LEPT - BACSU - GREMLIN Contacts

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LEPT - Signal peptidase I T

UniProt:	P71013	Sequences: MTEEKNTNTEKTAKKKTNTYLEWGKAIVIAVLLALLIRHFLFEPYLVEGSSMYPTLHDGERLFVNKTVNYIGELKRGDIVIINGETSKIHYVKRLIGKPGETVQMKDDTLYINGKKVAEPYLSKNKKEAEKLGVSLTGDFGPVKVPKGKYFVMGDNRLNSMDSRNGLGLIAEDRIVGTSKFVFFPFNEMRQTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	193 (166)
Sequences:	6773 (4618)
Seq/√Len:	358.5

ECOLI - LEP
BACSU - LEPT LEPU 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
109_T	116_K	3.558	1.00
150_Y	172_E	3.126	1.00
102_T	142_P	2.976	1.00
101_E	113_N	2.961	1.00
50_S	53_Y	2.739	1.00
104_Q	142_P	2.704	1.00
149_K	171_A	2.629	1.00
150_Y	175_I	2.550	1.00
76_R	98_K	2.431	1.00
149_K	169_L	2.389	1.00
74_L	95_L	2.344	1.00
80_V	152_V	2.311	1.00
102_T	144_K	2.272	1.00
65_N	68_V	2.148	1.00
76_R	101_E	1.980	1.00
49_G	58_D	1.974	1.00
53_Y	57_H	1.947	1.00
69_N	74_L	1.946	1.00
95_L	152_V	1.844	1.00
76_R	112_I	1.837	1.00
51_S	93_K	1.811	1.00
84_G	91_Y	1.811	1.00
38_R	43_E	1.776	1.00
92_V	179_S	1.764	1.00
43_E	66_K	1.761	1.00
145_V	169_L	1.722	1.00
64_V	177_G	1.717	1.00
111_Y	116_K	1.673	1.00
80_V	175_I	1.665	1.00
171_A	174_R	1.661	1.00
110_L	117_V	1.660	1.00
93_K	160_S	1.659	1.00
65_N	180_K	1.642	1.00
30_A	34_A	1.638	1.00
90_H	176_V	1.623	1.00
154_G	160_S	1.581	1.00
56_L	92_V	1.556	1.00
64_V	81_I	1.518	1.00
21_L	25_K	1.505	1.00
99_P	150_Y	1.504	1.00
146_P	169_L	1.472	1.00
46_L	61_R	1.456	1.00
98_K	101_E	1.383	1.00
145_V	149_K	1.381	1.00
148_G	172_E	1.353	1.00
105_M	110_L	1.347	1.00
26_A	30_A	1.320	1.00
106_K	111_Y	1.319	1.00
44_P	183_F	1.313	1.00
78_D	178_T	1.292	1.00
68_V	72_G	1.285	1.00
47_V	56_L	1.276	1.00
82_I	91_Y	1.275	1.00
167_L	170_I	1.275	1.00
161_M	165_N	1.268	1.00
104_Q	111_Y	1.260	1.00
146_P	149_K	1.249	1.00
60_E	188_E	1.234	1.00
102_T	114_G	1.213	1.00
50_S	58_D	1.210	1.00
103_V	112_I	1.202	1.00
99_P	172_E	1.187	1.00
19_T	23_W	1.182	1.00
60_E	182_V	1.172	1.00
82_I	152_V	1.169	1.00
53_Y	58_D	1.167	1.00
69_N	178_T	1.165	1.00
42_F	180_K	1.152	1.00
143_V	169_L	1.118	1.00
47_V	62_L	1.098	1.00
48_E	58_D	1.093	1.00
83_N	176_V	1.092	1.00
93_K	154_G	1.082	1.00
73_E	172_E	1.079	1.00
52_M	79_I	1.078	1.00
37_I	41_L	1.066	1.00
101_E	112_I	1.065	1.00
83_N	90_H	1.061	1.00
72_G	78_D	1.049	1.00
106_K	109_T	1.029	1.00
16_K	20_Y	1.024	1.00
16_K	19_T	1.010	1.00
62_L	179_S	1.009	1.00
51_S	160_S	1.009	1.00
19_T	22_E	0.999	1.00
80_V	95_L	0.979	1.00
110_L	153_M	0.979	1.00
128_E	164_R	0.967	1.00
119_E	122_L	0.967	1.00
61_R	184_F	0.957	1.00
119_E	157_R	0.950	1.00
151_F	163_S	0.945	1.00
17_T	21_L	0.943	1.00
37_I	42_F	0.934	1.00
20_Y	24_G	0.929	1.00
84_G	167_L	0.920	1.00
172_E	175_I	0.919	1.00
97_G	103_V	0.913	1.00
18_N	21_L	0.908	1.00
179_S	182_V	0.889	1.00
61_R	183_F	0.880	1.00
38_R	44_P	0.877	1.00
42_F	63_F	0.871	1.00
140_F	143_V	0.871	1.00
85_E	174_R	0.867	1.00
113_N	117_V	0.859	1.00
95_L	98_K	0.856	1.00
62_L	182_V	0.855	1.00
45_Y	64_V	0.853	1.00
123_S	126_K	0.852	1.00
23_W	26_A	0.851	1.00
91_Y	167_L	0.842	1.00
51_S	154_G	0.837	1.00
50_S	159_N	0.836	1.00
49_G	167_L	0.833	1.00
113_N	116_K	0.830	1.00
99_P	147_K	0.827	1.00
182_V	188_E	0.825	1.00
49_G	56_L	0.824	1.00
84_G	87_S	0.823	1.00
25_K	29_I	0.819	1.00
45_Y	90_H	0.818	1.00
81_I	90_H	0.816	1.00
54_P	57_H	0.816	1.00
22_E	26_A	0.815	1.00
23_W	27_I	0.806	1.00
108_D	158_L	0.804	1.00
41_L	67_T	0.799	1.00
21_L	24_G	0.794	1.00
77_G	121_Y	0.792	1.00
104_Q	114_G	0.787	1.00
56_L	79_I	0.787	1.00
96_I	110_L	0.777	1.00
65_N	70_Y	0.770	1.00
53_Y	156_N	0.765	1.00
24_G	28_V	0.764	1.00
35_L	39_H	0.757	1.00
153_M	157_R	0.757	1.00
44_P	61_R	0.753	1.00
54_P	123_S	0.748	1.00
87_S	174_R	0.739	1.00
67_T	70_Y	0.739	1.00
95_L	150_Y	0.737	1.00
97_G	101_E	0.735	1.00
48_E	56_L	0.733	1.00
84_G	90_H	0.729	1.00
83_N	174_R	0.728	1.00
79_I	179_S	0.721	0.99
91_Y	161_M	0.714	0.99
148_G	171_A	0.714	0.99
163_S	168_G	0.713	0.99
57_H	188_E	0.711	0.99
48_E	60_E	0.707	0.99
136_L	139_D	0.703	0.99
20_Y	23_W	0.701	0.99
68_V	71_I	0.698	0.99
56_L	179_S	0.695	0.99
36_L	40_F	0.694	0.99
96_I	153_M	0.693	0.99
91_Y	170_I	0.691	0.99
125_N	128_E	0.686	0.99
152_V	170_I	0.686	0.99
137_T	165_N	0.684	0.99
34_A	38_R	0.680	0.99
57_H	185_P	0.679	0.99
161_M	167_L	0.678	0.99
47_V	58_D	0.677	0.99
31_V	35_L	0.675	0.99
114_G	117_V	0.673	0.99
124_K	127_K	0.672	0.99
65_N	178_T	0.672	0.99
103_V	151_F	0.670	0.99
135_S	138_G	0.668	0.99
50_S	57_H	0.662	0.99
47_V	92_V	0.662	0.99
33_L	36_L	0.660	0.99
145_V	148_G	0.659	0.99
182_V	185_P	0.659	0.99
156_N	159_N	0.653	0.99
137_T	140_F	0.652	0.99
45_Y	81_I	0.645	0.99
151_F	169_L	0.644	0.99
57_H	60_E	0.643	0.99
27_I	31_V	0.642	0.99
62_L	92_V	0.641	0.99
103_V	145_V	0.636	0.99
33_L	37_I	0.630	0.99
117_V	121_Y	0.627	0.99
112_I	157_R	0.624	0.99
74_L	98_K	0.623	0.99
68_V	178_T	0.622	0.98
76_R	97_G	0.617	0.98
81_I	176_V	0.616	0.98
72_G	75_K	0.615	0.98
185_P	188_E	0.611	0.98
45_Y	62_L	0.611	0.98
81_I	179_S	0.604	0.98
63_F	180_K	0.602	0.98
74_L	175_I	0.601	0.98
75_K	147_K	0.595	0.98
45_Y	182_V	0.594	0.98
113_N	120_P	0.592	0.98
67_T	71_I	0.590	0.98
82_I	170_I	0.590	0.98
50_S	156_N	0.588	0.98
45_Y	176_V	0.587	0.98
49_G	154_G	0.581	0.98
55_T	79_I	0.580	0.98
112_I	117_V	0.577	0.98
37_I	40_F	0.577	0.98
115_K	147_K	0.577	0.98
18_N	22_E	0.573	0.97
50_S	59_G	0.571	0.97
29_I	33_L	0.568	0.97
123_S	156_N	0.567	0.97
30_A	33_L	0.567	0.97
32_L	35_L	0.561	0.97
17_T	20_Y	0.553	0.97
103_V	153_M	0.552	0.97
121_Y	124_K	0.551	0.97
71_I	74_L	0.546	0.97
53_Y	60_E	0.545	0.97
143_V	151_F	0.541	0.96
77_G	97_G	0.540	0.96
96_I	103_V	0.538	0.96
17_T	25_K	0.538	0.96
28_V	32_L	0.532	0.96
104_Q	140_F	0.532	0.96
27_I	30_A	0.531	0.96
85_E	88_K	0.529	0.96
94_R	155_D	0.527	0.96
104_Q	141_G	0.525	0.96
119_E	123_S	0.524	0.96
172_E	176_V	0.522	0.96
75_K	178_T	0.522	0.96
19_T	24_G	0.522	0.96
38_R	45_Y	0.515	0.95
139_D	142_P	0.515	0.95
81_I	177_G	0.513	0.95
49_G	60_E	0.512	0.95
41_L	44_P	0.510	0.95
82_I	93_K	0.507	0.95
79_I	93_K	0.504	0.95
72_G	178_T	0.503	0.95
22_E	25_K	0.503	0.95
49_G	91_Y	0.501	0.95
126_K	158_L	0.501	0.95
25_K	28_V	0.500	0.94
135_S	139_D	0.500	0.94

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	0.8031	100	0.226	Contact Map
4nv4A	2	0.5751	100	0.231	Contact Map
4me8A	1	0.5699	100	0.281	Contact Map
4n31A	5	0.7306	100	0.314	Contact Map
4k8wA	2	0.6062	100	0.367	Contact Map
1kcaA	6	0.4922	98.9	0.785	Contact Map
1umuA	2	0.544	98.5	0.814	Contact Map
3bdnA	2	0.6736	98.3	0.826	Contact Map
2hnfA	1	0.6062	97.6	0.851	Contact Map
3k2zA	2	0.6632	97.3	0.86	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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