YAFS - ECOLI - GREMLIN Contacts

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YAFS - Uncharacterized protein YafS

UniProt:	P75672	Sequences: MKPARVPQTVVAPDCWGDLPWGKLYRKALERQLNPWFTKMYGFHLLKIGNLSAEINCEACAVSHQVNVSAQGMPVQVQADPLHLPFADKSVDVCLLAHTLPWCTDPHRLLREADRVLIDDGWLVISGFNPISFMGLRKLVPVLRKTSPYNSRMFTLMRQLDWLSLLNFEVLHASRFHVLPWNKHGGKLLNAHIPALGCLQLIVARKRTIPLTLNPMKQSKNKPRIRQAVGATRQCRKPQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13331
Length:	240 (212)
Sequences:	1163 (887)
Seq/√Len:	60.9

ECOLI - YAFS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_F	91_V	4.182	1.00
94_C	113_A	4.026	1.00
96_L	113_A	3.396	1.00
45_L	93_V	3.340	1.00
112_E	115_R	3.278	1.00
46_L	94_C	3.248	1.00
84_L	116_V	3.057	1.00
113_A	123_L	2.875	1.00
48_I	84_L	2.753	1.00
161_D	165_L	2.694	1.00
175_R	197_G	2.630	1.00
68_V	79_A	2.595	1.00
114_D	168_F	2.533	1.00
33_L	126_S	2.491	1.00
127_G	200_Q	2.431	1.00
163_L	204_A	2.405	1.00
122_W	203_V	2.324	1.00
169_E	207_R	2.268	1.00
44_H	64_H	2.193	1.00
122_W	205_R	2.183	1.00
101_P	151_S	2.105	1.00
117_L	121_G	2.090	1.00
178_V	189_L	1.995	1.00
186_G	189_L	1.992	1.00
68_V	86_F	1.983	1.00
107_H	165_L	1.937	1.00
46_L	91_V	1.926	1.00
181_W	185_G	1.924	1.00
82_L	108_R	1.837	1.00
215_P	219_S	1.803	1.00
77_V	86_F	1.784	0.99
158_R	161_D	1.762	0.99
87_A	90_S	1.752	0.99
134_M	198_C	1.749	0.99
162_W	166_L	1.681	0.99
107_H	162_W	1.668	0.99
32_Q	35_P	1.649	0.99
111_R	165_L	1.647	0.99
16_W	132_S	1.597	0.99
137_R	141_P	1.562	0.99
161_D	166_L	1.523	0.98
120_D	207_R	1.513	0.98
89_K	119_D	1.510	0.98
126_S	201_L	1.471	0.98
130_P	158_R	1.470	0.98
171_L	205_R	1.467	0.98
163_L	202_I	1.467	0.98
81_P	109_L	1.454	0.98
19_L	22_G	1.444	0.98
111_R	166_L	1.423	0.97
132_S	135_G	1.389	0.97
149_Y	153_M	1.380	0.97
217_K	221_N	1.356	0.97
173_A	202_I	1.352	0.97
120_D	205_R	1.330	0.96
211_L	214_N	1.313	0.96
39_K	43_F	1.299	0.96
158_R	165_L	1.291	0.95
112_E	132_S	1.290	0.95
117_L	206_K	1.280	0.95
148_P	151_S	1.276	0.95
189_L	193_I	1.269	0.95
180_P	189_L	1.262	0.95
102_W	151_S	1.254	0.95
220_K	223_P	1.240	0.94
178_V	186_G	1.240	0.94
162_W	165_L	1.231	0.94
47_K	53_A	1.226	0.94
156_L	173_A	1.225	0.94
112_E	116_V	1.210	0.94
182_N	185_G	1.209	0.94
111_R	162_W	1.201	0.93
91_V	94_C	1.199	0.93
46_L	116_V	1.196	0.93
163_L	168_F	1.187	0.93
106_P	162_W	1.181	0.93
96_L	123_L	1.171	0.92
95_L	126_S	1.159	0.92
47_K	51_L	1.158	0.92
32_Q	174_S	1.157	0.92
124_V	201_L	1.153	0.92
209_I	213_L	1.149	0.92
46_L	86_F	1.135	0.91
107_H	161_D	1.131	0.91
118_I	197_G	1.124	0.91
29_L	98_H	1.106	0.90
48_I	81_P	1.103	0.90
122_W	171_L	1.102	0.90
96_L	99_T	1.097	0.90
66_V	91_V	1.095	0.90
21_W	134_M	1.090	0.89
46_L	68_V	1.089	0.89
67_N	70_A	1.086	0.89
25_Y	199_L	1.084	0.89
209_I	212_T	1.079	0.89
107_H	111_R	1.074	0.89
111_R	161_D	1.065	0.88
32_Q	201_L	1.054	0.88
47_K	97_A	1.050	0.88
156_L	202_I	1.044	0.87
106_P	110_L	1.041	0.87
101_P	127_G	1.040	0.87
16_W	128_F	1.033	0.87
158_R	162_W	1.026	0.86
91_V	116_V	1.024	0.86
107_H	110_L	1.002	0.85
32_Q	176_F	1.002	0.85
96_L	100_L	0.996	0.85
108_R	166_L	0.982	0.84
101_P	129_N	0.958	0.82
35_P	38_T	0.949	0.82
58_E	69_S	0.941	0.81
214_N	218_Q	0.941	0.81
107_H	166_L	0.935	0.81
171_L	203_V	0.934	0.81
54_E	57_C	0.932	0.81
13_P	51_L	0.920	0.80
79_A	85_P	0.919	0.80
167_N	211_L	0.918	0.80
41_Y	44_H	0.914	0.79
219_S	223_P	0.912	0.79
107_H	158_R	0.912	0.79
89_K	213_L	0.911	0.79
215_P	218_Q	0.905	0.79
88_D	115_R	0.903	0.78
33_L	94_C	0.903	0.78
125_I	171_L	0.895	0.78
45_L	62_V	0.894	0.78
49_G	154_F	0.894	0.78
127_G	130_P	0.893	0.78
183_K	222_K	0.892	0.78
141_P	155_T	0.884	0.77
39_K	61_A	0.878	0.76
212_T	217_K	0.874	0.76
49_G	101_P	0.865	0.75
41_Y	165_L	0.865	0.75
49_G	97_A	0.862	0.75
24_L	86_F	0.862	0.75
13_P	17_G	0.859	0.75
77_V	119_D	0.857	0.75
18_D	123_L	0.856	0.75
68_V	77_V	0.851	0.74
44_H	63_S	0.847	0.74
117_L	123_L	0.838	0.73
94_C	116_V	0.837	0.73
41_Y	111_R	0.836	0.73
46_L	84_L	0.828	0.72
48_I	168_F	0.825	0.72
114_D	167_N	0.822	0.72
55_I	155_T	0.820	0.71
130_P	162_W	0.814	0.71
98_H	128_F	0.813	0.71
43_F	118_I	0.813	0.71
47_K	50_N	0.804	0.70
106_P	154_F	0.799	0.69
30_E	34_N	0.794	0.69
151_S	203_V	0.789	0.68
141_P	177_H	0.789	0.68
111_R	158_R	0.780	0.68
21_W	33_L	0.779	0.67
92_D	118_I	0.775	0.67
36_W	105_D	0.772	0.67
167_N	202_I	0.768	0.66
28_A	32_Q	0.768	0.66
218_Q	221_N	0.768	0.66
138_K	153_M	0.767	0.66
13_P	19_L	0.765	0.66
178_V	192_H	0.765	0.66
169_E	205_R	0.764	0.66
215_P	220_K	0.764	0.66
214_N	219_S	0.763	0.66
138_K	149_Y	0.762	0.66
20_P	217_K	0.760	0.66
37_F	203_V	0.757	0.65
50_N	53_A	0.751	0.65
130_P	200_Q	0.749	0.64
98_H	101_P	0.746	0.64
54_E	97_A	0.737	0.63
180_P	186_G	0.734	0.63
33_L	95_L	0.734	0.63
25_Y	29_L	0.732	0.63
31_R	34_N	0.725	0.62
48_I	113_A	0.725	0.62
17_G	176_F	0.724	0.62
20_P	123_L	0.722	0.62
41_Y	62_V	0.721	0.61
43_F	61_A	0.721	0.61
188_L	221_N	0.720	0.61
120_D	169_E	0.718	0.61
170_V	202_I	0.714	0.61
89_K	206_K	0.711	0.60
210_P	214_N	0.709	0.60
36_W	201_L	0.704	0.60
173_A	192_H	0.701	0.59
42_G	204_A	0.700	0.59
218_Q	222_K	0.699	0.59
33_L	124_V	0.688	0.58
125_I	189_L	0.678	0.57
93_V	98_H	0.677	0.57
36_W	126_S	0.673	0.56
161_D	169_E	0.672	0.56
217_K	222_K	0.669	0.56
167_N	207_R	0.668	0.56
37_F	93_V	0.665	0.55
98_H	133_F	0.663	0.55
121_G	206_K	0.650	0.54
128_F	154_F	0.650	0.54
188_L	193_I	0.648	0.53
97_A	126_S	0.647	0.53
176_F	201_L	0.646	0.53
28_A	176_F	0.646	0.53
168_F	202_I	0.644	0.53
104_T	172_H	0.643	0.53
89_K	150_N	0.642	0.53
132_S	149_Y	0.641	0.53
71_Q	78_Q	0.641	0.53
14_D	155_T	0.641	0.53
26_R	31_R	0.637	0.52
82_L	95_L	0.636	0.52
17_G	210_P	0.635	0.52
129_N	196_L	0.634	0.52
105_D	108_R	0.632	0.52
212_T	215_P	0.631	0.51
102_W	128_F	0.630	0.51
17_G	89_K	0.630	0.51
68_V	84_L	0.627	0.51
185_G	222_K	0.622	0.50
52_S	68_V	0.619	0.50
139_L	197_G	0.618	0.50
216_M	219_S	0.617	0.50
216_M	222_K	0.608	0.49
34_N	61_A	0.608	0.49
101_P	134_M	0.605	0.48
51_L	120_D	0.604	0.48
66_V	152_R	0.602	0.48
37_F	40_M	0.600	0.48
94_C	117_L	0.598	0.48
159_Q	197_G	0.598	0.48
219_S	222_K	0.597	0.48
98_H	132_S	0.596	0.47
32_Q	38_T	0.594	0.47
191_A	195_A	0.594	0.47
98_H	168_F	0.593	0.47
48_I	78_Q	0.593	0.47
126_S	151_S	0.590	0.47
40_M	203_V	0.589	0.47
37_F	45_L	0.585	0.46
37_F	95_L	0.584	0.46
16_W	102_W	0.584	0.46
57_C	60_C	0.583	0.46
218_Q	223_P	0.582	0.46
120_D	210_P	0.581	0.46
87_A	222_K	0.580	0.46
105_D	210_P	0.579	0.46
11_V	15_C	0.579	0.46
217_K	220_K	0.578	0.45
175_R	191_A	0.578	0.45
172_H	201_L	0.575	0.45
34_N	41_Y	0.573	0.45
136_L	140_V	0.572	0.45
178_V	190_N	0.571	0.45
79_A	212_T	0.571	0.45
82_L	103_C	0.569	0.44
10_V	63_S	0.566	0.44
123_L	204_A	0.565	0.44
110_L	113_A	0.563	0.44
29_L	126_S	0.562	0.44
77_V	90_S	0.562	0.44
111_R	163_L	0.561	0.44
109_L	125_I	0.557	0.43
26_R	29_L	0.554	0.43
80_D	152_R	0.554	0.43
55_I	64_H	0.553	0.43
56_N	59_A	0.552	0.43
98_H	127_G	0.550	0.42
98_H	158_R	0.549	0.42
50_N	54_E	0.548	0.42
38_T	181_W	0.546	0.42
135_G	149_Y	0.546	0.42
28_A	34_N	0.541	0.41
61_A	192_H	0.538	0.41
75_V	222_K	0.536	0.41
63_S	197_G	0.536	0.41
46_L	95_L	0.534	0.41
216_M	223_P	0.532	0.40
207_R	210_P	0.528	0.40
41_Y	214_N	0.527	0.40
166_L	170_V	0.526	0.40
213_L	220_K	0.525	0.40
82_L	216_M	0.524	0.39
29_L	97_A	0.523	0.39
44_H	170_V	0.522	0.39
106_P	152_R	0.521	0.39
50_N	70_A	0.521	0.39
46_L	104_T	0.519	0.39
154_F	159_Q	0.519	0.39
177_H	198_C	0.517	0.39
75_V	80_D	0.514	0.38
134_M	153_M	0.514	0.38
95_L	195_A	0.513	0.38
31_R	35_P	0.513	0.38
132_S	153_M	0.511	0.38
188_L	196_L	0.511	0.38
26_R	56_N	0.511	0.38
22_G	100_L	0.510	0.38
181_W	184_H	0.510	0.38
80_D	109_L	0.509	0.38
96_L	125_I	0.509	0.38
17_G	198_C	0.508	0.38
127_G	159_Q	0.508	0.38
139_L	157_M	0.505	0.37
41_Y	118_I	0.504	0.37
128_F	149_Y	0.504	0.37
197_G	212_T	0.502	0.37
29_L	199_L	0.501	0.37
134_M	180_P	0.500	0.37
80_D	104_T	0.500	0.37
17_G	29_L	0.500	0.37

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
2gs9A	2	0.8167	100	0.528	Contact Map
4htfA	2	0.8458	99.9	0.589	Contact Map
2p7iA	6	0.7875	99.9	0.593	Contact Map
4kdcA	1	0.7917	99.9	0.602	Contact Map
1vlmA	1	0.8208	99.9	0.606	Contact Map
2avnA	3	0.8458	99.9	0.606	Contact Map
4kdrA	1	0.7708	99.9	0.62	Contact Map
3cc8A	2	0.7542	99.9	0.625	Contact Map
3l8dA	2	0.7792	99.9	0.628	Contact Map
4pneA	2	0.8542	99.9	0.63	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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