LEPU - BACSU - GREMLIN Contacts

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LEPU - Signal peptidase I U

UniProt:	P42959	Sequences: MNAKTITLKKKRKIKTIVVLSIIMIAALIFTIRLVFYKPFLIEGSSMAPTLKDSERILVDKAVKWTGGFHRGDIIVIHDKKSGRSFVKRLIGLPGDSIKMKNDQLYINDKKVEEPYLKEYKQEVKESGVTLTGDFEVEVPSGKYFVMGDNRLNSLDSRNGMGMPSEDDIIGTESLVFYPFGEMRQAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	187 (165)
Sequences:	6774 (4752)
Seq/√Len:	369.9

ECOLI - LEP
BACSU - LEPU LEPT LEPS LEPV

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
104_Q	111_K	3.661	1.00
144_Y	166_E	3.102	1.00
97_S	136_E	3.083	1.00
96_D	108_N	2.956	1.00
144_Y	169_I	2.732	1.00
45_S	48_A	2.731	1.00
99_K	136_E	2.688	1.00
143_K	165_S	2.655	1.00
71_R	93_L	2.500	1.00
143_K	163_M	2.497	1.00
69_F	90_L	2.396	1.00
60_D	63_V	2.249	1.00
97_S	138_E	2.244	1.00
75_I	146_V	2.237	1.00
48_A	52_K	2.015	1.00
64_K	69_F	1.990	1.00
71_R	96_D	1.939	1.00
46_S	88_K	1.861	1.00
44_G	53_D	1.823	1.00
38_K	61_K	1.809	1.00
33_R	38_K	1.800	1.00
90_L	146_V	1.771	1.00
71_R	107_I	1.765	1.00
139_V	163_M	1.750	1.00
79_D	86_F	1.747	1.00
60_D	174_S	1.734	1.00
87_V	173_E	1.732	1.00
105_L	112_V	1.712	1.00
59_V	171_G	1.701	1.00
25_I	29_I	1.680	1.00
85_S	170_I	1.651	1.00
165_S	168_D	1.642	1.00
75_I	169_I	1.631	1.00
106_Y	111_K	1.623	1.00
88_K	154_S	1.601	1.00
148_G	154_S	1.566	1.00
140_P	163_M	1.563	1.00
59_V	76_V	1.519	1.00
16_T	20_L	1.504	1.00
94_P	144_Y	1.494	1.00
51_L	87_V	1.470	1.00
139_V	143_K	1.460	1.00
21_S	25_I	1.447	1.00
41_L	56_R	1.438	1.00
93_L	96_D	1.421	1.00
100_M	105_L	1.398	1.00
142_G	166_E	1.388	1.00
101_K	106_Y	1.381	1.00
39_P	177_F	1.353	1.00
77_I	86_F	1.308	1.00
73_D	172_T	1.304	1.00
161_M	164_P	1.295	1.00
140_P	143_K	1.290	1.00
155_L	159_N	1.256	1.00
45_S	53_D	1.253	1.00
77_I	146_V	1.243	1.00
99_K	106_Y	1.238	1.00
97_S	109_D	1.227	1.00
42_I	51_L	1.217	1.00
48_A	53_D	1.198	1.00
64_K	172_T	1.189	1.00
55_E	182_E	1.182	1.00
98_I	107_I	1.164	1.00
14_I	18_V	1.158	1.00
55_E	176_V	1.157	1.00
94_P	166_E	1.151	1.00
37_Y	174_S	1.121	1.00
137_V	163_M	1.112	1.00
78_H	85_S	1.107	1.00
108_N	112_V	1.101	1.00
78_H	170_I	1.101	1.00
42_I	57_I	1.093	1.00
108_N	111_K	1.092	1.00
12_R	16_T	1.077	1.00
32_I	36_F	1.076	1.00
68_G	166_E	1.066	1.00
46_S	154_S	1.065	1.00
88_K	148_G	1.059	1.00
96_D	107_I	1.050	1.00
47_M	74_I	1.043	1.00
67_G	73_D	1.039	1.00
43_E	53_D	1.030	1.00
57_I	173_E	1.022	1.00
56_R	178_Y	1.013	1.00
14_I	17_I	1.008	1.00
166_E	169_I	0.979	1.00
15_K	19_V	0.975	1.00
105_L	147_M	0.971	1.00
101_K	104_Q	0.969	1.00
18_V	21_S	0.958	1.00
32_I	37_Y	0.956	1.00
134_D	137_V	0.945	1.00
13_K	16_T	0.945	1.00
75_I	90_L	0.930	1.00
173_E	176_V	0.922	1.00
128_G	133_G	0.921	1.00
37_Y	58_L	0.919	1.00
92_G	98_I	0.911	1.00
46_S	148_G	0.909	1.00
127_S	130_T	0.909	1.00
33_R	39_P	0.893	1.00
56_R	177_F	0.891	1.00
80_K	168_D	0.889	1.00
57_I	176_V	0.881	1.00
145_F	157_S	0.881	1.00
86_F	161_M	0.871	1.00
49_P	52_K	0.868	1.00
49_P	118_K	0.862	1.00
45_S	153_N	0.855	1.00
90_L	93_L	0.855	1.00
114_E	151_R	0.851	1.00
79_D	161_M	0.849	1.00
40_F	85_S	0.849	1.00
76_V	85_S	0.849	1.00
176_V	182_E	0.842	1.00
79_D	82_S	0.841	1.00
44_G	51_L	0.841	1.00
18_V	22_I	0.819	1.00
36_F	62_A	0.814	1.00
132_T	158_R	0.811	1.00
103_D	152_L	0.811	1.00
91_I	105_L	0.807	1.00
62_A	65_W	0.799	1.00
17_I	21_S	0.798	1.00
40_F	59_V	0.797	1.00
99_K	109_D	0.795	1.00
94_P	141_S	0.793	1.00
16_T	19_V	0.792	1.00
72_G	116_Y	0.783	1.00
19_V	23_I	0.781	1.00
51_L	74_I	0.780	1.00
30_F	34_L	0.774	1.00
20_L	24_M	0.771	1.00
39_P	56_R	0.770	1.00
142_G	165_S	0.770	1.00
44_G	161_M	0.766	1.00
109_D	112_V	0.765	1.00
92_G	96_D	0.758	1.00
74_I	173_E	0.754	1.00
63_V	67_G	0.752	1.00
90_L	144_Y	0.745	1.00
157_S	162_G	0.728	1.00
131_L	134_D	0.725	1.00
79_D	83_G	0.723	1.00
26_A	30_F	0.713	1.00
48_A	150_N	0.713	1.00
51_L	173_E	0.709	0.99
146_V	164_P	0.708	0.99
139_V	142_G	0.707	0.99
31_T	35_V	0.705	0.99
86_F	155_L	0.705	0.99
86_F	164_P	0.703	0.99
60_D	172_T	0.703	0.99
147_M	151_R	0.698	0.99
78_H	168_D	0.696	0.99
42_I	53_D	0.696	0.99
79_D	85_S	0.692	0.99
179_P	182_E	0.687	0.99
43_E	51_L	0.681	0.99
57_I	87_V	0.680	0.99
28_L	32_I	0.678	0.99
131_L	159_N	0.674	0.99
91_I	147_M	0.670	0.99
52_K	182_E	0.664	0.99
13_K	17_I	0.664	0.99
25_I	28_L	0.663	0.99
43_E	55_E	0.662	0.99
114_E	117_L	0.660	0.99
176_V	179_P	0.659	0.99
29_I	33_R	0.654	0.99
45_S	150_N	0.648	0.99
69_F	169_I	0.644	0.99
145_F	163_M	0.642	0.99
60_D	65_W	0.638	0.99
40_F	76_V	0.636	0.99
52_K	179_P	0.634	0.99
42_I	87_V	0.633	0.99
40_F	176_V	0.627	0.99
52_K	55_E	0.627	0.99
150_N	153_N	0.625	0.99
128_G	131_L	0.625	0.99
15_K	18_V	0.624	0.99
98_I	139_V	0.622	0.99
118_K	150_N	0.620	0.99
28_L	31_T	0.616	0.99
45_S	52_K	0.613	0.99
58_L	174_S	0.612	0.98
76_V	170_I	0.612	0.98
129_V	132_T	0.609	0.98
22_I	26_A	0.608	0.98
99_K	135_F	0.607	0.98
13_K	20_L	0.601	0.98
155_L	161_M	0.597	0.98
107_I	112_V	0.595	0.98
76_V	173_E	0.592	0.98
100_M	103_D	0.592	0.98
50_T	74_I	0.589	0.98
40_F	57_I	0.589	0.98
118_K	121_K	0.588	0.98
24_M	28_L	0.578	0.98
69_F	93_L	0.578	0.98
71_R	92_G	0.573	0.98
110_K	141_S	0.572	0.98
32_I	35_V	0.569	0.98
98_I	145_F	0.566	0.97
33_R	40_F	0.566	0.97
44_G	55_E	0.565	0.97
44_G	148_G	0.560	0.97
96_D	139_V	0.560	0.97
117_L	120_Y	0.559	0.97
107_I	151_R	0.557	0.97
45_S	54_S	0.555	0.97
63_V	174_S	0.553	0.97
63_V	172_T	0.550	0.97
66_T	69_F	0.549	0.97
82_S	168_D	0.548	0.97
70_H	141_S	0.546	0.97
36_F	39_P	0.544	0.97
27_A	30_F	0.543	0.97
40_F	170_I	0.542	0.97
130_T	133_G	0.542	0.97
127_S	131_L	0.538	0.97
77_I	164_P	0.536	0.97
121_K	152_L	0.534	0.96
115_P	118_K	0.533	0.96
74_I	88_K	0.529	0.96
92_G	107_I	0.529	0.96
21_S	24_M	0.529	0.96
77_I	88_K	0.529	0.96
14_I	19_V	0.527	0.96
80_K	161_M	0.527	0.96
132_T	135_F	0.525	0.96
128_G	137_V	0.524	0.96
133_G	136_E	0.523	0.96
12_R	20_L	0.520	0.96
76_V	171_G	0.518	0.96
99_K	134_D	0.518	0.96
67_G	70_H	0.516	0.96
105_L	151_R	0.516	0.96
40_F	87_V	0.514	0.96
79_D	84_R	0.513	0.96
17_I	20_L	0.512	0.96
70_H	172_T	0.509	0.95
116_Y	119_E	0.506	0.95
100_M	158_R	0.505	0.95
88_K	146_V	0.504	0.95
158_R	164_P	0.501	0.95
44_G	86_F	0.500	0.95

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
1b12A	1	0.8235	100	0.223	Contact Map
4nv4A	2	0.5882	100	0.227	Contact Map
4me8A	1	0.5829	100	0.279	Contact Map
4n31A	5	0.754	100	0.318	Contact Map
4k8wA	2	0.6257	100	0.37	Contact Map
1kcaA	6	0.508	98.9	0.785	Contact Map
1umuA	2	0.5615	98.5	0.815	Contact Map
3bdnA	2	0.6684	98.4	0.82	Contact Map
2hnfA	1	0.5775	97.7	0.848	Contact Map
1jhfA	2	0.6631	97.3	0.859	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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