YECM - ECOLI - GREMLIN Contacts

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YECM - Protein YecM

UniProt:	P52007	Sequences: MANWQSIDELQDIASDLPRFIHALDELSRRLGLNITPLTADHISLRCHQNATAERWRRGFEQCGELLSENMINGRPICLFKLHEPVQVAHWQFSIVELPWPGEKRYPHEGWEHIEIVLPGDPETLNARALALLSDEGLSLPGISVKTSSPKGEHERLPNPTLAVTDGKTTIKFHPWSIEEIVASEQSA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13405
Length:	188 (177)
Sequences:	256 (170)
Seq/√Len:	12.7

ECOLI - YECM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_K	179_E	7.711	1.00
52_T	109_E	3.669	0.99
27_L	169_T	3.602	0.99
66_L	69_E	3.533	0.99
69_E	78_C	3.404	0.98
180_E	183_A	2.934	0.96
95_I	116_I	2.880	0.95
57_R	69_E	2.781	0.94
40_A	116_I	2.702	0.93
30_R	166_D	2.455	0.90
61_E	66_L	2.383	0.88
27_L	94_S	2.341	0.87
57_R	78_C	2.321	0.87
70_N	154_H	2.188	0.83
72_I	152_G	2.173	0.83
65_E	81_K	2.018	0.78
51_A	54_E	2.007	0.77
10_L	59_G	1.957	0.75
171_I	179_E	1.903	0.73
40_A	91_W	1.871	0.72
110_G	181_I	1.803	0.69
40_A	114_I	1.765	0.67
152_G	156_R	1.744	0.66
57_R	66_L	1.733	0.66
149_S	171_I	1.732	0.66
51_A	87_Q	1.714	0.65
35_I	38_L	1.641	0.61
107_P	119_P	1.625	0.61
47_C	80_F	1.588	0.59
22_H	37_P	1.559	0.57
71_M	180_E	1.431	0.51
120_G	131_A	1.419	0.50
43_I	88_V	1.388	0.48
29_R	87_Q	1.368	0.47
57_R	100_W	1.368	0.47
34_N	62_Q	1.357	0.47
17_L	142_G	1.351	0.47
34_N	37_P	1.312	0.45
66_L	88_V	1.289	0.43
93_F	171_I	1.286	0.43
150_P	161_T	1.284	0.43
59_G	62_Q	1.283	0.43
62_Q	167_G	1.279	0.43
87_Q	90_H	1.272	0.43
127_A	143_I	1.271	0.42
56_W	128_R	1.269	0.42
49_Q	182_V	1.264	0.42
121_D	135_D	1.262	0.42
64_G	80_F	1.252	0.42
82_L	96_V	1.240	0.41
102_G	182_V	1.237	0.41
56_W	79_L	1.232	0.41
29_R	89_A	1.226	0.40
124_T	127_A	1.219	0.40
51_A	135_D	1.217	0.40
95_I	107_P	1.217	0.40
33_L	89_A	1.209	0.39
150_P	155_E	1.198	0.39
87_Q	92_Q	1.191	0.38
44_S	107_P	1.187	0.38
150_P	163_A	1.183	0.38
47_C	56_W	1.160	0.37
156_R	184_S	1.158	0.37
67_L	95_I	1.141	0.36
42_H	46_R	1.119	0.35
38_L	63_C	1.117	0.35
106_Y	163_A	1.113	0.35
82_L	94_S	1.108	0.35
95_I	100_W	1.106	0.34
162_L	170_T	1.106	0.34
69_E	136_E	1.094	0.34
48_H	170_T	1.085	0.33
104_K	150_P	1.072	0.33
46_R	112_E	1.064	0.32
114_I	171_I	1.060	0.32
66_L	78_C	1.047	0.32
42_H	112_E	1.045	0.32
40_A	67_L	1.042	0.31
84_E	92_Q	1.034	0.31
10_L	96_V	1.023	0.31
58_R	105_R	1.020	0.31
105_R	141_P	1.019	0.30
61_E	69_E	1.015	0.30
129_A	162_L	1.014	0.30
38_L	137_G	1.013	0.30
16_D	19_R	0.974	0.29
123_E	151_K	0.971	0.28
50_N	54_E	0.963	0.28
29_R	153_E	0.962	0.28
69_E	114_I	0.954	0.28
29_R	121_D	0.945	0.27
60_F	82_L	0.944	0.27
79_L	178_I	0.939	0.27
102_G	128_R	0.935	0.27
29_R	61_E	0.931	0.27
91_W	114_I	0.925	0.27
132_L	181_I	0.912	0.26
47_C	166_D	0.907	0.26
101_P	115_E	0.907	0.26
36_T	83_H	0.897	0.25
85_P	157_L	0.897	0.25
32_G	110_G	0.896	0.25
93_F	114_I	0.896	0.25
78_C	173_F	0.893	0.25
84_E	124_T	0.891	0.25
83_H	183_A	0.887	0.25
94_S	179_E	0.880	0.25
29_R	36_T	0.877	0.25
12_D	59_G	0.873	0.24
11_Q	19_R	0.869	0.24
136_E	139_S	0.868	0.24
48_H	106_Y	0.859	0.24
148_S	163_A	0.854	0.24
67_L	132_L	0.854	0.24
34_N	127_A	0.854	0.24
38_L	181_I	0.853	0.24
46_R	115_E	0.852	0.24
15_S	84_E	0.845	0.23
65_E	87_Q	0.844	0.23
90_H	126_N	0.839	0.23
118_L	162_L	0.839	0.23
128_R	164_V	0.839	0.23
122_P	164_V	0.838	0.23
42_H	115_E	0.836	0.23
47_C	125_L	0.832	0.23
106_Y	150_P	0.830	0.23
60_F	79_L	0.828	0.23
46_R	172_K	0.825	0.23
57_R	178_I	0.822	0.23
25_D	62_Q	0.819	0.22
30_R	136_E	0.814	0.22
42_H	172_K	0.807	0.22
25_D	34_N	0.804	0.22
69_E	80_F	0.804	0.22
95_I	147_T	0.798	0.22
27_L	64_G	0.797	0.22
43_I	93_F	0.793	0.22
14_A	63_C	0.786	0.21
157_L	160_P	0.784	0.21
73_N	148_S	0.782	0.21
29_R	90_H	0.774	0.21
112_E	115_E	0.772	0.21
49_Q	109_E	0.770	0.21
28_S	142_G	0.769	0.21
100_W	176_W	0.765	0.21
25_D	134_S	0.764	0.21
47_C	130_L	0.762	0.20
26_E	37_P	0.756	0.20
15_S	136_E	0.755	0.20
56_W	182_V	0.751	0.20
50_N	105_R	0.751	0.20
112_E	172_K	0.744	0.20
71_M	178_I	0.744	0.20
71_M	140_L	0.742	0.20
53_A	148_S	0.742	0.20
86_V	165_T	0.741	0.20
165_T	183_A	0.740	0.20
11_Q	169_T	0.739	0.20
53_A	106_Y	0.736	0.20
28_S	171_I	0.734	0.20
55_R	59_G	0.733	0.20
93_F	158_P	0.724	0.19
107_P	176_W	0.720	0.19
146_K	150_P	0.720	0.19
104_K	163_A	0.720	0.19
44_S	148_S	0.720	0.19
70_N	183_A	0.716	0.19
56_W	89_A	0.716	0.19
17_L	53_A	0.712	0.19
18_P	171_I	0.709	0.19
125_L	128_R	0.702	0.19
17_L	79_L	0.700	0.18
142_G	178_I	0.698	0.18
105_R	118_L	0.694	0.18
127_A	183_A	0.687	0.18
44_S	53_A	0.675	0.18
130_L	182_V	0.675	0.18
53_A	111_W	0.670	0.18
96_V	105_R	0.669	0.18
96_V	185_E	0.668	0.17
16_D	62_Q	0.666	0.17
24_L	80_F	0.665	0.17
41_D	97_E	0.664	0.17
97_E	113_H	0.664	0.17
41_D	113_H	0.664	0.17
41_D	75_R	0.664	0.17
75_R	97_E	0.664	0.17
75_R	113_H	0.664	0.17
143_I	177_S	0.663	0.17
127_A	180_E	0.661	0.17
73_N	104_K	0.658	0.17
86_V	119_P	0.653	0.17
120_G	128_R	0.648	0.17
32_G	144_S	0.641	0.17
158_P	165_T	0.640	0.17
106_Y	111_W	0.639	0.17
20_F	73_N	0.638	0.17
32_G	36_T	0.637	0.17
141_P	145_V	0.630	0.16
98_L	145_V	0.628	0.16
126_N	147_T	0.627	0.16
96_V	116_I	0.623	0.16
111_W	175_P	0.619	0.16
77_I	144_S	0.617	0.16
35_I	86_V	0.612	0.16
157_L	163_A	0.608	0.16
111_W	161_T	0.608	0.16
146_K	155_E	0.607	0.16
56_W	165_T	0.607	0.16
17_L	158_P	0.603	0.16
44_S	139_S	0.601	0.16
161_T	184_S	0.599	0.16
106_Y	184_S	0.599	0.16
67_L	182_V	0.598	0.15
16_D	28_S	0.598	0.15
29_R	114_I	0.598	0.15
163_A	184_S	0.596	0.15
36_T	92_Q	0.594	0.15
13_I	129_A	0.593	0.15
153_E	156_R	0.593	0.15
60_F	93_F	0.589	0.15
64_G	118_L	0.589	0.15
29_R	50_N	0.586	0.15
51_A	80_F	0.580	0.15
65_E	84_E	0.579	0.15
14_A	88_V	0.578	0.15
134_S	141_P	0.576	0.15
19_R	121_D	0.576	0.15
20_F	146_K	0.575	0.15
68_S	146_K	0.574	0.15
18_P	63_C	0.573	0.15
135_D	158_P	0.573	0.15
78_C	100_W	0.572	0.15
62_Q	151_K	0.569	0.15
34_N	50_N	0.564	0.15
136_E	140_L	0.563	0.15
22_H	32_G	0.561	0.15
26_E	114_I	0.553	0.14
57_R	171_I	0.549	0.14
95_I	176_W	0.548	0.14
30_R	85_P	0.546	0.14
115_E	172_K	0.546	0.14
62_Q	65_E	0.541	0.14
34_N	59_G	0.540	0.14
133_L	136_E	0.539	0.14
29_R	119_P	0.538	0.14
52_T	130_L	0.536	0.14
31_L	161_T	0.534	0.14
103_E	141_P	0.531	0.14
33_L	65_E	0.525	0.14
106_Y	109_E	0.520	0.13
94_S	116_I	0.519	0.13
148_S	159_N	0.518	0.13
45_L	52_T	0.516	0.13
19_R	135_D	0.515	0.13
53_A	170_T	0.512	0.13
35_I	171_I	0.511	0.13
13_I	116_I	0.510	0.13
50_N	76_P	0.509	0.13
33_L	80_F	0.508	0.13
159_N	163_A	0.507	0.13
69_E	84_E	0.506	0.13
44_S	170_T	0.505	0.13
73_N	109_E	0.503	0.13
95_I	131_A	0.502	0.13
44_S	48_H	0.500	0.13

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
1k4nA	1	0.9521	100	0.025	Contact Map
1f9zA	2	0.6596	50.4	0.952	Contact Map
4ljxA	1	0.5851	48.6	0.952	Contact Map
4mtsA	2	0.6649	38.5	0.955	Contact Map
2rk0A	4	0.7021	37.4	0.955	Contact Map
2lm1A	1	0.5372	34.5	0.956	Contact Map
1ig6A	1	0.5266	33.4	0.956	Contact Map
1r9cA	2	0.6596	32.7	0.957	Contact Map
4huzA	2	0.7766	31.7	0.957	Contact Map
2li6A	1	0.5745	26.7	0.958	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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