LEPS - BACSU - GREMLIN Contacts

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LEPS - Signal peptidase I S

UniProt:	P28628	Sequences: MKSENVSKKKSILEWAKAIVIAVVLALLIRNFIFAPYVVDGDSMYPTLHNRERVFVNMTVKYIGEFDRGDIVVLNGDDVHYVKRIIGLPGDTVEMKNDQLYINGKKVDEPYLAANKKRAKQDGFDHLTDDFGPVKVPDNKYFVMGDNRRNSMDSRNGLGLFTKKQIAGTSKFVFYPFNEMRKTN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	184 (161)
Sequences:	6789 (4625)
Seq/√Len:	364.5

ECOLI - LEP
BACSU - LEPS LEPU LEPT 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
99_Q	106_K	3.581	1.00
141_Y	163_K	3.162	1.00
92_T	133_P	3.034	1.00
91_D	103_N	2.890	1.00
42_D	45_Y	2.797	1.00
94_E	133_P	2.729	1.00
140_K	162_T	2.654	1.00
141_Y	166_I	2.556	1.00
140_K	160_L	2.509	1.00
68_R	88_L	2.416	1.00
72_V	143_V	2.363	1.00
66_F	85_I	2.338	1.00
92_T	135_K	2.246	1.00
57_N	60_V	2.164	1.00
68_R	91_D	2.042	1.00
61_K	66_F	2.024	1.00
45_Y	49_H	1.973	1.00
41_G	50_N	1.925	1.00
43_S	83_K	1.841	1.00
85_I	143_V	1.803	1.00
68_R	102_I	1.790	1.00
30_R	35_A	1.774	1.00
56_V	168_G	1.769	1.00
35_A	58_M	1.754	1.00
57_N	171_K	1.722	1.00
162_T	165_Q	1.719	1.00
22_A	26_A	1.693	1.00
82_V	170_S	1.688	1.00
80_H	167_A	1.674	1.00
136_V	160_L	1.669	1.00
101_Y	106_K	1.658	1.00
83_K	151_S	1.651	1.00
72_V	166_I	1.615	1.00
145_G	151_S	1.614	1.00
48_L	82_V	1.577	1.00
100_L	107_V	1.567	1.00
56_V	73_V	1.525	1.00
13_L	17_K	1.524	1.00
38_V	53_R	1.504	1.00
89_P	141_Y	1.504	1.00
137_P	160_L	1.493	1.00
18_A	22_A	1.487	1.00
158_L	161_F	1.412	1.00
95_M	100_L	1.392	1.00
139_N	163_K	1.387	1.00
136_V	140_K	1.386	1.00
96_K	101_Y	1.372	1.00
36_P	174_F	1.353	1.00
74_L	81_Y	1.351	1.00
70_D	169_T	1.351	1.00
88_L	91_D	1.349	1.00
137_P	140_K	1.265	1.00
152_M	156_N	1.265	1.00
61_K	169_T	1.243	1.00
92_T	104_G	1.223	1.00
42_D	50_N	1.217	1.00
94_E	101_Y	1.214	1.00
52_E	179_E	1.203	1.00
89_P	163_K	1.189	1.00
39_V	48_L	1.183	1.00
93_V	102_I	1.172	1.00
75_N	167_A	1.168	1.00
60_V	64_G	1.166	1.00
52_E	173_V	1.164	1.00
11_S	15_W	1.162	1.00
34_F	171_K	1.151	1.00
75_N	80_H	1.141	1.00
74_L	143_V	1.133	1.00
134_V	160_L	1.096	1.00
83_K	145_G	1.089	1.00
45_Y	50_N	1.087	1.00
39_V	54_V	1.074	1.00
103_N	107_V	1.070	1.00
40_D	50_N	1.063	1.00
91_D	102_I	1.041	1.00
64_G	70_D	1.039	1.00
44_M	71_I	1.036	1.00
65_E	163_K	1.012	1.00
103_N	106_K	1.010	1.00
11_S	14_E	1.001	1.00
43_S	151_S	0.997	1.00
163_K	166_I	0.984	1.00
29_I	33_I	0.980	1.00
54_V	170_S	0.980	1.00
96_K	99_Q	0.978	1.00
113_A	116_K	0.969	1.00
72_V	85_I	0.969	1.00
87_G	93_V	0.960	1.00
53_R	175_Y	0.953	1.00
29_I	34_F	0.944	1.00
109_E	148_R	0.941	1.00
12_I	16_A	0.939	1.00
109_E	112_L	0.931	1.00
100_L	144_M	0.929	1.00
81_Y	158_L	0.907	1.00
30_R	36_P	0.899	1.00
34_F	55_F	0.896	1.00
53_R	174_F	0.895	1.00
43_S	145_G	0.889	1.00
10_K	13_L	0.887	1.00
13_L	16_A	0.871	1.00
54_V	173_V	0.869	1.00
170_S	173_V	0.868	1.00
14_E	18_A	0.863	1.00
129_D	155_R	0.862	1.00
142_F	154_S	0.862	1.00
41_G	158_L	0.861	1.00
15_W	18_A	0.849	1.00
37_Y	56_V	0.848	1.00
46_P	49_H	0.844	1.00
131_F	134_V	0.841	1.00
85_I	88_L	0.840	1.00
89_P	138_D	0.836	1.00
15_W	19_I	0.830	1.00
173_V	179_E	0.811	1.00
37_Y	80_H	0.811	1.00
17_K	21_I	0.794	1.00
41_G	48_L	0.793	1.00
59_T	62_Y	0.789	1.00
42_D	150_N	0.789	1.00
98_D	149_R	0.788	1.00
57_N	62_Y	0.784	1.00
86_I	100_L	0.783	1.00
73_V	80_H	0.778	1.00
33_I	59_T	0.778	1.00
16_A	20_V	0.775	1.00
27_L	31_N	0.771	1.00
69_G	111_Y	0.762	1.00
81_Y	161_F	0.760	1.00
48_L	71_I	0.756	1.00
36_P	53_R	0.750	1.00
127_L	130_D	0.750	1.00
152_M	158_L	0.749	1.00
75_N	165_Q	0.738	1.00
144_M	148_R	0.738	1.00
94_E	104_G	0.736	1.00
139_N	162_T	0.731	1.00
77_D	165_Q	0.727	1.00
45_Y	147_N	0.727	1.00
49_H	176_P	0.721	1.00
71_I	170_S	0.721	1.00
104_G	107_V	0.719	1.00
128_T	156_N	0.718	1.00
39_V	50_N	0.713	0.99
46_P	113_A	0.711	0.99
49_H	52_E	0.709	0.99
49_H	179_E	0.706	0.99
85_I	141_Y	0.705	0.99
40_D	48_L	0.695	0.99
86_I	144_M	0.694	0.99
114_A	117_K	0.689	0.99
107_V	111_Y	0.688	0.99
28_L	32_F	0.685	0.99
154_S	159_G	0.685	0.99
142_F	160_L	0.683	0.99
136_V	139_N	0.680	0.99
87_G	91_D	0.676	0.99
12_I	15_W	0.676	0.99
143_V	161_F	0.671	0.99
57_N	169_T	0.665	0.99
37_Y	173_V	0.665	0.99
19_I	23_V	0.661	0.99
81_Y	152_M	0.661	0.99
37_Y	73_V	0.661	0.99
26_A	30_R	0.659	0.99
93_V	136_V	0.657	0.99
68_R	87_G	0.655	0.99
23_V	27_L	0.653	0.99
176_P	179_E	0.648	0.99
60_V	63_I	0.645	0.99
47_T	71_I	0.638	0.99
73_V	167_A	0.635	0.99
42_D	49_H	0.632	0.99
10_K	14_E	0.632	0.99
40_D	52_E	0.631	0.99
37_Y	54_V	0.629	0.99
147_N	150_N	0.629	0.99
48_L	170_S	0.625	0.99
39_V	82_V	0.625	0.99
103_N	110_P	0.622	0.99
173_V	176_P	0.621	0.99
17_K	20_V	0.621	0.99
25_L	29_I	0.615	0.98
25_L	28_L	0.607	0.98
42_D	147_N	0.606	0.98
128_T	131_F	0.606	0.98
73_V	170_S	0.605	0.98
54_V	82_V	0.604	0.98
126_H	129_D	0.599	0.98
66_F	166_I	0.596	0.98
93_V	142_F	0.593	0.98
74_L	83_K	0.593	0.98
60_V	169_T	0.588	0.98
94_E	132_G	0.588	0.98
10_K	17_K	0.587	0.98
11_S	16_A	0.586	0.98
29_I	32_F	0.585	0.98
113_A	117_K	0.585	0.98
102_I	148_R	0.577	0.98
20_V	24_V	0.575	0.98
19_I	22_A	0.574	0.98
95_M	98_D	0.570	0.97
102_I	107_V	0.569	0.97
64_G	67_D	0.568	0.97
66_F	88_L	0.565	0.97
22_A	25_L	0.565	0.97
74_L	161_F	0.561	0.97
155_R	159_G	0.560	0.97
42_D	51_R	0.560	0.97
67_D	138_D	0.560	0.97
134_V	142_F	0.558	0.97
93_V	144_M	0.558	0.97
21_I	25_L	0.547	0.97
33_I	36_P	0.546	0.97
105_K	138_D	0.543	0.97
71_I	83_K	0.543	0.97
55_F	171_K	0.541	0.97
59_T	63_I	0.539	0.96
163_K	167_A	0.535	0.96
30_R	37_Y	0.530	0.96
114_A	149_R	0.530	0.96
126_H	130_D	0.529	0.96
87_G	102_I	0.528	0.96
67_D	169_T	0.527	0.96
14_E	17_K	0.526	0.96
74_L	158_L	0.526	0.96
112_L	116_K	0.525	0.96
76_G	79_V	0.516	0.96
116_K	149_R	0.515	0.95
41_G	145_G	0.512	0.95
73_V	168_G	0.511	0.95
64_G	169_T	0.509	0.95
130_D	133_P	0.509	0.95
63_I	66_F	0.508	0.95
94_E	131_F	0.508	0.95
18_A	21_I	0.508	0.95
24_V	27_L	0.506	0.95
155_R	161_F	0.506	0.95
37_Y	167_A	0.506	0.95
111_Y	114_A	0.503	0.95
35_A	80_H	0.500	0.95
127_L	131_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	0.837	100	0.22	Contact Map
4nv4A	2	0.6033	100	0.222	Contact Map
4me8A	1	0.5924	100	0.279	Contact Map
4n31A	5	0.7663	100	0.301	Contact Map
4k8wA	2	0.6359	100	0.356	Contact Map
1kcaA	6	0.5109	98.9	0.781	Contact Map
1umuA	2	0.5707	98.6	0.806	Contact Map
3bdnA	2	0.6576	98.4	0.814	Contact Map
2hnfA	1	0.587	97.8	0.842	Contact Map
3k2zA	2	0.6522	97.6	0.849	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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