RFAY - ECOLI - GREMLIN Contacts

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RFAY - Lipopolysaccharide core heptose(II) kinase RfaY

UniProt:	P27240	Sequences: MIQKSKIKDLVVFTDENNSKYLNVLNDFLSYNINIIKVFRSIDDTKVMLIDTDYGKLILKVFSPKVKRNERFFKSLLKGDYYERLFEQTQKVRNEGLNTLNDFYLLAERKTLRFVHTYIMIIEYIDGIELCDMPDIDDALKNKIQQSINALHQHGMVSGDPHRGNFIIKNGEVRIIDLSGKRASAQRKAKDRIDLERHYGIKNEIRDLGYYLLVYRKKMRNFMRRLKGKPAR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11425
Length:	232 (188)
Sequences:	414 (303)
Seq/√Len:	22.1

ECOLI - RFAY RFAP INAA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
144_I	173_V	3.911	1.00
58_I	124_Y	3.592	1.00
127_G	130_L	3.158	1.00
109_R	117_T	3.041	1.00
213_L	216_R	2.949	0.99
83_E	87_E	2.717	0.99
158_S	161_P	2.618	0.99
161_P	166_F	2.580	0.98
157_V	184_S	2.572	0.98
59_L	121_I	2.456	0.98
150_A	154_H	2.364	0.97
125_I	174_R	2.349	0.97
55_G	123_E	2.321	0.97
82_Y	103_F	2.214	0.96
81_Y	179_S	2.094	0.94
91_K	95_E	1.995	0.93
29_L	32_N	1.900	0.91
30_S	33_I	1.876	0.90
151_L	175_I	1.855	0.90
209_G	213_L	1.797	0.88
89_T	99_T	1.792	0.88
158_S	166_F	1.789	0.88
57_L	104_Y	1.756	0.87
186_Q	190_K	1.754	0.87
52_T	57_L	1.727	0.86
62_F	120_M	1.709	0.86
212_L	216_R	1.673	0.84
62_F	179_S	1.668	0.84
76_L	114_F	1.619	0.82
85_L	120_M	1.603	0.82
85_L	178_L	1.599	0.81
62_F	81_Y	1.595	0.81
88_Q	192_R	1.585	0.81
152_H	195_L	1.538	0.79
51_D	56_K	1.536	0.79
33_I	106_L	1.493	0.77
132_D	150_A	1.484	0.76
45_T	81_Y	1.483	0.76
148_I	161_P	1.480	0.76
160_D	177_D	1.461	0.75
82_Y	118_Y	1.443	0.74
45_T	179_S	1.436	0.74
45_T	164_G	1.423	0.73
96_G	176_I	1.413	0.72
134_P	138_D	1.412	0.72
207_D	214_V	1.401	0.72
148_I	192_R	1.385	0.71
44_D	162_H	1.383	0.71
103_F	118_Y	1.375	0.70
87_E	126_D	1.343	0.69
209_G	216_R	1.336	0.68
45_T	173_V	1.330	0.68
62_F	164_G	1.320	0.67
80_D	108_E	1.288	0.65
211_Y	214_V	1.288	0.65
115_V	118_Y	1.285	0.65
147_S	173_V	1.273	0.64
92_V	156_M	1.267	0.64
82_Y	85_L	1.257	0.63
206_R	214_V	1.248	0.63
85_L	167_I	1.244	0.62
152_H	167_I	1.238	0.62
49_L	56_K	1.232	0.62
158_S	176_I	1.231	0.62
110_K	115_V	1.229	0.61
130_L	195_L	1.216	0.61
165_N	177_D	1.208	0.60
73_F	97_L	1.206	0.60
208_L	212_L	1.202	0.60
89_T	120_M	1.201	0.60
204_E	214_V	1.178	0.58
162_H	191_D	1.178	0.58
89_T	178_L	1.171	0.58
84_R	168_I	1.135	0.55
60_K	177_D	1.127	0.55
208_L	214_V	1.125	0.55
166_F	175_I	1.122	0.54
50_I	119_I	1.122	0.54
52_T	55_G	1.117	0.54
162_H	178_L	1.114	0.54
45_T	180_G	1.113	0.54
103_F	175_I	1.066	0.51
126_D	186_Q	1.050	0.49
164_G	179_S	1.048	0.49
206_R	211_Y	1.047	0.49
208_L	216_R	1.047	0.49
65_K	166_F	1.044	0.49
53_D	212_L	1.040	0.49
145_Q	188_K	1.034	0.48
64_P	151_L	1.033	0.48
47_V	159_G	1.029	0.48
25_L	104_Y	1.026	0.48
81_Y	162_H	1.021	0.47
142_N	146_Q	1.016	0.47
149_N	153_Q	1.014	0.47
85_L	89_T	1.013	0.47
29_L	34_N	1.010	0.47
39_F	47_V	1.007	0.47
102_D	123_E	1.006	0.46
160_D	165_N	1.005	0.46
30_S	34_N	1.001	0.46
44_D	152_H	0.992	0.46
208_L	213_L	0.991	0.45
134_P	137_D	0.988	0.45
32_N	36_I	0.988	0.45
207_D	210_Y	0.983	0.45
44_D	179_S	0.977	0.45
67_K	104_Y	0.967	0.44
38_V	41_S	0.957	0.43
27_D	34_N	0.955	0.43
149_N	168_I	0.951	0.43
84_R	100_L	0.951	0.43
26_N	30_S	0.950	0.43
152_H	173_V	0.949	0.43
173_V	183_A	0.940	0.42
86_F	162_H	0.933	0.42
47_V	58_I	0.930	0.41
85_L	179_S	0.928	0.41
27_D	121_I	0.922	0.41
91_K	106_L	0.919	0.41
65_K	159_G	0.914	0.40
155_G	166_F	0.912	0.40
191_D	196_E	0.909	0.40
90_Q	195_L	0.906	0.40
191_D	194_D	0.904	0.40
60_K	108_E	0.903	0.40
146_Q	186_Q	0.903	0.40
185_A	189_A	0.900	0.39
60_K	160_D	0.897	0.39
45_T	162_H	0.889	0.39
128_I	132_D	0.884	0.38
81_Y	164_G	0.878	0.38
210_Y	215_Y	0.875	0.38
208_L	215_Y	0.874	0.38
39_F	51_D	0.873	0.38
47_V	144_I	0.864	0.37
121_I	170_N	0.857	0.37
88_Q	196_E	0.854	0.36
92_V	103_F	0.852	0.36
131_C	134_P	0.852	0.36
161_P	176_I	0.845	0.36
97_L	147_S	0.845	0.36
88_Q	191_D	0.840	0.36
111_T	195_L	0.835	0.35
210_Y	214_V	0.835	0.35
168_I	191_D	0.831	0.35
209_G	212_L	0.829	0.35
62_F	180_G	0.829	0.35
104_Y	121_I	0.827	0.35
144_I	174_R	0.827	0.35
144_I	147_S	0.821	0.34
204_E	208_L	0.816	0.34
182_R	187_R	0.812	0.34
65_K	69_N	0.804	0.33
203_N	207_D	0.799	0.33
65_K	148_I	0.798	0.33
161_P	192_R	0.790	0.33
99_T	178_L	0.786	0.32
169_K	174_R	0.775	0.32
192_R	195_L	0.766	0.31
149_N	158_S	0.762	0.31
179_S	194_D	0.757	0.31
149_N	188_K	0.747	0.30
100_L	105_L	0.746	0.30
97_L	175_I	0.743	0.30
45_T	74_K	0.742	0.30
210_Y	216_R	0.739	0.30
45_T	65_K	0.739	0.30
209_G	215_Y	0.738	0.29
27_D	30_S	0.737	0.29
58_I	181_K	0.734	0.29
107_A	121_I	0.731	0.29
65_K	147_S	0.718	0.28
162_H	179_S	0.713	0.28
105_L	193_I	0.710	0.28
77_L	186_Q	0.708	0.28
95_E	109_R	0.707	0.28
87_E	146_Q	0.706	0.28
63_S	82_Y	0.703	0.28
69_N	179_S	0.698	0.27
44_D	74_K	0.696	0.27
74_K	180_G	0.695	0.27
51_D	126_D	0.694	0.27
67_K	103_F	0.690	0.27
151_L	194_D	0.689	0.27
112_L	126_D	0.689	0.27
42_I	47_V	0.687	0.27
50_I	125_I	0.679	0.26
123_E	215_Y	0.678	0.26
60_K	119_I	0.675	0.26
27_D	31_Y	0.674	0.26
74_K	152_H	0.674	0.26
56_K	210_Y	0.673	0.26
83_E	112_L	0.665	0.26
127_G	171_G	0.657	0.25
121_I	139_A	0.656	0.25
111_T	116_H	0.656	0.25
80_D	100_L	0.656	0.25
212_L	215_Y	0.653	0.25
45_T	70_E	0.649	0.25
74_K	144_I	0.645	0.24
85_L	158_S	0.643	0.24
29_L	35_I	0.640	0.24
51_D	110_K	0.639	0.24
82_Y	89_T	0.639	0.24
65_K	179_S	0.639	0.24
56_K	86_F	0.638	0.24
88_Q	181_K	0.635	0.24
31_Y	34_N	0.633	0.24
121_I	171_G	0.633	0.24
81_Y	173_V	0.628	0.24
47_V	156_M	0.627	0.24
113_R	129_E	0.626	0.24
34_N	116_H	0.626	0.24
125_I	150_A	0.625	0.23
110_K	113_R	0.625	0.23
151_L	192_R	0.624	0.23
96_G	150_A	0.623	0.23
152_H	155_G	0.618	0.23
138_D	142_N	0.618	0.23
157_V	182_R	0.616	0.23
53_D	139_A	0.616	0.23
31_Y	53_D	0.610	0.23
91_K	94_N	0.610	0.23
97_L	144_I	0.609	0.23
143_K	146_Q	0.605	0.23
80_D	156_M	0.601	0.22
77_L	141_K	0.598	0.22
35_I	50_I	0.595	0.22
86_F	191_D	0.593	0.22
172_E	204_E	0.585	0.22
73_F	173_V	0.585	0.22
87_E	95_E	0.585	0.22
66_V	181_K	0.582	0.21
31_Y	134_P	0.582	0.21
69_N	115_V	0.579	0.21
38_V	126_D	0.579	0.21
90_Q	141_K	0.578	0.21
97_L	170_N	0.574	0.21
81_Y	180_G	0.573	0.21
81_Y	158_S	0.573	0.21
43_D	143_K	0.572	0.21
40_R	159_G	0.569	0.21
115_V	143_K	0.566	0.21
75_S	102_D	0.565	0.21
73_F	121_I	0.556	0.20
81_Y	178_L	0.553	0.20
60_K	165_N	0.552	0.20
130_L	151_L	0.550	0.20
210_Y	213_L	0.549	0.20
84_R	119_I	0.547	0.20
135_D	139_A	0.545	0.20
82_Y	194_D	0.542	0.20
171_G	182_R	0.542	0.20
84_R	189_A	0.541	0.20
211_Y	215_Y	0.540	0.20
44_D	167_I	0.540	0.20
201_I	215_Y	0.539	0.20
144_I	161_P	0.539	0.20
50_I	114_F	0.539	0.20
78_K	181_K	0.537	0.19
50_I	59_L	0.537	0.19
60_K	78_K	0.536	0.19
81_Y	118_Y	0.534	0.19
147_S	183_A	0.532	0.19
84_R	183_A	0.528	0.19
94_N	155_G	0.528	0.19
37_K	96_G	0.524	0.19
40_R	46_K	0.521	0.19
171_G	204_E	0.515	0.19
122_I	127_G	0.513	0.18
144_I	175_I	0.511	0.18
128_I	131_C	0.509	0.18
75_S	162_H	0.509	0.18
93_R	146_Q	0.508	0.18
53_D	127_G	0.507	0.18
80_D	118_Y	0.506	0.18
51_D	214_V	0.506	0.18
145_Q	158_S	0.506	0.18
149_N	191_D	0.504	0.18
205_I	208_L	0.504	0.18
55_G	91_K	0.500	0.18

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
4gyiA	1	0.8966	99.6	0.733	Contact Map
1zarA	1	0.8319	99.5	0.741	Contact Map
3tm0A	1	0.8362	99.5	0.746	Contact Map
3atsA	1	0.8707	99.5	0.747	Contact Map
2olcA	3	0.8707	99.5	0.75	Contact Map
1zthA	1	0.8319	99.5	0.75	Contact Map
4h05A	1	0.8448	99.5	0.752	Contact Map
3dxpA	2	0.8405	99.4	0.756	Contact Map
3w0oA	1	0.8233	99.4	0.759	Contact Map
2pywA	2	0.9138	99.4	0.761	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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