SPC22 - PFAM28P - GREMLIN Contacts

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SPC22 - Signal peptidase subunit

PFAM:	PF04573	Sequences: VLSRANAVFAFALTVLAVLAALIALSTFFLDRPPGSIPVSNVQVKNVRDFGYSRKKNDLAFLTFDLDADLSPLFNWNTKQLFVYLTAEYETPKNSLNQVVLWDKIITRKEDAKLDLKNVKNKYPFWDQGNGLRGKEVTLTLHWNVMPNVGLLTYGEAAGSSSFTFPEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	168 (166)
Sequences:	550 (397)
Seq/√Len:	30.8
META:	0.255

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_D	115_D	5.778	1.00
144_N	152_L	3.766	1.00
88_E	98_Q	2.958	1.00
65_D	143_W	2.869	1.00
70_L	106_I	2.526	0.99
94_N	128_Q	2.407	0.99
14_T	18_V	2.404	0.99
101_L	125_F	2.269	0.99
109_K	112_A	2.172	0.98
80_Q	105_I	2.113	0.98
81_L	145_V	2.093	0.98
103_D	123_Y	2.040	0.98
74_F	82_F	2.009	0.97
103_D	122_K	1.875	0.96
23_I	27_T	1.850	0.96
67_D	113_K	1.792	0.95
144_N	154_Y	1.787	0.95
64_F	114_L	1.772	0.95
2_L	5_A	1.771	0.95
10_A	20_A	1.756	0.94
152_L	155_G	1.747	0.94
116_L	119_V	1.745	0.94
6_N	10_A	1.684	0.93
63_T	134_G	1.660	0.92
18_V	91_T	1.657	0.92
47_V	50_F	1.648	0.92
90_E	136_E	1.608	0.91
86_T	142_H	1.586	0.90
11_F	15_V	1.575	0.90
62_L	101_L	1.563	0.90
70_L	112_A	1.561	0.90
94_N	129_G	1.546	0.89
147_P	150_G	1.541	0.89
88_E	140_T	1.538	0.89
5_A	9_F	1.537	0.89
113_K	117_K	1.505	0.88
6_N	146_M	1.480	0.87
6_N	16_L	1.474	0.87
98_Q	142_H	1.470	0.87
73_L	78_T	1.458	0.86
46_N	50_F	1.427	0.85
84_Y	147_P	1.420	0.85
132_L	137_V	1.418	0.85
74_F	80_Q	1.409	0.84
27_T	75_N	1.406	0.84
90_E	95_S	1.402	0.84
47_V	59_L	1.396	0.84
143_W	156_E	1.374	0.83
108_R	112_A	1.368	0.82
131_G	135_K	1.357	0.82
20_A	27_T	1.353	0.82
89_Y	99_V	1.352	0.82
37_I	106_I	1.347	0.81
76_W	97_N	1.319	0.80
102_W	147_P	1.291	0.79
3_S	20_A	1.288	0.78
74_F	112_A	1.267	0.77
10_A	13_L	1.262	0.77
63_T	119_V	1.257	0.77
64_F	84_Y	1.252	0.76
108_R	111_D	1.251	0.76
76_W	103_D	1.249	0.76
28_F	92_P	1.244	0.76
127_D	143_W	1.228	0.75
91_T	127_D	1.227	0.75
3_S	58_D	1.222	0.75
85_L	141_L	1.221	0.75
80_Q	146_M	1.204	0.73
58_D	132_L	1.194	0.73
45_K	49_D	1.187	0.72
9_F	15_V	1.178	0.72
80_Q	106_I	1.176	0.72
18_V	25_L	1.172	0.71
73_L	81_L	1.151	0.70
8_V	21_A	1.148	0.70
52_Y	130_N	1.111	0.67
65_D	89_Y	1.106	0.67
83_V	100_V	1.095	0.66
137_V	148_N	1.074	0.65
56_K	160_S	1.074	0.65
90_E	138_T	1.067	0.64
60_A	101_L	1.058	0.63
65_D	117_K	1.042	0.62
46_N	49_D	1.027	0.61
60_A	106_I	1.026	0.61
50_F	99_V	1.001	0.59
65_D	131_G	0.998	0.59
65_D	157_A	0.995	0.59
88_E	96_L	0.993	0.58
74_F	79_K	0.992	0.58
87_A	125_F	0.985	0.58
89_Y	127_D	0.983	0.58
91_T	97_N	0.978	0.57
18_V	22_L	0.971	0.57
88_E	112_A	0.968	0.56
65_D	119_V	0.965	0.56
57_N	126_W	0.945	0.55
86_T	100_V	0.940	0.54
56_K	60_A	0.937	0.54
106_I	161_S	0.927	0.53
104_K	108_R	0.926	0.53
64_F	77_N	0.925	0.53
73_L	79_K	0.921	0.53
28_F	44_V	0.921	0.53
137_V	165_F	0.892	0.50
161_S	164_T	0.880	0.49
140_T	157_A	0.870	0.49
147_P	152_L	0.867	0.48
93_K	134_G	0.863	0.48
73_L	87_A	0.848	0.47
100_V	122_K	0.847	0.47
21_A	111_D	0.837	0.46
37_I	42_V	0.834	0.46
7_A	12_A	0.828	0.45
69_D	113_K	0.828	0.45
100_V	129_G	0.824	0.45
66_L	138_T	0.823	0.45
61_F	121_N	0.821	0.45
36_S	72_P	0.817	0.44
42_V	95_S	0.808	0.44
20_A	23_I	0.801	0.43
113_K	164_T	0.800	0.43
27_T	145_V	0.800	0.43
138_T	158_A	0.784	0.42
22_L	151_L	0.781	0.42
64_F	102_W	0.781	0.42
62_L	80_Q	0.777	0.41
55_K	149_V	0.772	0.41
27_T	89_Y	0.767	0.40
62_L	106_I	0.762	0.40
7_A	131_G	0.759	0.40
20_A	24_A	0.759	0.40
146_M	149_V	0.757	0.40
28_F	162_S	0.751	0.39
78_T	109_K	0.748	0.39
81_L	100_V	0.738	0.38
45_K	54_R	0.733	0.38
46_N	140_T	0.733	0.38
33_P	39_V	0.731	0.38
103_D	132_L	0.730	0.38
47_V	72_P	0.728	0.37
106_I	116_L	0.725	0.37
102_W	144_N	0.716	0.37
9_F	145_V	0.715	0.36
128_Q	149_V	0.713	0.36
138_T	156_E	0.712	0.36
71_S	127_D	0.710	0.36
13_L	27_T	0.709	0.36
5_A	17_A	0.703	0.36
74_F	89_Y	0.702	0.36
72_P	113_K	0.688	0.34
118_N	163_F	0.688	0.34
73_L	105_I	0.686	0.34
99_V	103_D	0.684	0.34
152_L	157_A	0.681	0.34
18_V	40_S	0.681	0.34
75_N	78_T	0.680	0.34
98_Q	158_A	0.677	0.34
10_A	16_L	0.675	0.34
62_L	119_V	0.673	0.33
89_Y	143_W	0.673	0.33
86_T	110_E	0.672	0.33
76_W	127_D	0.672	0.33
142_H	156_E	0.672	0.33
48_R	51_G	0.671	0.33
29_F	138_T	0.669	0.33
67_D	117_K	0.667	0.33
87_A	129_G	0.666	0.33
12_A	15_V	0.665	0.33
70_L	75_N	0.663	0.33
100_V	103_D	0.663	0.33
26_S	76_W	0.663	0.33
126_W	143_W	0.662	0.33
95_S	104_K	0.661	0.33
10_A	145_V	0.660	0.32
44_V	122_K	0.659	0.32
23_I	148_N	0.659	0.32
34_P	114_L	0.658	0.32
16_L	43_Q	0.656	0.32
70_L	84_Y	0.655	0.32
34_P	95_S	0.654	0.32
82_F	102_W	0.646	0.31
27_T	41_N	0.643	0.31
15_V	115_D	0.642	0.31
22_L	106_I	0.640	0.31
52_Y	104_K	0.636	0.31
66_L	86_T	0.635	0.31
139_L	163_F	0.633	0.31
36_S	104_K	0.632	0.31
18_V	21_A	0.630	0.30
11_F	126_W	0.628	0.30
50_F	88_E	0.622	0.30
117_K	158_A	0.617	0.30
78_T	81_L	0.614	0.29
8_V	13_L	0.610	0.29
147_P	166_P	0.608	0.29
12_A	59_L	0.606	0.29
10_A	165_F	0.605	0.29
42_V	129_G	0.604	0.29
79_K	112_A	0.601	0.28
107_T	125_F	0.596	0.28
62_L	93_K	0.595	0.28
5_A	32_R	0.590	0.28
48_R	105_I	0.590	0.28
51_G	58_D	0.589	0.28
106_I	117_K	0.589	0.28
22_L	92_P	0.583	0.27
59_L	121_N	0.581	0.27
40_S	93_K	0.578	0.27
71_S	112_A	0.576	0.27
21_A	54_R	0.572	0.27
48_R	63_T	0.570	0.26
45_K	98_Q	0.568	0.26
132_L	155_G	0.566	0.26
53_S	95_S	0.566	0.26
23_I	79_K	0.566	0.26
139_L	155_G	0.566	0.26
144_N	148_N	0.564	0.26
7_A	21_A	0.564	0.26
17_A	20_A	0.564	0.26
55_K	145_V	0.562	0.26
75_N	145_V	0.562	0.26
127_D	132_L	0.561	0.26
64_F	119_V	0.557	0.26
3_S	18_V	0.557	0.26
10_A	144_N	0.555	0.26
121_N	146_M	0.555	0.26
68_A	116_L	0.553	0.25
8_V	90_E	0.547	0.25
93_K	109_K	0.544	0.25
85_L	144_N	0.542	0.25
82_F	144_N	0.539	0.25
93_K	115_D	0.532	0.24
76_W	123_Y	0.532	0.24
12_A	70_L	0.531	0.24
64_F	68_A	0.530	0.24
123_Y	132_L	0.528	0.24
14_T	22_L	0.527	0.24
33_P	50_F	0.523	0.24
22_L	35_G	0.522	0.24
110_E	158_A	0.515	0.23
24_A	75_N	0.513	0.23
6_N	133_R	0.511	0.23
21_A	35_G	0.510	0.23
154_Y	158_A	0.510	0.23
30_L	67_D	0.507	0.23
10_A	59_L	0.503	0.22
90_E	120_K	0.500	0.22
3_S	27_T	0.500	0.22

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
3zqxA	1	0.4821	3.6	0.96	Contact Map
2mekA	1	0.2738	3	0.962	Contact Map
4kytB	2	0.0179	2.9	0.962	Contact Map
4y3uB	1	0.0179	2.2	0.965	Contact Map
3j45G	1	0.1369	2.2	0.965	Contact Map
4jdzB	1	0.3393	2.2	0.965	Contact Map
2f68X	1	0.3214	2.2	0.965	Contact Map
4qhpA	1	0.6667	2	0.965	Contact Map
1n7lA	1	0.1429	1.9	0.966	Contact Map
2lp1A	1	0.2024	1.8	0.966	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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