SYF2 - PFAM28P - GREMLIN Contacts

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SYF2 - SYF2 splicing factor

PFAM:	PF08231	Sequences: EAGEDFERKKALDWTAEEAERWDKKKKKKARRADFGFSDYEQAAYRAYKRQLKNLKPDLEAYEKQKEAAGEDKGAFYRTADSLLYGDHKPSKEAVDRLVADLEKQEEKRKKFSRRRKFDDDADVTYINERNKQFNKKLERFYDKYTAEIRQNLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	154 (151)
Sequences:	509 (355)
Seq/√Len:	28.9
META:	0.287

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
139_E	143_D	5.361	1.00
98_L	102_L	4.045	1.00
62_Y	66_K	3.460	1.00
137_K	140_R	2.735	1.00
130_R	140_R	2.466	0.99
101_D	105_Q	2.383	0.99
102_L	148_E	2.294	0.99
107_E	111_K	2.252	0.98
94_A	97_R	2.220	0.98
148_E	152_N	2.211	0.98
129_E	132_K	2.152	0.98
147_A	151_Q	2.032	0.97
90_P	94_A	2.032	0.97
47_A	51_Q	1.879	0.95
37_F	40_Y	1.847	0.95
130_R	138_L	1.841	0.95
91_S	95_V	1.802	0.94
134_F	137_K	1.802	0.94
143_D	150_R	1.757	0.93
58_D	62_Y	1.727	0.93
19_A	23_D	1.726	0.93
98_L	101_D	1.717	0.92
64_K	68_A	1.668	0.91
14_W	22_W	1.637	0.90
96_D	99_V	1.613	0.90
58_D	61_A	1.591	0.89
20_E	141_F	1.582	0.89
47_A	50_R	1.578	0.89
11_A	14_W	1.567	0.88
15_T	18_E	1.493	0.86
105_Q	108_K	1.486	0.85
64_K	67_E	1.457	0.84
77_Y	82_S	1.455	0.84
37_F	142_Y	1.443	0.84
131_N	135_N	1.437	0.83
21_R	24_K	1.432	0.83
91_S	94_A	1.396	0.82
139_E	150_R	1.378	0.81
113_S	116_R	1.372	0.80
95_V	99_V	1.347	0.79
54_N	104_K	1.335	0.79
63_E	67_E	1.330	0.78
45_Y	49_K	1.327	0.78
14_W	18_E	1.313	0.77
9_K	12_L	1.277	0.75
40_Y	142_Y	1.274	0.75
27_K	129_E	1.262	0.74
62_Y	76_F	1.244	0.73
21_R	64_K	1.241	0.73
63_E	66_K	1.231	0.73
51_Q	101_D	1.227	0.72
134_F	140_R	1.213	0.71
39_D	42_Q	1.211	0.71
66_K	71_E	1.200	0.71
60_E	64_K	1.193	0.70
99_V	102_L	1.189	0.70
17_E	25_K	1.177	0.69
34_D	38_S	1.161	0.68
19_A	29_K	1.150	0.67
146_T	149_I	1.118	0.65
78_R	82_S	1.116	0.65
18_E	22_W	1.111	0.65
6_F	9_K	1.106	0.64
95_V	98_L	1.100	0.64
76_F	82_S	1.098	0.64
10_K	18_E	1.097	0.64
138_L	142_Y	1.094	0.63
54_N	68_A	1.093	0.63
113_S	130_R	1.087	0.63
48_Y	127_I	1.086	0.63
10_K	19_A	1.077	0.62
96_D	103_E	1.076	0.62
36_G	152_N	1.075	0.62
102_L	124_V	1.071	0.62
146_T	150_R	1.069	0.62
143_D	146_T	1.067	0.61
16_A	19_A	1.034	0.59
148_E	151_Q	1.022	0.58
44_A	134_F	1.015	0.57
30_A	82_S	0.984	0.55
40_Y	43_A	0.971	0.54
13_D	151_Q	0.968	0.54
43_A	50_R	0.967	0.54
44_A	47_A	0.965	0.54
67_E	100_A	0.944	0.52
124_V	129_E	0.943	0.52
48_Y	90_P	0.937	0.51
103_E	106_E	0.931	0.51
38_S	42_Q	0.927	0.51
83_L	138_L	0.916	0.50
112_F	115_R	0.899	0.48
75_A	83_L	0.895	0.48
95_V	102_L	0.888	0.48
105_Q	109_R	0.880	0.47
118_F	132_K	0.878	0.47
45_Y	152_N	0.877	0.47
34_D	37_F	0.873	0.46
77_Y	86_G	0.866	0.46
64_K	102_L	0.861	0.46
65_Q	69_A	0.858	0.45
129_E	140_R	0.854	0.45
14_W	17_E	0.849	0.45
28_K	49_K	0.848	0.45
24_K	28_K	0.847	0.44
103_E	151_Q	0.836	0.44
37_F	48_Y	0.832	0.43
146_T	154_E	0.829	0.43
2_A	7_E	0.825	0.43
15_T	22_W	0.824	0.43
149_I	154_E	0.821	0.42
32_R	46_R	0.818	0.42
130_R	133_Q	0.815	0.42
19_A	22_W	0.810	0.42
136_K	140_R	0.803	0.41
39_D	50_R	0.802	0.41
11_A	16_A	0.796	0.41
57_P	62_Y	0.790	0.40
125_T	140_R	0.785	0.40
10_K	29_K	0.781	0.39
126_Y	132_K	0.774	0.39
44_A	138_L	0.773	0.39
81_D	89_K	0.771	0.39
39_D	51_Q	0.768	0.38
150_R	154_E	0.767	0.38
105_Q	130_R	0.763	0.38
108_K	152_N	0.763	0.38
59_L	63_E	0.762	0.38
132_K	136_K	0.758	0.38
79_T	148_E	0.757	0.38
12_L	15_T	0.756	0.38
110_K	120_D	0.756	0.38
122_A	150_R	0.748	0.37
46_R	116_R	0.744	0.37
41_E	44_A	0.744	0.37
48_Y	55_L	0.735	0.36
40_Y	51_Q	0.730	0.36
2_A	6_F	0.729	0.36
103_E	107_E	0.728	0.36
148_E	154_E	0.728	0.36
16_A	22_W	0.704	0.34
134_F	146_T	0.702	0.34
39_D	44_A	0.702	0.34
149_I	153_L	0.700	0.34
69_A	82_S	0.700	0.34
35_F	42_Q	0.696	0.33
119_D	134_F	0.693	0.33
145_Y	154_E	0.692	0.33
83_L	86_G	0.691	0.33
138_L	141_F	0.690	0.33
64_K	106_E	0.689	0.33
11_A	18_E	0.689	0.33
59_L	99_V	0.689	0.33
131_N	134_F	0.682	0.32
48_Y	57_P	0.682	0.32
13_D	82_S	0.679	0.32
95_V	142_Y	0.675	0.32
35_F	38_S	0.673	0.32
121_D	136_K	0.668	0.31
144_K	147_A	0.665	0.31
92_K	100_A	0.660	0.31
47_A	129_E	0.659	0.31
47_A	124_V	0.658	0.31
111_K	120_D	0.656	0.31
29_K	58_D	0.653	0.30
27_K	30_A	0.653	0.30
19_A	26_K	0.651	0.30
17_E	145_Y	0.649	0.30
11_A	15_T	0.648	0.30
14_W	23_D	0.646	0.30
94_A	121_D	0.633	0.29
69_A	78_R	0.628	0.29
43_A	126_Y	0.627	0.29
94_A	114_R	0.626	0.29
50_R	54_N	0.623	0.28
58_D	96_D	0.614	0.28
10_K	14_W	0.611	0.28
43_A	47_A	0.609	0.28
100_A	103_E	0.606	0.27
142_Y	145_Y	0.604	0.27
132_K	141_F	0.603	0.27
47_A	106_E	0.602	0.27
61_A	150_R	0.601	0.27
7_E	41_E	0.599	0.27
44_A	48_Y	0.598	0.27
24_K	49_K	0.597	0.27
70_G	76_F	0.595	0.27
41_E	90_P	0.591	0.26
145_Y	149_I	0.587	0.26
33_A	46_R	0.585	0.26
133_Q	138_L	0.584	0.26
24_K	60_E	0.582	0.26
120_D	148_E	0.580	0.26
8_R	12_L	0.578	0.26
63_E	77_Y	0.575	0.26
104_K	132_K	0.574	0.25
16_A	96_D	0.569	0.25
17_E	119_D	0.567	0.25
130_R	136_K	0.553	0.24
66_K	79_T	0.551	0.24
18_E	25_K	0.550	0.24
14_W	153_L	0.550	0.24
47_A	133_Q	0.548	0.24
64_K	148_E	0.543	0.24
15_T	20_E	0.539	0.23
11_A	98_L	0.538	0.23
15_T	29_K	0.535	0.23
133_Q	136_K	0.535	0.23
56_K	80_A	0.529	0.23
127_I	149_I	0.527	0.23
12_L	125_T	0.527	0.23
79_T	100_A	0.526	0.23
93_E	116_R	0.526	0.23
36_G	115_R	0.525	0.23
36_G	140_R	0.525	0.23
131_N	138_L	0.522	0.23
2_A	35_F	0.517	0.22
39_D	134_F	0.516	0.22
30_A	49_K	0.515	0.22
11_A	19_A	0.515	0.22
48_Y	142_Y	0.511	0.22
36_G	39_D	0.510	0.22
115_R	139_E	0.510	0.22
135_N	140_R	0.510	0.22
61_A	91_S	0.509	0.22
13_D	60_E	0.507	0.22
34_D	126_Y	0.500	0.21

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
2xs1A	1	0.8896	2.8	0.954	Contact Map
3tj1A	2	0.1039	1.9	0.958	Contact Map
4zriC	1	0.0974	1.8	0.958	Contact Map
1rzuA	1	0.3442	1.6	0.96	Contact Map
2mjgA	2	0.2987	1.4	0.961	Contact Map
3nuhB	1	0.2078	1.3	0.961	Contact Map
4zrkE	1	0.1169	1.3	0.962	Contact Map
2p58B	1	0	1.2	0.963	Contact Map
3basA	2	0.474	1.1	0.963	Contact Map
2v6eA	2	0.4091	1.1	0.964	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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