	0.649	0.28
70_P	77_R	0.649	0.28
23_H	32_P	0.642	0.27
31_T	37_K	0.627	0.26
1_M	7_C	0.621	0.26
8_H	49_D	0.615	0.26
20_E	25_V	0.615	0.26
22_Q	36_P	0.611	0.26
19_V	62_G	0.605	0.25
40_T	64_E	0.603	0.25
34_F	43_V	0.601	0.25
30_E	45_I	0.599	0.25
20_E	60_V	0.586	0.24
29_T	43_V	0.585	0.24
20_E	23_H	0.577	0.24
30_E	68_E	0.574	0.24
24_G	61_V	0.570	0.23
64_E	69_E	0.569	0.23
14_I	35_E	0.567	0.23
50_K	55_E	0.556	0.23
11_D	17_H	0.555	0.23
43_V	47_D	0.555	0.23
20_E	39_P	0.547	0.22
65_S	76_L	0.545	0.22
21_T	37_K	0.545	0.22
19_V	23_H	0.540	0.22
62_G	77_R	0.539	0.22
18_A	62_G	0.538	0.22
14_I	17_H	0.534	0.21
17_H	27_H	0.533	0.21
40_T	74_S	0.530	0.21
43_V	50_K	0.515	0.21
22_Q	41_I	0.500	0.20

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
3oh8A	1	0.3846	13.9	0.922	Contact Map
2azjA	2	0.5897	3.7	0.94	Contact Map
1zgkA	1	0.4615	2.3	0.946	Contact Map
3pkoA	2	0.7051	1.8	0.949	Contact Map
2rc5A	1	0.6667	1.7	0.95	Contact Map
1usyA	3	0.5513	1.5	0.952	Contact Map
3jqqA	2	0.6154	1.3	0.953	Contact Map
2j1pA	2	0.5769	1.3	0.954	Contact Map
2lcoA	1	0.1026	1.2	0.954	Contact Map
4c68A	1	0.8077	1.1	0.955	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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