TIP41 - PFAM28P - GREMLIN Contacts

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TIP41 - TIP41-like family

PFAM:	PF04176	Sequences: MIFGDNSLRLEHEPSGWKIEFNALDALKRVDKTGLPKVAYAEEWKKSREDSKEVVKPYDWTYTTDYKGTLEGLKWEPTDERIPLEKLKRRDPILFYDEVVLYEDELADNGISMLSVKIRVMPSCFFLLLRFFLRVDGVLVRIRDTRVYHEFGTNYVLREYTAREATYEELK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (170)
Sequences:	543 (371)
Seq/√Len:	28.4
META:	0.221

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_N	25_D	4.929	1.00
104_D	107_A	4.653	1.00
12_H	15_S	4.033	1.00
85_E	88_K	3.886	1.00
29_R	65_D	3.654	1.00
114_L	129_L	3.587	1.00
165_A	169_E	3.390	1.00
86_K	148_Y	3.004	1.00
140_V	170_L	2.897	1.00
25_D	69_T	2.873	1.00
12_H	16_G	2.735	1.00
91_D	123_S	2.722	1.00
98_E	115_S	2.575	0.99
78_T	157_L	2.486	0.99
97_D	117_K	2.325	0.99
86_K	150_E	2.304	0.99
10_L	127_L	2.223	0.98
124_C	148_Y	2.157	0.98
9_R	20_E	2.132	0.98
125_F	149_H	2.099	0.97
141_R	164_E	2.084	0.97
24_L	61_T	2.050	0.97
143_R	162_A	1.973	0.96
87_L	93_I	1.901	0.95
11_E	18_K	1.869	0.95
4_G	167_Y	1.714	0.92
83_P	150_E	1.666	0.91
98_E	116_V	1.635	0.90
37_K	45_K	1.622	0.90
40_Y	137_G	1.580	0.88
31_D	34_G	1.553	0.87
63_T	139_L	1.550	0.87
24_L	41_A	1.541	0.87
107_A	112_S	1.438	0.83
64_T	102_Y	1.427	0.82
67_K	158_R	1.393	0.81
116_V	129_L	1.389	0.81
104_D	167_Y	1.379	0.80
40_Y	109_N	1.366	0.80
8_L	125_F	1.304	0.76
94_L	151_F	1.303	0.76
108_D	136_D	1.286	0.75
39_A	112_S	1.269	0.74
166_T	169_E	1.263	0.74
97_D	100_V	1.259	0.74
67_K	160_Y	1.210	0.71
19_I	147_V	1.199	0.70
29_R	64_T	1.194	0.70
43_E	46_K	1.190	0.69
108_D	134_R	1.169	0.68
86_K	89_R	1.147	0.66
141_R	145_T	1.143	0.66
102_Y	120_V	1.138	0.66
80_E	157_L	1.137	0.66
22_N	111_I	1.129	0.65
64_T	114_L	1.128	0.65
126_F	144_D	1.121	0.65
76_E	79_D	1.117	0.64
44_W	48_R	1.102	0.63
143_R	160_Y	1.102	0.63
72_G	77_P	1.102	0.63
66_Y	69_T	1.086	0.62
22_N	69_T	1.078	0.62
30_V	57_P	1.056	0.60
75_W	78_T	1.046	0.59
78_T	81_R	1.039	0.59
119_R	146_R	1.030	0.58
40_Y	126_F	1.030	0.58
135_V	163_R	1.027	0.58
3_F	62_Y	1.020	0.57
24_L	169_E	1.011	0.57
82_I	144_D	1.006	0.56
30_V	33_T	0.996	0.55
80_E	155_Y	0.987	0.55
96_Y	117_K	0.974	0.54
105_E	133_L	0.964	0.53
8_L	12_H	0.961	0.53
2_I	23_A	0.950	0.52
74_K	77_P	0.947	0.52
19_I	102_Y	0.945	0.51
102_Y	141_R	0.944	0.51
153_T	170_L	0.938	0.51
5_D	62_Y	0.936	0.51
114_L	140_V	0.934	0.51
37_K	133_L	0.921	0.50
89_R	92_P	0.917	0.49
53_E	137_G	0.900	0.48
107_A	138_V	0.898	0.48
23_A	137_G	0.898	0.48
82_I	157_L	0.883	0.47
30_V	41_A	0.879	0.46
93_I	121_M	0.877	0.46
9_R	18_K	0.876	0.46
61_T	135_V	0.875	0.46
86_K	132_F	0.874	0.46
16_G	157_L	0.870	0.46
77_P	80_E	0.866	0.45
144_D	148_Y	0.862	0.45
64_T	94_L	0.853	0.44
40_Y	47_S	0.851	0.44
61_T	86_K	0.830	0.43
3_F	103_E	0.823	0.42
97_D	107_A	0.822	0.42
125_F	155_Y	0.822	0.42
40_Y	83_P	0.812	0.41
110_G	134_R	0.811	0.41
85_E	115_S	0.811	0.41
105_E	138_V	0.807	0.41
118_I	131_F	0.805	0.41
84_L	144_D	0.805	0.41
31_D	129_L	0.801	0.40
42_E	46_K	0.800	0.40
111_I	132_F	0.798	0.40
41_A	90_R	0.796	0.40
98_E	117_K	0.795	0.40
120_V	151_F	0.792	0.40
39_A	138_V	0.792	0.40
62_Y	83_P	0.787	0.39
37_K	142_I	0.786	0.39
139_L	142_I	0.784	0.39
97_D	132_F	0.778	0.39
88_K	163_R	0.776	0.39
109_N	138_V	0.773	0.38
97_D	163_R	0.772	0.38
84_L	148_Y	0.761	0.38
84_L	123_S	0.757	0.37
72_G	139_L	0.757	0.37
48_R	57_P	0.755	0.37
103_E	138_V	0.751	0.37
7_S	19_I	0.750	0.37
43_E	121_M	0.749	0.37
104_D	125_F	0.748	0.37
45_K	125_F	0.743	0.36
48_R	151_F	0.742	0.36
163_R	166_T	0.742	0.36
65_D	143_R	0.739	0.36
19_I	24_L	0.736	0.36
8_L	112_S	0.735	0.36
140_V	167_Y	0.732	0.35
105_E	109_N	0.731	0.35
5_D	12_H	0.730	0.35
87_L	119_R	0.729	0.35
40_Y	147_V	0.724	0.35
27_L	30_V	0.717	0.34
20_E	25_D	0.715	0.34
102_Y	151_F	0.714	0.34
73_L	79_D	0.709	0.34
103_E	108_D	0.708	0.34
104_D	110_G	0.708	0.34
155_Y	166_T	0.707	0.34
47_S	151_F	0.698	0.33
87_L	146_R	0.696	0.33
74_K	80_E	0.690	0.33
149_H	152_G	0.690	0.33
87_L	121_M	0.688	0.32
105_E	108_D	0.682	0.32
29_R	58_Y	0.680	0.32
63_T	141_R	0.675	0.32
112_S	131_F	0.673	0.31
8_L	129_L	0.673	0.31
32_K	156_V	0.672	0.31
162_A	170_L	0.671	0.31
28_K	32_K	0.671	0.31
103_E	106_L	0.671	0.31
129_L	170_L	0.670	0.31
125_F	167_Y	0.669	0.31
102_Y	116_V	0.668	0.31
95_F	132_F	0.666	0.31
124_C	149_H	0.664	0.31
92_P	109_N	0.653	0.30
50_D	129_L	0.643	0.29
30_V	34_G	0.642	0.29
110_G	136_D	0.641	0.29
62_Y	148_Y	0.639	0.29
147_V	156_V	0.638	0.29
132_F	145_T	0.630	0.29
75_W	80_E	0.629	0.29
65_D	162_A	0.623	0.28
106_L	133_L	0.623	0.28
70_L	137_G	0.617	0.28
38_V	138_V	0.617	0.28
70_L	75_W	0.616	0.28
148_Y	153_T	0.615	0.28
6_N	56_K	0.615	0.28
132_F	142_I	0.614	0.28
63_T	162_A	0.614	0.28
99_V	116_V	0.612	0.27
11_E	99_V	0.612	0.27
99_V	118_I	0.611	0.27
14_P	55_V	0.608	0.27
154_N	168_E	0.604	0.27
44_W	108_D	0.603	0.27
12_H	72_G	0.603	0.27
75_W	79_D	0.603	0.27
18_K	42_E	0.602	0.27
83_P	88_K	0.601	0.27
1_M	105_E	0.599	0.27
58_Y	97_D	0.599	0.27
139_L	164_E	0.598	0.27
26_A	38_V	0.597	0.27
4_G	58_Y	0.592	0.26
25_D	142_I	0.592	0.26
102_Y	143_R	0.591	0.26
101_L	141_R	0.590	0.26
75_W	156_V	0.589	0.26
99_V	157_L	0.584	0.26
23_A	113_M	0.583	0.26
71_E	147_V	0.582	0.26
42_E	76_E	0.579	0.25
4_G	99_V	0.578	0.25
34_G	102_Y	0.575	0.25
99_V	127_L	0.572	0.25
86_K	156_V	0.571	0.25
130_R	144_D	0.570	0.25
81_R	112_S	0.568	0.25
70_L	147_V	0.567	0.25
8_L	100_V	0.567	0.25
38_V	141_R	0.566	0.25
153_T	156_V	0.565	0.25
98_E	118_I	0.561	0.24
48_R	95_F	0.560	0.24
132_F	170_L	0.557	0.24
18_K	152_G	0.557	0.24
65_D	160_Y	0.551	0.24
4_G	151_F	0.549	0.24
73_L	102_Y	0.549	0.24
43_E	48_R	0.547	0.24
149_H	153_T	0.542	0.23
45_K	116_V	0.541	0.23
67_K	80_E	0.539	0.23
51_S	55_V	0.534	0.23
103_E	134_R	0.534	0.23
16_G	46_K	0.533	0.23
81_R	152_G	0.533	0.23
45_K	163_R	0.529	0.23
70_L	78_T	0.524	0.22
48_R	82_I	0.524	0.22
117_K	123_S	0.524	0.22
96_Y	153_T	0.523	0.22
61_T	116_V	0.522	0.22
30_V	105_E	0.521	0.22
41_A	96_Y	0.518	0.22
3_F	16_G	0.518	0.22
77_P	168_E	0.515	0.22
117_K	146_R	0.513	0.22
24_L	98_E	0.510	0.22
83_P	149_H	0.509	0.22
31_D	114_L	0.508	0.22
94_L	98_E	0.505	0.21
40_Y	107_A	0.504	0.21
83_P	91_D	0.502	0.21
81_R	117_K	0.502	0.21
161_T	166_T	0.502	0.21
114_L	131_F	0.501	0.21
126_F	149_H	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
4rydA	4	0.4561	4.1	0.969	Contact Map
3wbzA	5	0.3509	3.5	0.97	Contact Map
2kvkA	1	0.2807	3.3	0.97	Contact Map
2gibA	3	0.3216	3.1	0.971	Contact Map
4kgmA	5	0.3158	2.9	0.971	Contact Map
1t3yA	1	0.2398	2.9	0.971	Contact Map
1sr4A	1	0.3333	2.8	0.971	Contact Map
1sa3A	1	0.4035	2.8	0.971	Contact Map
4cknA	2	0.3801	2.8	0.971	Contact Map
3pimA	2	0.3392	2.7	0.971	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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