YBDM - ECOLI - GREMLIN Contacts

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YBDM - Uncharacterized protein YbdM

UniProt:	P77174	Sequences: MGDTMQQRLTQDLTQFLASLPEDDRIKAINEIRMAIHQVSPFREEPVDCVLWVKNSQLMPNDYNPNNVAPPEKKLLQKSIEIDGFTQPIVVTHTDKNAMEIVDGFHRHEIGKGSSSLKLRLKGYLPVTCLEGTRNQRIAATIRHNRARGRHQITAMSEIVRELSQLGWDDNKIGKELGMDSDEVLRLKQINGLQELFADRQYSRAWTVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13532
Length:	209 (164)
Sequences:	226 (114)
Seq/√Len:	8.9

ECOLI - YBDM

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_E	116_S	2.848	0.88
142_I	159_I	2.767	0.86
146_R	156_M	2.495	0.79
86_T	144_H	2.379	0.76
182_D	185_L	2.362	0.75
45_E	48_D	2.348	0.75
153_I	194_Q	2.230	0.71
48_D	52_W	2.205	0.70
168_W	176_E	2.186	0.69
72_E	143_R	2.138	0.68
57_Q	97_N	2.093	0.66
80_I	110_I	2.063	0.65
50_V	128_T	2.040	0.64
45_E	120_R	2.034	0.63
77_Q	116_S	1.853	0.56
127_V	142_I	1.844	0.56
67_N	150_R	1.827	0.55
129_C	138_I	1.803	0.54
168_W	172_K	1.764	0.52
189_Q	197_F	1.747	0.51
59_M	98_A	1.731	0.51
77_Q	114_S	1.714	0.50
68_V	73_K	1.712	0.50
53_V	162_E	1.700	0.49
83_D	140_A	1.688	0.49
177_L	184_V	1.663	0.48
154_T	194_Q	1.662	0.48
141_T	187_L	1.612	0.46
89_I	159_I	1.586	0.44
114_S	177_L	1.577	0.44
188_K	197_F	1.563	0.43
54_K	129_C	1.520	0.42
62_D	100_E	1.518	0.42
58_L	130_L	1.516	0.41
172_K	176_E	1.506	0.41
124_Y	168_W	1.490	0.40
58_L	99_M	1.486	0.40
141_T	188_K	1.481	0.40
189_Q	193_L	1.468	0.39
182_D	190_I	1.449	0.39
55_N	101_I	1.428	0.38
85_F	188_K	1.426	0.38
105_F	150_R	1.418	0.37
176_E	184_V	1.417	0.37
102_V	139_A	1.405	0.37
90_V	141_T	1.401	0.37
69_A	180_D	1.394	0.36
136_Q	204_R	1.378	0.36
150_R	153_I	1.377	0.36
155_A	194_Q	1.329	0.34
83_D	130_L	1.324	0.34
45_E	52_W	1.324	0.34
81_E	128_T	1.304	0.33
53_V	127_V	1.283	0.32
193_L	197_F	1.282	0.32
109_E	113_G	1.261	0.31
62_D	136_Q	1.249	0.31
47_V	130_L	1.249	0.31
146_R	167_G	1.241	0.31
60_P	101_I	1.213	0.30
121_L	176_E	1.211	0.30
174_G	177_L	1.196	0.29
163_L	189_Q	1.186	0.29
185_L	189_Q	1.184	0.29
94_T	100_E	1.179	0.28
174_G	184_V	1.173	0.28
192_G	197_F	1.169	0.28
68_V	80_I	1.167	0.28
176_E	191_N	1.163	0.28
168_W	184_V	1.162	0.28
141_T	156_M	1.141	0.27
184_V	206_W	1.127	0.27
89_I	101_I	1.127	0.27
47_V	80_I	1.124	0.26
60_P	162_E	1.112	0.26
94_T	97_N	1.095	0.26
112_K	202_Y	1.090	0.25
87_Q	143_R	1.084	0.25
78_K	101_I	1.075	0.25
135_N	196_L	1.074	0.25
55_N	111_G	1.063	0.24
83_D	144_H	1.062	0.24
101_I	165_Q	1.058	0.24
99_M	137_R	1.051	0.24
177_L	206_W	1.049	0.24
62_D	138_I	1.033	0.24
102_V	141_T	1.028	0.23
60_P	158_E	1.027	0.23
111_G	125_L	1.025	0.23
182_D	189_Q	1.022	0.23
63_Y	148_R	1.022	0.23
81_E	114_S	1.016	0.23
68_V	71_P	1.013	0.23
86_T	179_M	1.010	0.23
89_I	110_I	1.007	0.23
144_H	179_M	1.004	0.23
157_S	191_N	0.995	0.22
85_F	120_R	0.985	0.22
45_E	111_G	0.982	0.22
86_T	143_R	0.978	0.22
122_K	205_A	0.978	0.22
168_W	193_L	0.977	0.22
57_Q	93_H	0.973	0.22
88_P	143_R	0.967	0.22
109_E	174_G	0.957	0.21
77_Q	81_E	0.950	0.21
53_V	57_Q	0.940	0.21
72_E	88_P	0.929	0.20
158_E	171_N	0.927	0.20
95_D	175_K	0.920	0.20
115_S	133_T	0.918	0.20
117_L	155_A	0.918	0.20
82_I	201_Q	0.916	0.20
122_K	129_C	0.906	0.20
48_D	111_G	0.898	0.20
85_F	125_L	0.898	0.20
48_D	120_R	0.893	0.19
182_D	199_D	0.889	0.19
93_H	97_N	0.887	0.19
72_E	144_H	0.883	0.19
97_N	134_R	0.867	0.19
101_I	111_G	0.848	0.18
83_D	86_T	0.843	0.18
139_A	188_K	0.830	0.18
157_S	162_E	0.830	0.18
87_Q	146_R	0.830	0.18
185_L	199_D	0.825	0.18
144_H	148_R	0.823	0.18
186_R	192_G	0.819	0.18
72_E	87_Q	0.819	0.18
148_R	192_G	0.819	0.18
141_T	146_R	0.818	0.17
148_R	186_R	0.816	0.17
152_Q	184_V	0.797	0.17
51_L	128_T	0.793	0.17
52_W	146_R	0.790	0.17
81_E	85_F	0.788	0.17
144_H	193_L	0.787	0.17
158_E	181_S	0.779	0.17
179_M	186_R	0.776	0.16
92_T	142_I	0.774	0.16
144_H	186_R	0.773	0.16
52_W	156_M	0.767	0.16
164_S	173_I	0.765	0.16
53_V	129_C	0.764	0.16
187_L	205_A	0.760	0.16
186_R	193_L	0.757	0.16
168_W	177_L	0.752	0.16
156_M	159_I	0.749	0.16
88_P	144_H	0.748	0.16
118_K	123_G	0.748	0.16
45_E	121_L	0.748	0.16
156_M	167_G	0.748	0.16
54_K	97_N	0.746	0.16
96_K	159_I	0.740	0.16
46_P	84_G	0.730	0.15
83_D	142_I	0.729	0.15
92_T	130_L	0.728	0.15
83_D	132_G	0.705	0.15
80_I	136_Q	0.703	0.15
46_P	75_L	0.703	0.15
95_D	134_R	0.696	0.15
179_M	193_L	0.695	0.15
62_D	133_T	0.692	0.15
74_K	180_D	0.681	0.14
185_L	197_F	0.679	0.14
70_P	174_G	0.678	0.14
91_V	176_E	0.677	0.14
185_L	205_A	0.673	0.14
56_S	130_L	0.672	0.14
72_E	86_T	0.670	0.14
72_E	83_D	0.668	0.14
174_G	202_Y	0.667	0.14
64_N	151_H	0.667	0.14
65_P	151_H	0.667	0.14
90_V	186_R	0.665	0.14
139_A	196_L	0.660	0.14
44_E	49_C	0.658	0.14
53_V	131_E	0.656	0.14
121_L	168_W	0.654	0.14
75_L	84_G	0.651	0.14
160_V	195_E	0.651	0.14
62_D	205_A	0.651	0.14
177_L	186_R	0.650	0.14
77_Q	85_F	0.647	0.14
68_V	137_R	0.642	0.14
89_I	205_A	0.641	0.14
80_I	207_T	0.639	0.13
203_S	207_T	0.632	0.13
83_D	143_R	0.630	0.13
200_R	205_A	0.627	0.13
114_S	119_L	0.624	0.13
57_Q	131_E	0.621	0.13
105_F	128_T	0.618	0.13
105_F	204_R	0.617	0.13
112_K	181_S	0.615	0.13
110_I	125_L	0.615	0.13
59_M	169_D	0.613	0.13
60_P	167_G	0.611	0.13
59_M	100_E	0.610	0.13
87_Q	156_M	0.610	0.13
188_K	196_L	0.606	0.13
56_S	105_F	0.601	0.13
185_L	188_K	0.601	0.13
120_R	156_M	0.600	0.13
73_K	110_I	0.595	0.13
56_S	95_D	0.594	0.13
133_T	202_Y	0.593	0.13
114_S	117_L	0.592	0.13
128_T	198_A	0.586	0.12
78_K	110_I	0.582	0.12
86_T	148_R	0.581	0.12
49_C	165_Q	0.578	0.12
128_T	195_E	0.578	0.12
136_Q	207_T	0.578	0.12
118_K	128_T	0.573	0.12
101_I	131_E	0.573	0.12
81_E	118_K	0.567	0.12
153_I	195_E	0.562	0.12
135_N	157_S	0.561	0.12
186_R	202_Y	0.559	0.12
51_L	109_E	0.556	0.12
137_R	180_D	0.555	0.12
90_V	148_R	0.553	0.12
101_I	191_N	0.552	0.12
58_L	112_K	0.550	0.12
81_E	131_E	0.547	0.12
51_L	138_I	0.547	0.12
179_M	192_G	0.547	0.12
105_F	201_Q	0.541	0.12
124_Y	152_Q	0.536	0.12
54_K	138_I	0.535	0.12
124_Y	172_K	0.534	0.11
71_P	123_G	0.533	0.11
52_W	124_Y	0.529	0.11
142_I	179_M	0.526	0.11
85_F	108_H	0.523	0.11
102_V	165_Q	0.522	0.11
142_I	196_L	0.521	0.11
74_K	160_V	0.513	0.11
51_L	140_A	0.513	0.11
156_M	188_K	0.508	0.11
131_E	134_R	0.508	0.11
48_D	121_L	0.508	0.11
52_W	195_E	0.502	0.11
45_E	87_Q	0.500	0.11

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
1vz0A	3	0.7321	99.8	0.791	Contact Map
4umkA	2	0.7225	99.8	0.805	Contact Map
1vk1A	1	0.689	99.3	0.857	Contact Map
1xw3A	1	0.5024	99	0.876	Contact Map
1yzsA	1	0.555	98.7	0.887	Contact Map
1r71A	2	0.3541	89.3	0.947	Contact Map
4dyqA	5	0.2584	65.1	0.958	Contact Map
2m8eA	1	0.2727	59	0.96	Contact Map
2x48A	1	0.2536	56.7	0.96	Contact Map
1tc3C	1	0.244	44.3	0.963	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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