YCGM - ECOLI - GREMLIN Contacts

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YCGM - Uncharacterized protein YcgM

UniProt:	P76004	Sequences: MYQHHNWQGALLDYPVSKVVCVGSNYAKHIKEMGSAVPEEPVLFIKPETALCDLRQPLAIPSDFGSVHHEVELAVLIGATLRQATEEHVRKAIAGYGVALDLTLRDVQGKMKKAGQPWEKAKAFDNSCPLSGFIPAAEFTGDPQNTTLSLSVNGEQRQQGTTADMIHKIVPLIAYMSKFFTLKAGDVVLTGTPDGVGPLQSGDELTVTFDGHSLTTRVL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13894
Length:	219 (201)
Sequences:	9775 (5869)
Seq/√Len:	414.0

ECOLI - YCGM
BACSU - YISK
HALSA - Q9HQR6
SULSO - Q97V63 Q97VT9 Q97UR1 KDAD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
153_N	203_D	3.747	1.00
99_A	189_L	3.422	1.00
147_T	159_Q	3.236	1.00
149_S	208_T	2.995	1.00
151_S	156_Q	2.916	1.00
206_T	216_T	2.696	1.00
85_T	88_H	2.659	1.00
208_T	214_L	2.621	1.00
86_E	174_A	2.604	1.00
168_K	171_P	2.539	1.00
86_E	171_P	2.517	1.00
74_A	99_A	2.516	1.00
156_Q	159_Q	2.389	1.00
71_V	150_L	2.312	1.00
206_T	214_L	2.310	1.00
81_L	84_A	2.291	1.00
81_L	92_A	2.286	1.00
88_H	91_K	2.244	1.00
149_S	159_Q	2.194	1.00
71_V	207_V	2.186	1.00
90_R	93_I	2.114	1.00
147_T	210_D	2.109	1.00
84_A	92_A	2.098	1.00
125_D	181_T	2.060	1.00
151_S	206_T	2.054	1.00
80_T	183_K	1.986	1.00
160_G	164_D	1.949	1.00
204_E	216_T	1.909	1.00
28_K	194_D	1.861	1.00
59_A	126_N	1.847	1.00
80_T	184_A	1.779	1.00
151_S	208_T	1.752	1.00
47_P	123_A	1.750	1.00
147_T	161_T	1.731	1.00
75_V	169_I	1.689	1.00
74_A	189_L	1.661	1.00
86_E	168_K	1.643	1.00
49_T	183_K	1.632	1.00
90_R	170_V	1.625	1.00
152_V	157_R	1.624	1.00
74_A	97_G	1.606	1.00
130_L	187_V	1.577	1.00
145_N	161_T	1.543	1.00
27_A	31_K	1.536	1.00
60_I	67_V	1.536	1.00
149_S	156_Q	1.534	1.00
69_H	157_R	1.534	1.00
74_A	187_V	1.521	1.00
52_C	56_Q	1.518	1.00
99_A	128_C	1.459	1.00
98_V	209_F	1.445	1.00
152_V	199_L	1.432	1.00
45_I	119_E	1.418	1.00
96_Y	137_A	1.414	1.00
97_G	131_S	1.355	1.00
43_L	176_M	1.347	1.00
24_S	35_S	1.338	1.00
145_N	163_A	1.332	1.00
82_R	125_D	1.323	1.00
71_V	148_L	1.318	1.00
102_L	199_L	1.314	1.00
128_C	189_L	1.298	1.00
22_V	172_L	1.281	1.00
79_A	92_A	1.270	1.00
140_T	146_T	1.267	1.00
28_K	164_D	1.240	1.00
19_V	128_C	1.220	1.00
79_A	91_K	1.213	1.00
53_D	56_Q	1.210	1.00
77_I	173_I	1.188	1.00
30_I	37_V	1.185	1.00
17_S	183_K	1.185	1.00
50_A	128_C	1.184	1.00
64_F	67_V	1.177	1.00
52_C	126_N	1.149	1.00
144_Q	170_V	1.146	1.00
144_Q	168_K	1.146	1.00
142_D	145_N	1.122	1.00
119_E	123_A	1.119	1.00
73_L	209_F	1.114	1.00
65_G	106_D	1.111	1.00
20_V	176_M	1.107	1.00
24_S	33_M	1.094	1.00
80_T	92_A	1.087	1.00
64_F	106_D	1.083	1.00
68_H	105_R	1.078	1.00
22_V	43_L	1.064	1.00
167_H	171_P	1.057	1.00
97_G	130_L	1.045	1.00
102_L	129_P	1.043	1.00
82_R	181_T	1.040	1.00
86_E	170_V	1.038	1.00
60_I	201_S	1.034	1.00
77_I	182_L	1.020	1.00
151_S	214_L	1.018	1.00
26_Y	190_T	1.015	1.00
58_L	102_L	1.014	1.00
80_T	181_T	0.999	1.00
136_A	139_F	0.989	1.00
94_A	134_I	0.988	1.00
66_S	109_G	0.985	1.00
40_E	110_K	0.983	1.00
75_V	188_V	0.974	1.00
28_K	31_K	0.974	1.00
141_G	211_G	0.962	1.00
105_R	108_Q	0.958	1.00
99_A	130_L	0.956	1.00
58_L	205_L	0.950	1.00
104_L	127_S	0.947	1.00
85_T	174_A	0.945	1.00
107_V	124_F	0.943	1.00
78_G	94_A	0.942	1.00
73_L	162_T	0.942	1.00
144_Q	165_M	0.939	1.00
174_A	178_K	0.929	1.00
66_S	106_D	0.925	1.00
71_V	98_V	0.920	1.00
55_R	216_T	0.913	1.00
43_L	175_Y	0.911	1.00
146_T	162_T	0.908	1.00
120_K	179_F	0.896	1.00
62_S	83_Q	0.888	1.00
37_V	166_I	0.885	1.00
150_L	207_V	0.882	1.00
55_R	215_T	0.881	1.00
98_V	207_V	0.877	1.00
98_V	212_H	0.868	1.00
154_G	206_T	0.860	1.00
97_G	212_H	0.859	1.00
54_L	215_T	0.857	1.00
29_H	105_R	0.854	1.00
83_Q	178_K	0.845	1.00
18_K	125_D	0.838	1.00
100_L	205_L	0.837	1.00
76_L	134_I	0.834	1.00
171_P	174_A	0.828	1.00
24_S	30_I	0.811	1.00
67_V	127_S	0.807	1.00
58_L	126_N	0.804	1.00
41_P	172_L	0.802	1.00
172_L	190_T	0.792	1.00
124_F	127_S	0.791	1.00
75_V	96_Y	0.789	1.00
38_P	167_H	0.788	1.00
174_A	177_S	0.785	1.00
41_P	175_Y	0.783	1.00
76_L	95_G	0.782	1.00
61_P	127_S	0.779	1.00
69_H	197_G	0.779	1.00
164_D	194_D	0.776	1.00
176_M	188_V	0.772	1.00
115_G	120_K	0.766	1.00
63_D	83_Q	0.765	1.00
20_V	45_I	0.764	1.00
199_L	205_L	0.762	1.00
84_A	174_A	0.751	1.00
175_Y	178_K	0.749	1.00
146_T	209_F	0.749	1.00
36_A	39_E	0.747	1.00
182_L	188_V	0.746	1.00
63_D	178_K	0.740	1.00
154_G	204_E	0.740	1.00
95_G	134_I	0.738	1.00
16_V	51_L	0.734	1.00
35_S	109_G	0.730	1.00
120_K	180_F	0.725	1.00
29_H	32_E	0.725	1.00
130_L	189_L	0.724	1.00
170_V	174_A	0.723	1.00
76_L	97_G	0.721	1.00
151_S	154_G	0.716	1.00
173_I	188_V	0.711	1.00
20_V	180_F	0.709	1.00
135_P	212_H	0.708	1.00
42_V	118_W	0.707	1.00
42_V	116_Q	0.705	1.00
64_F	104_L	0.705	1.00
199_L	203_D	0.704	1.00
102_L	126_N	0.701	1.00
32_E	196_V	0.701	1.00
124_F	179_F	0.700	1.00
76_L	187_V	0.699	1.00
50_A	181_T	0.697	1.00
45_I	123_A	0.696	1.00
200_Q	203_D	0.693	1.00
143_P	162_T	0.692	1.00
73_L	169_I	0.689	1.00
24_S	42_V	0.687	1.00
74_A	130_L	0.687	1.00
152_V	205_L	0.683	1.00
17_S	49_T	0.675	1.00
77_I	80_T	0.673	1.00
24_S	28_K	0.672	0.99
120_K	178_K	0.671	0.99
46_K	128_C	0.671	0.99
133_F	212_H	0.671	0.99
31_K	37_V	0.669	0.99
66_S	198_P	0.668	0.99
160_G	194_D	0.667	0.99
51_L	130_L	0.666	0.99
22_V	176_M	0.665	0.99
172_L	188_V	0.664	0.99
52_C	58_L	0.663	0.99
21_C	189_L	0.663	0.99
19_V	51_L	0.663	0.99
33_M	103_T	0.661	0.99
18_K	47_P	0.659	0.99
80_T	84_A	0.657	0.99
75_V	173_I	0.657	0.99
27_A	166_I	0.654	0.99
100_L	207_V	0.653	0.99
149_S	210_D	0.653	0.99
132_G	135_P	0.652	0.99
96_Y	143_P	0.652	0.99
31_K	34_G	0.652	0.99
29_H	196_V	0.652	0.99
81_L	173_I	0.647	0.99
31_K	164_D	0.645	0.99
61_P	124_F	0.640	0.99
27_A	164_D	0.639	0.99
77_I	92_A	0.637	0.99
18_K	48_E	0.635	0.99
150_L	205_L	0.627	0.99
103_T	108_Q	0.626	0.99
146_T	161_T	0.626	0.99
27_A	37_V	0.624	0.99
12_L	97_G	0.622	0.99
79_A	184_A	0.622	0.99
93_I	96_Y	0.619	0.99
135_P	138_E	0.618	0.99
104_L	107_V	0.617	0.99
141_G	146_T	0.614	0.99
175_Y	179_F	0.614	0.99
165_M	172_L	0.611	0.99
52_C	55_R	0.609	0.99
137_A	141_G	0.608	0.99
22_V	25_N	0.601	0.99
89_V	173_I	0.600	0.99
88_H	92_A	0.598	0.99
73_L	96_Y	0.598	0.99
148_L	209_F	0.598	0.99
148_L	160_G	0.592	0.99
90_R	96_Y	0.592	0.99
49_T	125_D	0.589	0.99
33_M	109_G	0.584	0.99
59_A	82_R	0.583	0.99
60_I	200_Q	0.579	0.99
147_T	163_A	0.578	0.98
89_V	174_A	0.574	0.98
90_R	137_A	0.573	0.98
98_V	215_T	0.573	0.98
85_T	92_A	0.569	0.98
69_H	152_V	0.568	0.98
109_G	121_A	0.567	0.98
81_L	85_T	0.565	0.98
47_P	50_A	0.563	0.98
49_T	181_T	0.563	0.98
102_L	205_L	0.562	0.98
162_T	169_I	0.562	0.98
89_V	170_V	0.561	0.98
41_P	167_H	0.561	0.98
40_E	175_Y	0.560	0.98
23_G	26_Y	0.558	0.98
90_R	169_I	0.556	0.98
17_S	48_E	0.551	0.98
145_N	162_T	0.549	0.98
58_L	67_V	0.547	0.98
81_L	177_S	0.546	0.98
30_I	34_G	0.546	0.98
18_K	186_D	0.544	0.98
58_L	127_S	0.543	0.98
75_V	93_I	0.540	0.98
97_G	133_F	0.539	0.98
76_L	94_A	0.539	0.98
91_K	137_A	0.534	0.97
134_I	212_H	0.534	0.97
161_T	164_D	0.532	0.97
84_A	173_I	0.529	0.97
151_S	159_Q	0.527	0.97
176_M	180_F	0.527	0.97
87_E	174_A	0.527	0.97
120_K	175_Y	0.524	0.97
66_S	110_K	0.522	0.97
146_T	210_D	0.521	0.97
90_R	144_Q	0.520	0.97
29_H	68_H	0.519	0.97
169_I	190_T	0.519	0.97
171_P	175_Y	0.517	0.97
209_F	212_H	0.516	0.97
29_H	108_Q	0.515	0.97
67_V	102_L	0.515	0.97
67_V	124_F	0.515	0.97
67_V	104_L	0.514	0.97
89_V	93_I	0.512	0.97
60_I	64_F	0.511	0.97
23_G	29_H	0.510	0.97
108_Q	121_A	0.508	0.97
23_G	42_V	0.505	0.96
31_K	36_A	0.505	0.96
34_G	37_V	0.504	0.96
144_Q	169_I	0.503	0.96
56_Q	126_N	0.500	0.96

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
4dbfA	2	0.9269	100	0.137	Contact Map
3r6oA	2	0.9315	100	0.14	Contact Map
3rr6A	1	0.9635	100	0.143	Contact Map
1wzoA	4	0.9498	100	0.164	Contact Map
1gttA	1	0.9406	100	0.172	Contact Map
2dfuA	2	0.9224	100	0.177	Contact Map
4maqA	2	0.9498	100	0.192	Contact Map
3lzkA	2	0.9817	100	0.195	Contact Map
1sawA	2	0.9269	100	0.196	Contact Map
3s52A	2	0.9909	100	0.21	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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