SPC25 - PFAM28P - GREMLIN Contacts

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SPC25 - Microsomal signal peptidase 25 kDa subunit (SPC25)

PFAM:	PF06703	Sequences: DLKNALDDAVKEYLTSLGFKEDHTLTDVRLALGYIAVAIAAVAFFYDYKLPFPESKPVLIVCVVLYFILNGILTLYTYFVEKGIIFVGKRKDGSGRIPKLTISSSLKKFDPKYTLTITYKDGKSGGKSLEAKELTKSVTKFFDEDGVLVEDLFEKWVAKLIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	162 (161)
Sequences:	653 (496)
Seq/√Len:	39.1
META:	0.262

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_F	148_L	7.074	1.00
104_S	115_L	5.092	1.00
141_F	156_W	3.622	1.00
148_L	153_F	3.613	1.00
114_T	135_T	3.016	1.00
104_S	113_Y	2.690	1.00
23_H	26_T	2.524	1.00
44_F	47_D	2.479	1.00
7_D	113_Y	2.410	1.00
22_D	84_I	2.373	1.00
15_T	86_F	2.322	1.00
13_Y	19_F	2.295	1.00
142_F	153_F	2.160	0.99
143_D	147_V	2.140	0.99
3_K	7_D	2.121	0.99
106_L	138_V	2.118	0.99
8_D	13_Y	2.067	0.99
32_L	69_L	2.049	0.99
35_I	69_L	1.952	0.99
10_V	102_I	1.904	0.98
64_V	68_I	1.902	0.98
51_P	55_S	1.826	0.98
66_Y	70_N	1.749	0.97
14_L	104_S	1.733	0.97
78_Y	82_K	1.728	0.97
103_S	118_T	1.713	0.97
7_D	104_S	1.707	0.97
53_P	62_C	1.672	0.96
38_A	42_V	1.558	0.94
47_D	51_P	1.531	0.94
30_L	34_Y	1.526	0.94
95_G	98_P	1.509	0.93
43_A	59_L	1.507	0.93
36_A	69_L	1.505	0.93
85_I	104_S	1.490	0.93
115_L	157_V	1.477	0.93
52_F	143_D	1.450	0.92
93_G	98_P	1.436	0.91
154_E	158_A	1.418	0.91
47_D	55_S	1.369	0.89
19_F	90_R	1.368	0.89
136_K	156_W	1.346	0.89
45_F	49_K	1.346	0.89
94_S	98_P	1.338	0.88
46_Y	62_C	1.316	0.87
102_I	115_L	1.309	0.87
33_G	70_N	1.279	0.86
19_F	161_I	1.272	0.86
33_G	139_T	1.262	0.85
21_E	75_L	1.241	0.84
47_D	66_Y	1.236	0.84
6_L	113_Y	1.208	0.82
41_A	44_F	1.203	0.82
136_K	140_K	1.202	0.82
14_L	105_S	1.198	0.82
2_L	6_L	1.174	0.81
51_P	54_E	1.162	0.80
28_V	85_I	1.154	0.79
52_F	103_S	1.135	0.78
92_D	98_P	1.120	0.77
46_Y	55_S	1.111	0.77
42_V	80_V	1.096	0.76
52_F	66_Y	1.073	0.74
29_R	47_D	1.058	0.73
53_P	59_L	1.058	0.73
36_A	81_E	1.050	0.73
78_Y	141_F	1.042	0.72
8_D	11_K	1.020	0.70
84_I	99_K	1.018	0.70
127_K	130_E	1.016	0.70
38_A	157_V	1.009	0.69
24_T	28_V	1.008	0.69
22_D	89_K	0.996	0.68
121_D	126_G	0.987	0.68
30_L	142_F	0.986	0.68
50_L	54_E	0.982	0.67
2_L	19_F	0.957	0.65
155_K	159_K	0.956	0.65
92_D	97_I	0.956	0.65
4_N	76_Y	0.955	0.65
65_L	72_I	0.953	0.65
111_P	139_T	0.941	0.64
77_T	153_F	0.928	0.63
3_K	8_D	0.923	0.62
48_Y	56_K	0.913	0.62
71_G	75_L	0.912	0.62
9_A	81_E	0.909	0.61
18_G	117_I	0.901	0.61
10_V	14_L	0.892	0.60
59_L	62_C	0.888	0.59
11_K	29_R	0.885	0.59
18_G	82_K	0.884	0.59
29_R	48_Y	0.872	0.58
32_L	35_I	0.871	0.58
126_G	129_L	0.867	0.58
149_V	152_L	0.866	0.58
84_I	108_K	0.863	0.57
87_V	101_T	0.863	0.57
32_L	72_I	0.861	0.57
135_T	144_E	0.855	0.57
29_R	33_G	0.852	0.56
85_I	153_F	0.850	0.56
46_Y	148_L	0.848	0.56
91_K	154_E	0.848	0.56
131_A	135_T	0.848	0.56
134_L	141_F	0.847	0.56
51_P	62_C	0.838	0.55
45_F	135_T	0.818	0.53
39_I	51_P	0.817	0.53
4_N	8_D	0.806	0.52
69_L	127_K	0.802	0.52
29_R	74_T	0.797	0.51
36_A	63_V	0.794	0.51
107_K	145_D	0.791	0.51
44_F	62_C	0.779	0.50
38_A	83_G	0.773	0.49
68_I	120_K	0.772	0.49
88_G	100_L	0.770	0.49
106_L	110_D	0.767	0.49
85_I	113_Y	0.766	0.49
19_F	86_F	0.758	0.48
33_G	66_Y	0.756	0.48
133_E	157_V	0.756	0.48
46_Y	67_F	0.755	0.48
46_Y	156_W	0.755	0.48
60_I	85_I	0.750	0.47
133_E	155_K	0.744	0.47
28_V	72_I	0.742	0.46
6_L	50_L	0.736	0.46
7_D	69_L	0.734	0.46
74_T	85_I	0.726	0.45
12_E	16_S	0.725	0.45
101_T	118_T	0.722	0.45
4_N	70_N	0.719	0.44
53_P	106_L	0.716	0.44
87_V	99_K	0.716	0.44
57_P	61_V	0.715	0.44
155_K	161_I	0.714	0.44
70_N	77_T	0.713	0.44
27_D	63_V	0.713	0.44
26_T	31_A	0.706	0.43
97_I	129_L	0.705	0.43
8_D	136_K	0.705	0.43
25_L	47_D	0.699	0.42
2_L	138_V	0.699	0.42
90_R	101_T	0.699	0.42
36_A	70_N	0.697	0.42
32_L	141_F	0.696	0.42
75_L	79_F	0.696	0.42
26_T	33_G	0.695	0.42
114_T	133_E	0.694	0.42
36_A	60_I	0.693	0.42
39_I	65_L	0.690	0.42
41_A	151_D	0.690	0.42
74_T	81_E	0.687	0.41
78_Y	140_K	0.686	0.41
134_L	159_K	0.678	0.41
3_K	85_I	0.676	0.40
90_R	121_D	0.674	0.40
49_K	61_V	0.674	0.40
59_L	148_L	0.659	0.39
55_S	70_N	0.654	0.39
29_R	81_E	0.653	0.38
32_L	136_K	0.647	0.38
33_G	40_A	0.646	0.38
17_L	154_E	0.643	0.38
143_D	156_W	0.638	0.37
1_D	5_A	0.631	0.37
6_L	106_L	0.626	0.36
23_H	30_L	0.625	0.36
23_H	28_V	0.619	0.36
66_Y	108_K	0.619	0.36
61_V	140_K	0.618	0.36
112_K	135_T	0.615	0.35
49_K	92_D	0.613	0.35
88_G	99_K	0.613	0.35
93_G	97_I	0.613	0.35
143_D	149_V	0.611	0.35
15_T	141_F	0.607	0.35
13_Y	157_V	0.606	0.35
66_Y	100_L	0.602	0.34
43_A	81_E	0.601	0.34
54_E	155_K	0.598	0.34
32_L	80_V	0.598	0.34
1_D	21_E	0.595	0.34
27_D	73_L	0.593	0.33
47_D	108_K	0.592	0.33
1_D	4_N	0.591	0.33
45_F	102_I	0.590	0.33
35_I	123_K	0.590	0.33
68_I	72_I	0.586	0.33
12_E	119_Y	0.585	0.33
35_I	145_D	0.570	0.32
34_Y	161_I	0.569	0.32
2_L	110_D	0.568	0.31
60_I	64_V	0.568	0.31
8_D	101_T	0.562	0.31
152_L	155_K	0.559	0.31
140_K	152_L	0.559	0.31
2_L	154_E	0.559	0.31
85_I	102_I	0.558	0.31
29_R	149_V	0.556	0.31
86_F	157_V	0.554	0.30
102_I	116_T	0.551	0.30
124_S	155_K	0.550	0.30
70_N	74_T	0.548	0.30
27_D	56_K	0.548	0.30
86_F	90_R	0.545	0.30
32_L	96_R	0.544	0.30
6_L	153_F	0.544	0.30
15_T	21_E	0.543	0.30
46_Y	160_L	0.542	0.29
101_T	148_L	0.541	0.29
89_K	149_V	0.540	0.29
37_V	83_G	0.540	0.29
36_A	108_K	0.539	0.29
79_F	125_G	0.538	0.29
90_R	100_L	0.537	0.29
82_K	115_L	0.536	0.29
153_F	158_A	0.535	0.29
2_L	95_G	0.530	0.29
57_P	91_K	0.529	0.29
150_E	154_E	0.528	0.28
24_T	118_T	0.528	0.28
71_G	74_T	0.525	0.28
116_T	147_V	0.523	0.28
111_P	137_S	0.523	0.28
18_G	72_I	0.523	0.28
29_R	141_F	0.523	0.28
38_A	140_K	0.518	0.28
17_L	64_V	0.515	0.27
52_F	156_W	0.515	0.27
92_D	153_F	0.514	0.27
6_L	10_V	0.512	0.27
70_N	83_G	0.511	0.27
9_A	42_V	0.511	0.27
37_V	102_I	0.510	0.27
19_F	157_V	0.509	0.27
127_K	131_A	0.507	0.27
57_P	67_F	0.504	0.27
2_L	33_G	0.500	0.26
93_G	96_R	0.500	0.26

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
4e17B	1	0.0926	10	0.933	Contact Map
4ev6A	3	0.4938	7.1	0.938	Contact Map
4i0uA	4	0.4815	6.6	0.939	Contact Map
4oe7A	3	0.2099	4.3	0.944	Contact Map
1oedB	1	0.1543	4.2	0.944	Contact Map
1oedA	1	0.1543	3.8	0.945	Contact Map
4akrA	1	0.9012	3.5	0.946	Contact Map
1t6cA	1	0.3889	3.3	0.947	Contact Map
3si9A	3	0.2099	3	0.948	Contact Map
4ge1A	1	0.3086	3	0.948	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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