YURK - BACSU - GREMLIN Contacts

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YURK - Uncharacterized HTH-type transcriptional regulator YurK

UniProt:	O32152	Sequences: MLNNGSSTPLYIQLKQIITDDIKKGVYSPTAKLPTENELCTKYNVSRITVRKAILDLVEEGYLIRQQGKGTFVKSPKLKRELIAVNGYSEFMESTGKKPKHHVLSHDIIPASKPIAEKLQIQPESPVVELKRILYNDDQPLTFEVTHYPLDLFPGIDTFIADGVSMHDILKQQYKVVPTHNTKLLNVVYAQQEESKYLDCDIGDALFEIDKTAFTSNDQPIYCSLFLMHTNRVTFTINSPYT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	242 (195)
Sequences:	25513 (19795)
Seq/√Len:	1417.6

ECOLI - YIHL FRLR YIDP MNGR YEGW PHNF NANR UXUR FADR EXUR GLCC PDHR LLDR YIEP YJJM DGOR MCBR
BACSU - YURK YMFC YVOA YYDK TRER GMUR YBGA YCBG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_S	31_A	4.040	1.00
21_D	26_V	3.923	1.00
19_T	60_E	3.352	1.00
15_K	56_D	3.296	1.00
21_D	42_K	3.285	1.00
64_I	74_K	2.836	1.00
14_L	45_V	2.675	1.00
36_E	47_R	2.663	1.00
186_N	189_Y	2.648	1.00
17_I	21_D	2.530	1.00
65_R	71_T	2.488	1.00
66_Q	69_K	2.369	1.00
14_L	43_Y	2.292	1.00
15_K	60_E	2.281	1.00
20_D	24_K	2.160	1.00
32_K	72_F	2.142	1.00
112_S	115_I	2.091	1.00
8_T	16_Q	2.035	1.00
17_I	43_Y	1.989	1.00
15_K	19_T	1.958	1.00
105_S	191_Q	1.899	1.00
69_K	72_F	1.843	1.00
58_V	65_R	1.825	1.00
134_L	142_T	1.802	1.00
52_K	55_L	1.766	1.00
19_T	23_K	1.752	1.00
37_N	41_T	1.718	1.00
10_L	13_Q	1.685	1.00
121_I	125_S	1.685	1.00
38_E	42_K	1.673	1.00
17_I	20_D	1.603	1.00
191_Q	194_E	1.600	1.00
21_D	27_Y	1.592	1.00
58_V	63_L	1.592	1.00
191_Q	195_S	1.586	1.00
115_I	137_D	1.582	1.00
19_T	62_Y	1.552	1.00
35_T	38_E	1.548	1.00
39_L	50_V	1.533	1.00
66_Q	72_F	1.526	1.00
13_Q	17_I	1.524	1.00
63_L	71_T	1.489	1.00
22_I	73_V	1.475	1.00
36_E	51_R	1.469	1.00
54_I	63_L	1.465	1.00
181_N	189_Y	1.448	1.00
130_L	146_T	1.435	1.00
131_K	134_L	1.416	1.00
27_Y	73_V	1.401	1.00
55_L	65_R	1.395	1.00
109_I	187_V	1.390	1.00
189_Y	193_E	1.385	1.00
64_I	72_F	1.377	1.00
111_A	116_A	1.373	1.00
122_Q	125_S	1.362	1.00
100_K	135_Y	1.344	1.00
11_Y	56_D	1.340	1.00
45_V	50_V	1.331	1.00
91_F	139_Q	1.321	1.00
98_K	102_H	1.310	1.00
38_E	41_T	1.282	1.00
56_D	59_E	1.267	1.00
8_T	13_Q	1.266	1.00
192_Q	196_K	1.263	1.00
29_P	75_S	1.250	1.00
179_T	183_K	1.245	1.00
102_H	135_Y	1.244	1.00
111_A	115_I	1.238	1.00
55_L	59_E	1.233	1.00
21_D	25_G	1.230	1.00
9_P	12_I	1.225	1.00
55_L	58_V	1.210	1.00
187_V	191_Q	1.208	1.00
115_I	147_H	1.190	1.00
130_L	134_L	1.190	1.00
23_K	62_Y	1.170	1.00
129_E	145_V	1.162	1.00
143_F	147_H	1.139	1.00
109_I	129_E	1.113	1.00
66_Q	70_G	1.108	1.00
54_I	71_T	1.108	1.00
32_K	70_G	1.101	1.00
104_L	108_I	1.101	1.00
56_D	60_E	1.095	1.00
140_P	151_D	1.080	1.00
176_V	180_H	1.074	1.00
91_F	95_T	1.064	1.00
21_D	43_Y	1.052	1.00
27_Y	31_A	1.044	1.00
107_D	129_E	1.042	1.00
116_A	183_K	1.039	1.00
12_I	56_D	1.036	1.00
127_V	131_K	1.021	1.00
120_Q	123_P	1.019	1.00
143_F	194_E	1.014	1.00
180_H	184_L	1.010	1.00
12_I	16_Q	1.008	1.00
167_H	171_K	1.003	1.00
89_S	93_E	0.999	1.00
116_A	119_L	0.996	1.00
97_K	101_H	0.989	1.00
189_Y	192_Q	0.975	1.00
133_I	145_V	0.970	1.00
177_V	193_E	0.955	1.00
131_K	145_V	0.954	1.00
195_S	199_D	0.952	1.00
132_R	182_T	0.945	1.00
11_Y	15_K	0.940	1.00
166_M	170_L	0.933	1.00
10_L	49_T	0.932	1.00
168_D	172_Q	0.920	1.00
165_S	168_D	0.915	1.00
52_K	56_D	0.913	1.00
113_K	117_E	0.908	1.00
68_G	71_T	0.907	1.00
111_A	185_L	0.904	1.00
131_K	135_Y	0.902	1.00
105_S	129_E	0.900	1.00
16_Q	19_T	0.896	1.00
30_T	64_I	0.891	1.00
116_A	179_T	0.889	1.00
124_E	127_V	0.887	1.00
96_G	100_K	0.882	1.00
184_L	189_Y	0.882	1.00
32_K	35_T	0.882	1.00
201_D	204_D	0.881	1.00
18_I	39_L	0.879	1.00
118_K	131_K	0.877	1.00
108_I	150_L	0.866	1.00
39_L	54_I	0.866	1.00
46_S	49_T	0.864	1.00
171_K	177_V	0.857	1.00
105_S	131_K	0.856	1.00
157_D	160_I	0.854	1.00
8_T	12_I	0.853	1.00
142_T	146_T	0.845	1.00
100_K	138_D	0.843	1.00
97_K	199_D	0.833	1.00
36_E	65_R	0.831	1.00
94_S	110_P	0.828	1.00
54_I	58_V	0.816	1.00
105_S	187_V	0.814	1.00
40_C	50_V	0.807	1.00
188_V	194_E	0.804	1.00
29_P	74_K	0.804	1.00
126_P	150_L	0.799	1.00
113_K	116_A	0.792	1.00
180_H	183_K	0.790	1.00
190_A	200_C	0.783	1.00
30_T	75_S	0.780	1.00
128_V	132_R	0.779	1.00
136_N	142_T	0.777	1.00
114_P	118_K	0.772	1.00
17_I	42_K	0.768	1.00
166_M	169_I	0.763	1.00
11_Y	52_K	0.761	1.00
129_E	175_K	0.758	1.00
131_K	193_E	0.758	1.00
188_V	191_Q	0.757	1.00
33_L	63_L	0.753	1.00
158_T	161_A	0.749	1.00
90_E	93_E	0.746	1.00
156_I	159_F	0.744	1.00
121_I	124_E	0.743	1.00
26_V	42_K	0.742	1.00
125_S	151_D	0.740	1.00
188_V	192_Q	0.738	1.00
96_G	99_P	0.736	1.00
16_Q	20_D	0.734	1.00
130_L	149_P	0.731	1.00
88_Y	92_M	0.730	1.00
120_Q	124_E	0.727	1.00
108_I	126_P	0.727	1.00
106_H	109_I	0.725	1.00
105_S	188_V	0.721	1.00
112_S	116_A	0.721	1.00
102_H	105_S	0.717	1.00
128_V	179_T	0.717	1.00
144_E	147_H	0.717	1.00
92_M	136_N	0.709	1.00
14_L	17_I	0.709	1.00
21_D	24_K	0.709	1.00
87_G	90_E	0.707	1.00
27_Y	33_L	0.705	1.00
123_P	127_V	0.704	1.00
90_E	94_S	0.701	1.00
192_Q	195_S	0.700	1.00
14_L	50_V	0.698	1.00
95_T	144_E	0.690	1.00
156_I	160_I	0.682	1.00
41_T	44_N	0.679	1.00
178_P	194_E	0.678	1.00
43_Y	50_V	0.677	1.00
18_I	27_Y	0.673	1.00
151_D	154_P	0.667	1.00
193_E	196_K	0.667	1.00
177_V	180_H	0.667	1.00
34_P	42_K	0.666	1.00
84_A	139_Q	0.666	1.00
115_I	118_K	0.665	1.00
194_E	197_Y	0.658	1.00
145_V	149_P	0.658	1.00
169_I	172_Q	0.657	1.00
101_H	104_L	0.656	1.00
116_A	185_L	0.654	1.00
178_P	193_E	0.652	1.00
101_H	195_S	0.651	1.00
140_P	143_F	0.650	1.00
37_N	40_C	0.648	1.00
181_N	186_N	0.647	1.00
110_P	126_P	0.647	1.00
176_V	179_T	0.644	1.00
40_C	43_Y	0.642	1.00
101_H	191_Q	0.642	1.00
159_F	162_D	0.639	1.00
149_P	152_L	0.638	1.00
39_L	43_Y	0.635	1.00
36_E	71_T	0.625	1.00
129_E	132_R	0.623	1.00
112_S	119_L	0.623	1.00
101_H	105_S	0.622	1.00
172_Q	200_C	0.621	1.00
165_S	169_I	0.617	1.00
200_C	204_D	0.616	1.00
97_K	195_S	0.612	1.00
136_N	141_L	0.599	1.00
7_S	13_Q	0.597	1.00
111_A	127_V	0.596	1.00
98_K	191_Q	0.595	1.00
108_I	128_V	0.593	1.00
54_I	65_R	0.589	1.00
177_V	189_Y	0.587	1.00
130_L	142_T	0.585	1.00
105_S	109_I	0.583	1.00
104_L	133_I	0.583	1.00
150_L	154_P	0.580	1.00
190_A	204_D	0.575	1.00
50_V	63_L	0.572	1.00
14_L	18_I	0.570	1.00
106_H	110_P	0.569	1.00
126_P	149_P	0.567	1.00
97_K	137_D	0.566	1.00
115_I	119_L	0.564	1.00
58_V	71_T	0.564	1.00
105_S	108_I	0.564	1.00
111_A	135_Y	0.562	1.00
153_F	156_I	0.560	1.00
111_A	119_L	0.559	1.00
153_F	157_D	0.559	1.00
135_Y	138_D	0.558	1.00
94_S	106_H	0.556	1.00
15_K	53_A	0.553	1.00
152_L	155_G	0.553	1.00
190_A	195_S	0.552	1.00
195_S	203_G	0.551	1.00
49_T	53_A	0.551	1.00
100_K	103_V	0.551	1.00
14_L	53_A	0.549	1.00
196_K	200_C	0.549	1.00
32_K	69_K	0.547	1.00
119_L	131_K	0.547	1.00
35_T	68_G	0.546	1.00
189_Y	204_D	0.545	1.00
175_K	197_Y	0.543	1.00
97_K	100_K	0.543	1.00
40_C	48_I	0.540	1.00
49_T	52_K	0.539	1.00
127_V	130_L	0.537	1.00
190_A	203_G	0.537	1.00
194_E	198_L	0.531	1.00
20_D	23_K	0.531	1.00
48_I	52_K	0.529	1.00
107_D	111_A	0.528	1.00
77_K	80_R	0.527	1.00
102_H	133_I	0.526	1.00
40_C	47_R	0.526	1.00
115_I	134_L	0.525	1.00
133_I	149_P	0.513	1.00
12_I	15_K	0.512	1.00
118_K	134_L	0.511	1.00
72_F	75_S	0.509	1.00
67_Q	70_G	0.508	1.00
37_N	47_R	0.507	1.00
34_P	49_T	0.507	1.00
93_E	96_G	0.507	1.00
151_D	155_G	0.507	1.00
102_H	106_H	0.505	1.00
103_V	107_D	0.505	1.00
98_K	141_L	0.504	1.00
20_D	26_V	0.503	1.00
106_H	112_S	0.500	1.00
190_A	194_E	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
4u0wA	2	0.9959	100	0.128	Contact Map
2ra5A	2	0.6116	100	0.153	Contact Map
3f8mA	2	0.9421	100	0.173	Contact Map
3edpA	2	0.9132	100	0.19	Contact Map
3eetA	2	0.9545	100	0.2	Contact Map
3bwgA	2	0.9421	100	0.208	Contact Map
1hw1A	2	0.8099	100	0.451	Contact Map
4p96A	2	0.8926	99.9	0.459	Contact Map
3c7jA	4	0.8512	99.9	0.466	Contact Map
3f8lA	2	0.6694	99.9	0.467	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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