Intron_maturas2 - PFAM28P - GREMLIN Contacts

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Intron_maturas2 - Type II intron maturase

PFAM:	PF01348	Sequences: TKKFDTIVPIIPLIGSLAKAKFCNVLKGKGHPISKPVWADLSDSDIIDRFNRICRNLSHYYSGSSNKKSLYSRIKYILRLSCAKTLARKHKSRTVRKFLKRLGKKLSEFLTEEFFTEEEQVKLKPKLSLIFPKTSSSSRT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (110)
Sequences:	1661 (806)
Seq/√Len:	76.8
META:	0.43

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_D	90_H	4.540	1.00
23_C	77_I	3.694	1.00
83_A	99_L	3.663	1.00
92_S	98_F	3.082	1.00
80_L	95_V	2.813	1.00
18_A	23_C	2.810	1.00
34_S	88_R	2.715	1.00
86_L	90_H	2.686	1.00
22_F	78_L	2.559	1.00
43_D	86_L	2.221	1.00
36_P	88_R	2.075	1.00
32_P	80_L	1.788	1.00
50_F	81_S	1.707	1.00
15_G	19_K	1.638	1.00
56_N	59_H	1.636	1.00
107_S	110_L	1.635	1.00
9_P	61_Y	1.508	0.99
82_C	86_L	1.505	0.99
84_K	94_T	1.478	0.99
51_N	54_C	1.473	0.99
99_L	103_G	1.472	0.99
32_P	76_Y	1.470	0.99
11_I	15_G	1.453	0.99
90_H	102_L	1.440	0.99
35_K	38_W	1.438	0.99
22_F	53_I	1.433	0.99
113_E	116_T	1.422	0.99
38_W	49_R	1.405	0.99
14_I	30_G	1.392	0.99
114_F	119_E	1.349	0.98
112_E	118_E	1.292	0.98
17_L	23_C	1.291	0.98
58_S	67_K	1.265	0.97
110_L	113_E	1.235	0.97
114_F	117_E	1.218	0.97
76_Y	80_L	1.216	0.97
14_I	57_L	1.214	0.97
98_F	102_L	1.140	0.95
118_E	121_V	1.132	0.95
112_E	117_E	1.114	0.95
75_K	79_R	1.107	0.95
116_T	120_Q	1.102	0.94
39_A	88_R	1.101	0.94
92_S	97_K	1.097	0.94
86_L	102_L	1.095	0.94
95_V	98_F	1.090	0.94
92_S	95_V	1.074	0.94
49_R	53_I	1.073	0.94
112_E	116_T	1.052	0.93
16_S	66_N	1.023	0.92
107_S	114_F	1.021	0.92
110_L	114_F	1.019	0.92
17_L	78_L	1.007	0.91
16_S	56_N	1.004	0.91
112_E	115_F	1.003	0.91
55_R	59_H	0.997	0.91
22_F	38_W	0.991	0.91
9_P	60_Y	0.963	0.89
11_I	56_N	0.957	0.89
23_C	75_K	0.951	0.89
116_T	119_E	0.937	0.88
68_K	71_Y	0.917	0.87
50_F	78_L	0.909	0.86
53_I	78_L	0.903	0.86
48_D	52_R	0.899	0.86
51_N	55_R	0.887	0.85
74_I	78_L	0.885	0.85
52_R	55_R	0.881	0.85
24_N	76_Y	0.867	0.84
6_T	64_S	0.864	0.83
96_R	100_K	0.858	0.83
9_P	70_L	0.849	0.82
34_S	84_K	0.823	0.80
50_F	82_C	0.823	0.80
46_I	82_C	0.818	0.80
109_F	114_F	0.805	0.79
45_D	48_D	0.805	0.79
77_I	94_T	0.803	0.79
41_L	54_C	0.802	0.79
54_C	75_K	0.797	0.78
19_K	56_N	0.787	0.77
30_G	73_R	0.782	0.77
110_L	115_F	0.772	0.76
117_E	120_Q	0.771	0.76
6_T	63_G	0.770	0.76
8_V	58_S	0.766	0.75
46_I	89_K	0.765	0.75
22_F	49_R	0.764	0.75
20_A	47_I	0.761	0.75
12_P	15_G	0.756	0.74
67_K	70_L	0.755	0.74
17_L	74_I	0.752	0.74
36_P	85_T	0.750	0.74
14_I	23_C	0.744	0.73
115_F	121_V	0.744	0.73
79_R	83_A	0.743	0.73
73_R	77_I	0.741	0.73
43_D	46_I	0.732	0.72
80_L	99_L	0.730	0.72
54_C	58_S	0.719	0.71
44_S	48_D	0.715	0.70
30_G	77_I	0.692	0.68
116_T	121_V	0.685	0.67
114_F	121_V	0.682	0.67
57_L	63_G	0.676	0.66
107_S	112_E	0.675	0.66
18_A	25_V	0.673	0.66
113_E	117_E	0.669	0.65
113_E	119_E	0.666	0.65
117_E	121_V	0.663	0.64
40_D	69_S	0.663	0.64
49_R	77_I	0.661	0.64
80_L	84_K	0.649	0.63
23_C	30_G	0.647	0.62
84_K	95_V	0.644	0.62
14_I	73_R	0.640	0.62
84_K	90_H	0.632	0.61
21_K	48_D	0.629	0.60
109_F	118_E	0.626	0.60
8_V	66_N	0.623	0.60
46_I	85_T	0.620	0.59
68_K	100_K	0.615	0.59
23_C	73_R	0.613	0.58
55_R	97_K	0.605	0.57
109_F	117_E	0.604	0.57
112_E	119_E	0.602	0.57
11_I	14_I	0.601	0.57
80_L	85_T	0.597	0.56
112_E	121_V	0.597	0.56
92_S	103_G	0.592	0.56
40_D	45_D	0.589	0.55
40_D	86_L	0.588	0.55
68_K	95_V	0.585	0.55
62_S	67_K	0.580	0.54
71_Y	79_R	0.577	0.54
109_F	112_E	0.577	0.54
33_I	36_P	0.577	0.54
42_S	45_D	0.575	0.54
45_D	54_C	0.573	0.53
67_K	71_Y	0.570	0.53
6_T	65_S	0.570	0.53
108_E	119_E	0.569	0.53
13_L	75_K	0.565	0.52
57_L	70_L	0.565	0.52
84_K	87_A	0.563	0.52
10_I	69_S	0.561	0.52
54_C	74_I	0.556	0.51
12_P	16_S	0.552	0.51
43_D	85_T	0.551	0.51
115_F	120_Q	0.549	0.50
11_I	19_K	0.542	0.49
21_K	97_K	0.541	0.49
109_F	113_E	0.541	0.49
91_K	115_F	0.531	0.48
112_E	120_Q	0.530	0.48
8_V	13_L	0.516	0.46
114_F	118_E	0.515	0.46
89_K	102_L	0.514	0.46
6_T	71_Y	0.512	0.46
24_N	33_I	0.510	0.45
46_I	102_L	0.507	0.45
83_A	95_V	0.505	0.45
40_D	50_F	0.502	0.44
10_I	73_R	0.502	0.44
47_I	73_R	0.500	0.44

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
2w50A	1	0.2286	5.7	0.94	Contact Map
2k4bA	1	0.2786	4.4	0.943	Contact Map
3kk7A	1	0.5571	3.9	0.945	Contact Map
2dulA	2	0.35	3.8	0.945	Contact Map
2x5qA	2	0.4714	3.5	0.946	Contact Map
1gkuB	1	0.5357	3.2	0.947	Contact Map
1rcuA	3	0.3357	3	0.948	Contact Map
3quaA	2	0.3357	2.6	0.95	Contact Map
3kylA	1	0.8357	2.5	0.95	Contact Map
1hsjA	2	0.4143	2.1	0.952	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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