YFBP - ECOLI - GREMLIN Contacts

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YFBP - Uncharacterized protein YfbP

UniProt:	P76486	Sequences: MKLIPRSSDISPGIDGICPGPFPPNGFTVLTDAAYGNGDCFGLYWPIGQEHKLPIVCETYHDEWRIVPAFSSIKKFEEWLEVNDDDPHENGISIEDQDFAANLFRVARKCLSTGRLDDALPLLQRATEQLPEVSEYWLALAIQYRRCKKTEAAAQAALNAYLGNWAFGVPDNKVIHLLSQAADVPNFQDDPVIQCIKEQGLDLSFGGTKENNNYPLMQMCVDTYFAQRKPLQALTLLHNYAWIMSSETTAFQERYDFNIDEWRAKFRQLCLEYFGDSRTQFT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14100
Length:	282 (215)
Sequences:	897 (843)
Seq/√Len:	57.5

ECOLI - YFBP LPSRP NLPI BAMD HEMY
BACSU - YVCD RAPD RAPK YPIA RAPF RAPC RAPE RAPG RAPJ RAPB RAPH RAPI RAPA YSOA YRRB
HALSA - Q9HMM8
SULSO - Q97V36 Q97WM3 Q97ZS3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
115_R	118_D	5.987	1.00
229_K	232_Q	5.759	1.00
149_K	152_A	5.333	1.00
107_A	123_L	4.927	1.00
81_E	84_D	4.790	1.00
183_D	186_N	4.261	1.00
73_I	89_E	3.658	1.00
141_A	157_A	3.423	1.00
106_V	122_L	3.230	1.00
110_C	118_D	2.975	1.00
104_F	139_A	2.758	1.00
221_V	237_L	2.747	1.00
174_V	178_L	2.704	1.00
106_V	110_C	2.691	1.00
120_L	143_Q	2.367	1.00
140_L	144_Y	2.305	1.00
76_F	81_E	2.275	1.00
89_E	105_R	2.094	1.00
118_D	121_P	2.080	1.00
178_L	224_Y	2.052	1.00
120_L	140_L	1.934	1.00
144_Y	152_A	1.914	1.00
90_N	106_V	1.902	1.00
76_F	84_D	1.902	1.00
160_A	170_P	1.890	1.00
92_I	102_N	1.890	1.00
124_Q	140_L	1.851	1.00
144_Y	149_K	1.824	0.99
137_W	159_N	1.804	0.99
154_A	174_V	1.803	0.99
134_S	141_A	1.776	0.99
140_L	156_A	1.765	0.99
93_S	103_L	1.757	0.99
66_I	70_F	1.750	0.99
86_D	90_N	1.744	0.99
103_L	122_L	1.642	0.99
224_Y	232_Q	1.614	0.99
141_A	160_A	1.564	0.98
127_T	137_W	1.530	0.98
77_E	109_K	1.481	0.98
126_A	129_Q	1.439	0.97
93_S	118_D	1.415	0.97
100_A	126_A	1.415	0.97
210_E	213_N	1.367	0.96
173_K	219_M	1.360	0.96
134_S	160_A	1.356	0.96
74_K	105_R	1.352	0.96
178_L	186_N	1.324	0.95
103_L	126_A	1.324	0.95
80_L	148_K	1.321	0.95
123_L	140_L	1.320	0.95
107_A	122_L	1.280	0.94
141_A	153_A	1.278	0.94
86_D	106_V	1.241	0.93
220_C	236_L	1.234	0.93
154_A	158_L	1.230	0.93
214_Y	240_Y	1.228	0.93
52_K	55_I	1.217	0.93
228_R	233_A	1.205	0.92
107_A	126_A	1.192	0.92
175_I	223_T	1.174	0.91
28_T	31_T	1.171	0.91
206_G	209_K	1.158	0.91
138_L	173_K	1.153	0.91
46_P	51_H	1.150	0.90
140_L	220_C	1.145	0.90
214_Y	221_V	1.145	0.90
217_M	240_Y	1.136	0.90
34_A	37_N	1.131	0.90
221_V	233_A	1.129	0.90
217_M	236_L	1.126	0.90
92_I	95_E	1.121	0.89
123_L	139_A	1.115	0.89
227_Q	235_T	1.113	0.89
154_A	177_L	1.096	0.88
73_I	92_I	1.091	0.88
139_A	142_I	1.080	0.87
29_V	32_D	1.074	0.87
29_V	34_A	1.070	0.87
66_I	92_I	1.062	0.87
102_N	109_K	1.058	0.86
161_Y	170_P	1.053	0.86
126_A	136_Y	1.049	0.86
31_T	37_N	1.043	0.86
35_Y	41_F	1.041	0.85
77_E	89_E	1.040	0.85
193_I	223_T	1.035	0.85
84_D	87_P	1.032	0.85
110_C	122_L	1.023	0.84
234_L	238_H	1.005	0.83
76_F	88_H	1.001	0.83
109_K	113_T	0.993	0.83
142_I	157_A	0.992	0.83
72_S	76_F	0.991	0.83
161_Y	174_V	0.987	0.82
237_L	241_A	0.979	0.82
120_L	124_Q	0.978	0.82
30_L	34_A	0.976	0.82
44_Y	47_I	0.963	0.81
151_E	155_Q	0.957	0.80
201_L	204_S	0.945	0.79
216_L	220_C	0.944	0.79
158_L	174_V	0.943	0.79
208_T	212_N	0.942	0.79
208_T	220_C	0.939	0.79
137_W	160_A	0.938	0.79
194_Q	197_K	0.933	0.79
222_D	237_L	0.933	0.79
225_F	230_P	0.927	0.78
120_L	154_A	0.917	0.77
221_V	240_Y	0.906	0.76
111_L	123_L	0.903	0.76
236_L	240_Y	0.896	0.76
157_A	161_Y	0.894	0.76
70_F	123_L	0.886	0.75
235_T	239_N	0.884	0.75
54_P	57_C	0.884	0.75
134_S	168_G	0.884	0.75
36_G	44_Y	0.883	0.75
89_E	237_L	0.879	0.74
134_S	214_Y	0.871	0.74
108_R	139_A	0.870	0.74
29_V	41_F	0.865	0.73
225_F	237_L	0.862	0.73
103_L	137_W	0.860	0.73
216_L	226_A	0.859	0.73
154_A	181_A	0.852	0.72
119_A	123_L	0.846	0.71
147_C	227_Q	0.840	0.71
205_F	213_N	0.837	0.71
200_G	204_S	0.830	0.70
124_Q	128_E	0.829	0.70
130_L	133_V	0.827	0.70
188_Q	193_I	0.825	0.69
118_D	186_N	0.815	0.69
86_D	110_C	0.809	0.68
203_L	229_K	0.807	0.68
154_A	234_L	0.806	0.68
133_V	137_W	0.805	0.68
72_S	110_C	0.804	0.68
220_C	224_Y	0.800	0.67
207_G	211_N	0.799	0.67
116_L	150_T	0.799	0.67
139_A	173_K	0.795	0.67
28_T	38_G	0.795	0.67
180_Q	235_T	0.794	0.67
84_D	185_P	0.791	0.66
54_P	58_E	0.788	0.66
137_W	156_A	0.787	0.66
46_P	69_A	0.786	0.66
203_L	230_P	0.785	0.66
121_P	124_Q	0.785	0.66
219_M	223_T	0.784	0.66
141_A	221_V	0.780	0.65
36_G	39_D	0.779	0.65
219_M	222_D	0.773	0.64
213_N	217_M	0.771	0.64
125_R	128_E	0.766	0.64
120_L	144_Y	0.765	0.64
142_I	173_K	0.751	0.62
130_L	136_Y	0.745	0.62
133_V	136_Y	0.740	0.61
197_K	220_C	0.739	0.61
31_T	40_C	0.737	0.61
45_W	49_Q	0.737	0.61
85_D	109_K	0.730	0.60
35_Y	40_C	0.728	0.60
57_C	159_N	0.727	0.60
121_P	153_A	0.725	0.59
28_T	32_D	0.723	0.59
158_L	211_N	0.720	0.59
116_L	120_L	0.720	0.59
221_V	236_L	0.718	0.59
32_D	37_N	0.717	0.59
105_R	125_R	0.713	0.58
108_R	111_L	0.712	0.58
103_L	171_D	0.712	0.58
218_Q	221_V	0.709	0.58
168_G	175_I	0.706	0.57
131_P	145_R	0.704	0.57
117_D	148_K	0.703	0.57
29_V	37_N	0.703	0.57
152_A	155_Q	0.702	0.57
223_T	227_Q	0.702	0.57
33_A	44_Y	0.701	0.57
110_C	178_L	0.698	0.57
30_L	36_G	0.697	0.56
167_F	171_D	0.696	0.56
70_F	102_N	0.695	0.56
121_P	155_Q	0.692	0.56
173_K	176_H	0.690	0.56
31_T	35_Y	0.690	0.56
74_K	89_E	0.689	0.56
80_L	105_R	0.689	0.56
28_T	33_A	0.688	0.56
160_A	175_I	0.682	0.55
93_S	175_I	0.682	0.55
208_T	229_K	0.680	0.55
196_I	204_S	0.678	0.54
138_L	160_A	0.675	0.54
70_F	73_I	0.675	0.54
185_P	227_Q	0.672	0.54
47_I	50_E	0.672	0.54
44_Y	51_H	0.664	0.53
74_K	77_E	0.663	0.53
32_D	41_F	0.663	0.53
117_D	147_C	0.662	0.53
122_L	126_A	0.660	0.52
120_L	147_C	0.657	0.52
47_I	73_I	0.655	0.52
92_I	126_A	0.654	0.52
161_Y	171_D	0.653	0.52
89_E	157_A	0.650	0.51
215_P	221_V	0.648	0.51
205_F	211_N	0.647	0.51
65_R	68_P	0.647	0.51
140_L	174_V	0.645	0.51
182_A	187_F	0.642	0.50
226_A	240_Y	0.641	0.50
208_T	211_N	0.641	0.50
176_H	219_M	0.636	0.50
115_R	129_Q	0.633	0.49
31_T	51_H	0.632	0.49
46_P	54_P	0.630	0.49
213_N	220_C	0.630	0.49
41_F	46_P	0.628	0.49
242_W	245_S	0.627	0.49
205_F	245_S	0.627	0.49
207_G	223_T	0.626	0.49
193_I	196_I	0.625	0.49
207_G	221_V	0.623	0.48
92_I	109_K	0.622	0.48
118_D	122_L	0.620	0.48
179_S	219_M	0.617	0.48
46_P	63_E	0.616	0.48
141_A	156_A	0.615	0.48
185_P	231_L	0.614	0.47
104_F	126_A	0.613	0.47
172_N	244_M	0.612	0.47
187_F	241_A	0.612	0.47
84_D	88_H	0.611	0.47
102_N	105_R	0.611	0.47
173_K	179_S	0.610	0.47
33_A	41_F	0.607	0.47
107_A	187_F	0.601	0.46
159_N	239_N	0.601	0.46
213_N	228_R	0.601	0.46
34_A	38_G	0.601	0.46
28_T	34_A	0.596	0.45
129_Q	163_G	0.595	0.45
33_A	37_N	0.594	0.45
143_Q	147_C	0.591	0.45
70_F	186_N	0.580	0.44
41_F	48_G	0.578	0.43
206_G	211_N	0.576	0.43
224_Y	229_K	0.576	0.43
196_I	210_E	0.576	0.43
77_E	93_S	0.576	0.43
28_T	37_N	0.575	0.43
157_A	170_P	0.575	0.43
157_A	184_V	0.575	0.43
67_V	70_F	0.569	0.43
48_G	59_T	0.569	0.43
37_N	41_F	0.569	0.43
210_E	216_L	0.565	0.42
87_P	90_N	0.564	0.42
73_I	212_N	0.562	0.42
244_M	247_E	0.562	0.42
73_I	85_D	0.562	0.42
77_E	82_V	0.561	0.42
154_A	169_V	0.559	0.41
35_Y	39_D	0.556	0.41
158_L	231_L	0.556	0.41
168_G	185_P	0.556	0.41
85_D	153_A	0.556	0.41
44_Y	48_G	0.556	0.41
89_E	109_K	0.550	0.40
158_L	186_N	0.550	0.40
114_G	224_Y	0.550	0.40
209_K	212_N	0.549	0.40
39_D	43_L	0.547	0.40
117_D	120_L	0.544	0.40
217_M	239_N	0.542	0.40
220_C	226_A	0.542	0.40
60_Y	125_R	0.541	0.40
110_C	115_R	0.539	0.39
204_S	208_T	0.538	0.39
35_Y	38_G	0.538	0.39
101_A	109_K	0.537	0.39
42_G	51_H	0.535	0.39
28_T	44_Y	0.534	0.39
139_A	148_K	0.534	0.39
205_F	230_P	0.534	0.39
53_L	227_Q	0.533	0.39
58_E	183_D	0.531	0.38
79_W	84_D	0.530	0.38
83_N	159_N	0.528	0.38
39_D	70_F	0.527	0.38
53_L	56_V	0.524	0.38
52_K	58_E	0.522	0.38
106_V	113_T	0.522	0.38
160_A	163_G	0.522	0.38
143_Q	225_F	0.521	0.37
77_E	92_I	0.520	0.37
103_L	129_Q	0.520	0.37
29_V	39_D	0.519	0.37
142_I	146_R	0.517	0.37
233_A	237_L	0.517	0.37
35_Y	43_L	0.517	0.37
174_V	177_L	0.516	0.37
124_Q	240_Y	0.513	0.37
207_G	215_P	0.512	0.37
221_V	230_P	0.511	0.36
233_A	244_M	0.510	0.36
67_V	79_W	0.510	0.36
188_Q	221_V	0.507	0.36
55_I	119_A	0.504	0.36
89_E	93_S	0.503	0.36
57_C	60_Y	0.503	0.36
48_G	56_V	0.502	0.36
69_A	97_Q	0.501	0.35
144_Y	156_A	0.500	0.35

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
3q7aA	1	0.8865	99.9	0.395	Contact Map
3dssA	1	0.8936	99.9	0.402	Contact Map
4l9pA	1	0.8369	99.9	0.414	Contact Map
3draA	1	0.8901	99.9	0.424	Contact Map
3urzA	1	0.6738	99.9	0.427	Contact Map
1w3bA	2	0.8901	99.9	0.429	Contact Map
4gywA	2	0.7376	99.9	0.436	Contact Map
1dceA	1	0.9397	99.9	0.438	Contact Map
2h6fA	1	0.8901	99.9	0.44	Contact Map
4ui9C	2	0.883	99.9	0.442	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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