YRAR - ECOLI - GREMLIN Contacts

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YRAR - Uncharacterized protein YraR

UniProt:	P45469	Sequences: MSQVLITGATGLVGGHLLRMLINEPKVNAIAAPTRRPLGDMPGVFNPHDPQLSDALAQVTDPIDIVFCCLGTTRREAGSKEAFIHADYTLVVDTALTGRRLGAQHMLVVSAMGANAHSPFFYNRVKGEMEEALIAQNWPKLTIARPSMLLGDRSKQRMNETLFAPLFRLLPGNWKSIDARDVARVMLAESMRPEHEGVTILSSSELRKRAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12783
Length:	211 (192)
Sequences:	48950 (33678)
Seq/√Len:	2430.5

ECOLI - YRAR RMLB2 GM4D YEEZ YBJS GALE RMLB1 HLDD YFCH FCL QOR2 RMLD YBJT ARNA
BACSU - YWNB RMLB YFNG YHFK YTCB GALE YFHF YTBQ YHEG SPSK YESF EPSC
HALSA - Q9HSU9 Q9HNV3 Q9HML4 Q9HSV1 Q9HRD1 Q9HS50 Q9HR86 Q9HSQ3 Q9HSE7 Q9HPF1
SULSO - Q97VN5 Q97XJ9 Q980W1 Q97XG1 Q7LXE8 Q97UM3 Q7LXG5 Q7LX44

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_A	32_A	3.383	1.00
3_Q	29_A	2.958	1.00
20_M	184_R	2.610	1.00
57_A	100_R	2.462	1.00
85_H	89_T	2.394	1.00
33_P	50_P	2.204	1.00
65_I	190_S	2.200	1.00
109_V	186_M	2.132	1.00
31_A	63_I	2.075	1.00
105_H	140_K	2.045	1.00
20_M	24_E	1.981	1.00
5_L	63_I	1.974	1.00
146_P	186_M	1.972	1.00
79_S	82_A	1.955	1.00
6_I	18_L	1.935	1.00
68_C	108_V	1.922	1.00
31_A	46_N	1.914	1.00
67_F	190_S	1.860	1.00
7_T	68_C	1.839	1.00
3_Q	31_A	1.834	1.00
24_E	191_M	1.827	1.00
29_A	46_N	1.774	1.00
20_M	187_L	1.764	1.00
133_L	141_L	1.739	1.00
53_S	85_H	1.737	1.00
184_R	188_A	1.725	1.00
31_A	48_H	1.689	1.00
144_A	189_E	1.684	1.00
17_L	183_A	1.661	1.00
95_A	136_Q	1.647	1.00
110_S	114_A	1.629	1.00
92_V	96_L	1.549	1.00
69_C	109_V	1.547	1.00
17_L	67_F	1.539	1.00
92_V	132_A	1.537	1.00
64_D	104_Q	1.505	1.00
57_A	97_T	1.504	1.00
17_L	69_C	1.500	1.00
13_V	149_L	1.497	1.00
91_V	129_M	1.490	1.00
89_T	92_V	1.481	1.00
36_R	47_P	1.457	1.00
10_T	34_T	1.448	1.00
127_G	131_E	1.433	1.00
84_I	128_E	1.409	1.00
20_M	23_N	1.405	1.00
157_R	160_E	1.395	1.00
18_L	32_A	1.384	1.00
57_A	101_L	1.383	1.00
105_H	142_T	1.381	1.00
87_D	125_V	1.379	1.00
19_R	153_R	1.334	1.00
144_A	186_M	1.308	1.00
137_N	141_L	1.300	1.00
20_M	183_A	1.296	1.00
98_G	106_M	1.295	1.00
52_L	90_L	1.292	1.00
67_F	186_M	1.288	1.00
68_C	91_V	1.278	1.00
94_T	106_M	1.267	1.00
24_E	187_L	1.267	1.00
150_L	178_D	1.263	1.00
187_L	191_M	1.259	1.00
158_M	162_L	1.259	1.00
4_V	28_N	1.248	1.00
122_Y	126_K	1.245	1.00
66_V	98_G	1.243	1.00
188_A	192_R	1.239	1.00
109_V	146_P	1.228	1.00
28_N	191_M	1.227	1.00
131_E	134_I	1.225	1.00
165_P	170_L	1.225	1.00
107_L	144_A	1.207	1.00
81_E	85_H	1.205	1.00
24_E	28_N	1.199	1.00
61_D	101_L	1.195	1.00
9_A	18_L	1.187	1.00
177_I	182_V	1.185	1.00
130_E	145_R	1.175	1.00
4_V	21_L	1.172	1.00
5_L	33_P	1.171	1.00
4_V	65_I	1.167	1.00
108_V	129_M	1.153	1.00
16_H	180_R	1.151	1.00
32_A	45_F	1.150	1.00
69_C	186_M	1.145	1.00
7_T	94_T	1.134	1.00
22_I	45_F	1.130	1.00
179_A	183_A	1.117	1.00
160_E	163_F	1.117	1.00
98_G	103_A	1.108	1.00
96_L	99_R	1.103	1.00
58_Q	61_D	1.098	1.00
146_P	182_V	1.093	1.00
95_A	106_M	1.093	1.00
134_I	143_I	1.091	1.00
52_L	70_L	1.088	1.00
20_M	180_R	1.081	1.00
108_V	133_L	1.080	1.00
56_L	97_T	1.069	1.00
19_R	23_N	1.067	1.00
60_T	66_V	1.062	1.00
55_A	96_L	1.054	1.00
124_R	128_E	1.049	1.00
156_Q	160_E	1.048	1.00
160_E	164_A	1.031	1.00
25_P	28_N	1.029	1.00
66_V	94_T	1.028	1.00
86_A	90_L	1.018	1.00
178_D	181_D	1.018	1.00
160_E	166_L	0.998	1.00
89_T	93_D	0.995	1.00
31_A	62_P	0.994	1.00
36_R	39_G	0.989	1.00
96_L	100_R	0.985	1.00
161_T	165_P	0.981	1.00
164_A	168_R	0.970	1.00
95_A	132_A	0.967	1.00
106_M	133_L	0.965	1.00
17_L	21_L	0.962	1.00
33_P	56_L	0.960	1.00
21_L	187_L	0.960	1.00
149_L	182_V	0.959	1.00
3_Q	28_N	0.957	1.00
108_V	143_I	0.950	1.00
57_A	61_D	0.945	1.00
22_I	44_V	0.941	1.00
60_T	63_I	0.938	1.00
112_M	147_S	0.929	1.00
110_S	130_E	0.926	1.00
72_T	86_A	0.924	1.00
132_A	135_A	0.922	1.00
3_Q	63_I	0.919	1.00
4_V	67_F	0.919	1.00
157_R	161_T	0.914	1.00
88_Y	128_E	0.913	1.00
34_T	47_P	0.910	1.00
95_A	133_L	0.901	1.00
12_L	179_A	0.899	1.00
96_L	136_Q	0.896	1.00
97_T	101_L	0.896	1.00
84_I	89_T	0.894	1.00
83_F	125_V	0.891	1.00
99_R	139_P	0.891	1.00
93_D	96_L	0.883	1.00
166_L	169_L	0.879	1.00
166_L	170_L	0.873	1.00
60_T	101_L	0.871	1.00
142_T	189_E	0.870	1.00
60_T	97_T	0.863	1.00
35_R	51_Q	0.856	1.00
15_G	153_R	0.847	1.00
33_P	59_V	0.841	1.00
16_H	179_A	0.840	1.00
159_N	163_F	0.840	1.00
99_R	136_Q	0.836	1.00
12_L	151_G	0.824	1.00
163_F	166_L	0.814	1.00
168_R	171_P	0.807	1.00
7_T	70_L	0.806	1.00
3_Q	64_D	0.803	1.00
42_P	45_F	0.802	1.00
37_P	49_D	0.801	1.00
134_I	141_L	0.797	1.00
147_S	175_K	0.797	1.00
60_T	98_G	0.790	1.00
22_I	30_I	0.787	1.00
84_I	88_Y	0.787	1.00
16_H	20_M	0.784	1.00
36_R	49_D	0.779	1.00
144_A	185_V	0.774	1.00
97_T	100_R	0.773	1.00
18_L	30_I	0.770	1.00
152_D	178_D	0.768	1.00
193_P	196_E	0.762	1.00
188_A	191_M	0.761	1.00
25_P	44_V	0.761	1.00
72_T	83_F	0.752	1.00
162_L	165_P	0.746	1.00
48_H	59_V	0.745	1.00
56_L	93_D	0.737	1.00
55_A	93_D	0.732	1.00
184_R	187_L	0.732	1.00
91_V	133_L	0.724	1.00
129_M	133_L	0.720	1.00
4_V	190_S	0.720	1.00
104_Q	140_K	0.720	1.00
131_E	135_A	0.718	1.00
156_Q	159_N	0.717	1.00
28_N	64_D	0.716	1.00
135_A	139_P	0.716	1.00
17_L	186_M	0.708	1.00
66_V	106_M	0.707	1.00
162_L	166_L	0.706	1.00
134_I	138_W	0.705	1.00
157_R	162_L	0.702	1.00
165_P	169_L	0.701	1.00
16_H	19_R	0.696	1.00
82_A	85_H	0.696	1.00
142_T	193_P	0.696	1.00
124_R	135_A	0.692	1.00
120_F	123_N	0.691	1.00
5_L	60_T	0.688	1.00
10_T	36_R	0.687	1.00
105_H	193_P	0.687	1.00
113_G	123_N	0.686	1.00
84_I	124_R	0.679	1.00
161_T	164_A	0.676	1.00
160_E	165_P	0.672	1.00
5_L	50_P	0.670	1.00
167_F	170_L	0.666	1.00
16_H	183_A	0.665	1.00
159_N	162_L	0.665	1.00
115_N	145_R	0.665	1.00
36_R	41_M	0.663	1.00
146_P	149_L	0.658	1.00
156_Q	161_T	0.655	1.00
114_A	145_R	0.652	1.00
162_L	169_L	0.646	1.00
13_V	182_V	0.646	1.00
149_L	177_I	0.645	1.00
72_T	87_D	0.638	1.00
53_S	86_A	0.633	1.00
65_I	105_H	0.633	1.00
21_L	190_S	0.633	1.00
84_I	125_V	0.629	1.00
69_C	146_P	0.629	1.00
160_E	170_L	0.628	1.00
160_E	168_R	0.627	1.00
29_A	44_V	0.623	1.00
128_E	131_E	0.622	1.00
183_A	187_L	0.617	1.00
161_T	166_L	0.615	1.00
59_V	63_I	0.613	1.00
3_Q	62_P	0.609	1.00
158_M	161_T	0.608	1.00
132_A	136_Q	0.608	1.00
90_L	93_D	0.602	1.00
124_R	131_E	0.601	1.00
148_M	176_S	0.597	1.00
128_E	132_A	0.596	1.00
32_A	47_P	0.594	1.00
114_A	130_E	0.591	1.00
135_A	138_W	0.591	1.00
157_R	169_L	0.589	1.00
24_E	188_A	0.587	1.00
72_T	82_A	0.587	1.00
163_F	167_F	0.583	1.00
24_E	184_R	0.582	1.00
92_V	136_Q	0.578	1.00
165_P	168_R	0.578	1.00
96_L	132_A	0.576	1.00
5_L	66_V	0.573	1.00
60_T	94_T	0.572	1.00
93_D	97_T	0.570	1.00
19_R	180_R	0.566	1.00
157_R	163_F	0.563	1.00
107_L	189_E	0.562	1.00
55_A	100_R	0.560	1.00
54_D	57_A	0.553	1.00
80_K	124_R	0.553	1.00
91_V	95_A	0.551	1.00
111_A	114_A	0.546	1.00
41_M	49_D	0.545	1.00
22_I	42_P	0.543	1.00
110_S	143_I	0.542	1.00
134_I	137_N	0.541	1.00
158_M	163_F	0.538	1.00
31_A	59_V	0.536	1.00
177_I	181_D	0.535	1.00
114_A	127_G	0.534	1.00
181_D	184_R	0.534	1.00
16_H	153_R	0.532	1.00
71_G	87_D	0.523	1.00
21_L	25_P	0.521	1.00
6_I	21_L	0.521	1.00
163_F	170_L	0.519	1.00
65_I	104_Q	0.518	1.00
107_L	190_S	0.515	1.00
28_N	65_I	0.514	1.00
65_I	107_L	0.514	1.00
140_K	195_H	0.512	1.00
121_F	125_V	0.506	1.00
160_E	169_L	0.505	1.00
88_Y	125_V	0.504	1.00
133_L	143_I	0.504	1.00
66_V	103_A	0.500	1.00
5_L	59_V	0.500	1.00

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
2x4gA	2	0.9242	100	0.248	Contact Map
2pzmA	2	0.981	100	0.256	Contact Map
2q1wA	2	0.9763	100	0.259	Contact Map
3m2pA	2	0.9621	100	0.26	Contact Map
1sb8A	2	0.9905	100	0.263	Contact Map
3rufA	2	0.9905	100	0.268	Contact Map
4wkgA	5	0.9858	100	0.268	Contact Map
1rkxA	3	0.9905	100	0.269	Contact Map
2q1sA	2	0.9573	100	0.271	Contact Map
1orrA	3	0.9858	100	0.271	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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