PINE - ECOLI - GREMLIN Contacts

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PINE - DNA-invertase from lambdoid prophage e14

UniProt:	P03014	Sequences: MLIGYVRVSTNDQNTDLQRNALNCAGCELIFEDKISGTKSERPGLKKLLRTLSAGDTLVVWKLDRLGRSMRHLVVLVEELRERGINFRSLTDSIDTSTPMGRFFFHVMGALAEMERELIVERTKAGLETARAQGRIGGRRPKLTPEQWAQAGRLIAAGTPRQKVAIIYDVGVSTLYKRFPAGDK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10737
Length:	184 (177)
Sequences:	9418 (6999)
Seq/√Len:	526.1

ECOLI - PINE PINR PINQ YAGL YBCK
BACSU - CISA YOKA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_G	47_K	3.341	1.00
31_F	51_T	3.053	1.00
154_L	167_I	2.934	1.00
33_D	44_G	2.723	1.00
48_L	58_L	2.591	1.00
6_V	19_R	2.360	1.00
19_R	23_N	2.288	1.00
150_Q	154_L	2.249	1.00
102_R	117_E	2.189	1.00
4_G	22_L	2.171	1.00
115_E	122_R	2.058	1.00
129_T	133_Q	2.027	1.00
19_R	32_E	2.027	1.00
38_T	116_R	1.955	1.00
130_A	135_R	1.941	1.00
89_S	92_D	1.921	1.00
162_Q	166_I	1.907	1.00
154_L	159_T	1.873	1.00
70_M	106_H	1.867	1.00
71_R	78_E	1.812	1.00
106_H	110_A	1.805	1.00
20_N	24_C	1.802	1.00
19_R	30_I	1.784	1.00
103_F	114_M	1.776	1.00
120_V	124_K	1.676	1.00
71_R	75_V	1.664	1.00
80_L	85_I	1.652	1.00
113_E	117_E	1.651	1.00
102_R	113_E	1.626	1.00
81_R	102_R	1.563	1.00
73_L	109_G	1.558	1.00
155_I	164_V	1.557	1.00
74_V	106_H	1.557	1.00
52_L	58_L	1.548	1.00
79_E	83_R	1.548	1.00
98_T	101_G	1.534	1.00
165_A	175_L	1.527	1.00
161_R	176_Y	1.521	1.00
77_V	105_F	1.516	1.00
45_L	76_L	1.488	1.00
155_I	179_F	1.469	1.00
52_L	85_I	1.439	1.00
3_I	48_L	1.428	1.00
3_I	51_T	1.426	1.00
159_T	167_I	1.409	1.00
60_V	89_S	1.388	1.00
4_G	30_I	1.379	1.00
116_R	119_I	1.377	1.00
29_L	47_K	1.377	1.00
123_T	127_L	1.374	1.00
103_F	110_A	1.364	1.00
41_E	46_K	1.363	1.00
172_V	176_Y	1.357	1.00
23_N	30_I	1.345	1.00
10_T	13_Q	1.342	1.00
160_P	163_K	1.339	1.00
128_E	132_A	1.337	1.00
67_G	73_L	1.323	1.00
162_Q	172_V	1.315	1.00
153_R	157_A	1.301	1.00
40_S	72_H	1.276	1.00
170_V	175_L	1.263	1.00
64_D	112_A	1.253	1.00
150_Q	167_I	1.248	1.00
116_R	120_V	1.242	1.00
78_E	82_E	1.239	1.00
70_M	74_V	1.227	1.00
57_T	88_R	1.221	1.00
60_V	87_F	1.208	1.00
154_L	164_V	1.200	1.00
129_T	132_A	1.197	1.00
20_N	129_T	1.184	1.00
144_T	147_Q	1.181	1.00
152_G	156_A	1.173	1.00
148_W	152_G	1.152	1.00
159_T	163_K	1.149	1.00
70_M	109_G	1.130	1.00
127_L	137_G	1.125	1.00
47_K	51_T	1.125	1.00
145_P	149_A	1.110	1.00
29_L	51_T	1.109	1.00
151_A	164_V	1.106	1.00
35_I	43_P	1.104	1.00
31_F	44_G	1.100	1.00
126_G	130_A	1.099	1.00
35_I	39_K	1.038	1.00
61_W	125_A	1.038	1.00
6_V	30_I	1.036	1.00
77_V	87_F	1.034	1.00
150_Q	153_R	1.022	1.00
45_L	48_L	1.017	1.00
155_I	161_R	1.012	1.00
154_L	157_A	1.011	1.00
115_E	119_I	1.009	1.00
170_V	178_R	1.005	1.00
17_L	61_W	0.992	1.00
6_V	32_E	0.987	1.00
175_L	178_R	0.975	1.00
21_A	61_W	0.975	1.00
151_A	175_L	0.975	1.00
31_F	48_L	0.961	1.00
86_N	97_S	0.957	1.00
22_L	59_V	0.951	1.00
49_L	79_E	0.950	1.00
57_T	86_N	0.949	1.00
6_V	22_L	0.946	1.00
49_L	76_L	0.944	1.00
171_G	174_T	0.932	1.00
127_L	131_R	0.928	1.00
131_R	137_G	0.920	1.00
64_D	122_R	0.913	1.00
118_L	122_R	0.902	1.00
124_K	127_L	0.900	1.00
63_L	112_A	0.897	1.00
147_Q	150_Q	0.892	1.00
103_F	111_L	0.891	1.00
143_L	146_E	0.887	1.00
6_V	15_T	0.878	1.00
61_W	91_T	0.871	1.00
66_L	76_L	0.870	1.00
119_I	123_T	0.870	1.00
58_L	80_L	0.867	1.00
107_V	110_A	0.865	1.00
114_M	118_L	0.862	1.00
163_K	166_I	0.857	1.00
128_E	131_R	0.837	1.00
53_S	79_E	0.837	1.00
149_A	153_R	0.835	1.00
8_V	13_Q	0.832	1.00
107_V	111_L	0.831	1.00
72_H	75_V	0.830	1.00
165_A	169_D	0.828	1.00
60_V	66_L	0.822	1.00
145_P	148_W	0.819	1.00
75_V	79_E	0.817	1.00
114_M	117_E	0.815	1.00
54_A	84_G	0.815	1.00
17_L	125_A	0.815	1.00
120_V	123_T	0.815	1.00
175_L	179_F	0.806	1.00
21_A	125_A	0.804	1.00
16_D	20_N	0.798	1.00
25_A	59_V	0.795	1.00
15_T	32_E	0.794	1.00
37_G	68_R	0.791	1.00
88_R	95_D	0.791	1.00
151_A	178_R	0.786	1.00
25_A	90_L	0.783	1.00
17_L	129_T	0.781	1.00
148_W	151_A	0.780	1.00
164_V	168_Y	0.779	1.00
161_R	172_V	0.778	1.00
21_A	24_C	0.774	1.00
146_E	150_Q	0.772	1.00
111_L	114_M	0.770	1.00
8_V	34_K	0.768	1.00
121_E	125_A	0.763	1.00
53_S	83_R	0.761	1.00
76_L	80_L	0.756	1.00
106_H	117_E	0.753	1.00
37_G	67_G	0.753	1.00
21_A	91_T	0.753	1.00
173_S	176_Y	0.752	1.00
143_L	147_Q	0.751	1.00
163_K	167_I	0.746	1.00
99_P	121_E	0.743	1.00
17_L	21_A	0.741	1.00
48_L	51_T	0.741	1.00
17_L	62_K	0.739	1.00
32_E	44_G	0.738	1.00
45_L	66_L	0.738	1.00
148_W	178_R	0.736	1.00
173_S	177_K	0.734	1.00
123_T	126_G	0.728	1.00
118_L	121_E	0.727	1.00
48_L	52_L	0.727	1.00
20_N	23_N	0.726	1.00
38_T	120_V	0.721	1.00
144_T	148_W	0.721	1.00
47_K	50_R	0.721	1.00
67_G	76_L	0.716	1.00
25_A	88_R	0.714	1.00
62_K	91_T	0.713	1.00
161_R	179_F	0.707	1.00
69_S	78_E	0.703	1.00
136_I	141_P	0.702	1.00
153_R	156_A	0.701	1.00
147_Q	151_A	0.696	1.00
100_M	103_F	0.689	1.00
3_I	31_F	0.689	1.00
124_K	128_E	0.684	1.00
147_Q	168_Y	0.680	1.00
104_F	108_M	0.680	1.00
70_M	113_E	0.677	1.00
119_I	126_G	0.674	1.00
15_T	34_K	0.670	1.00
103_F	107_V	0.666	1.00
136_I	139_R	0.653	1.00
164_V	175_L	0.651	1.00
171_G	176_Y	0.648	1.00
63_L	89_S	0.645	1.00
86_N	95_D	0.640	1.00
149_A	152_G	0.639	1.00
115_E	118_L	0.638	1.00
73_L	105_F	0.637	1.00
88_R	93_S	0.631	1.00
130_A	137_G	0.630	1.00
103_F	106_H	0.625	1.00
100_M	114_M	0.624	1.00
92_D	108_M	0.616	1.00
152_G	155_I	0.615	1.00
5_Y	33_D	0.613	1.00
151_A	168_Y	0.611	1.00
104_F	111_L	0.611	1.00
127_L	130_A	0.611	1.00
108_M	111_L	0.601	1.00
142_K	146_E	0.597	1.00
170_V	174_T	0.595	0.99
63_L	105_F	0.593	0.99
161_R	165_A	0.589	0.99
27_C	59_V	0.586	0.99
46_K	50_R	0.586	0.99
104_F	107_V	0.586	0.99
69_S	72_H	0.586	0.99
100_M	104_F	0.585	0.99
160_P	166_I	0.584	0.99
79_E	82_E	0.583	0.99
174_T	177_K	0.582	0.99
52_L	80_L	0.580	0.99
3_I	52_L	0.580	0.99
171_G	177_K	0.580	0.99
161_R	175_L	0.572	0.99
59_V	90_L	0.570	0.99
158_G	164_V	0.568	0.99
14_N	34_K	0.563	0.99
71_R	74_V	0.560	0.99
62_K	122_R	0.555	0.99
170_V	176_Y	0.549	0.99
62_K	118_L	0.548	0.99
150_Q	168_Y	0.546	0.99
45_L	49_L	0.543	0.99
70_M	110_A	0.538	0.99
146_E	149_A	0.534	0.99
78_E	81_R	0.534	0.99
75_V	78_E	0.533	0.99
165_A	172_V	0.531	0.99
122_R	125_A	0.531	0.99
164_V	167_I	0.531	0.99
62_K	92_D	0.527	0.99
142_K	147_Q	0.526	0.99
117_E	120_V	0.524	0.99
65_R	68_R	0.522	0.99
125_A	128_E	0.520	0.99
20_N	132_A	0.518	0.99
45_L	72_H	0.517	0.99
125_A	129_T	0.516	0.99
4_G	27_C	0.515	0.99
120_V	127_L	0.513	0.99
165_A	170_V	0.510	0.98
22_L	90_L	0.509	0.98
155_I	175_L	0.507	0.98
99_P	114_M	0.505	0.98
67_G	72_H	0.505	0.98
40_S	45_L	0.504	0.98
127_L	136_I	0.502	0.98
142_K	145_P	0.500	0.98

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
3uj3X	2	0.6739	100	0.113	Contact Map
2r0qC	3	0.962	100	0.13	Contact Map
1gdtA	2	0.9783	100	0.147	Contact Map
4bqqA	2	0.9565	100	0.242	Contact Map
2gm5A	4	0.663	100	0.34	Contact Map
3g13A	2	0.7554	100	0.344	Contact Map
3guvA	2	0.712	100	0.355	Contact Map
3lhkA	2	0.7337	100	0.414	Contact Map
3pkzA	4	0.625	100	0.414	Contact Map
3ilxA	2	0.6902	100	0.442	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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