KIPR - BACSU - GREMLIN Contacts

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KIPR - HTH-type transcriptional regulator KipR

UniProt:	P42968	Sequences: MQNKNKTVVKSMALLNLFLHKPSLTLSELVSLTGMPKTSVHRMVSSLEEMGFLSRDASGAYSLGLVFLEFGQLVADRLDIRKIAKPVMEELCREVDEAVQLIMRDGNEAIYVEKIEGTQTVRLYTAIGRRSPLYAGACARSILSFLPREEIEAYIKQTELISIGSGTITDPEKLLQEIDASVQNGYTVSYSELENYTAAIGAPIFNHERQVAAGISIAGFEARFTEDRLPYLTEKVKDAALQISRKIGYT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	250 (242)
Sequences:	12710 (9364)
Seq/√Len:	602.0

ECOLI - YJHI RHMR ALLR KDGR YAGI ICLR YIAJ MHPR
BACSU - KIPR
HALSA - Q9HHM8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_V	11_S	3.157	1.00
94_E	235_K	3.146	1.00
9_V	50_M	2.824	1.00
102_I	138_C	2.809	1.00
87_V	239_A	2.795	1.00
180_A	184_N	2.626	1.00
16_N	66_V	2.573	1.00
85_K	113_E	2.458	1.00
140_R	177_E	2.401	1.00
12_M	52_F	2.351	1.00
152_E	175_L	2.321	1.00
108_E	130_R	2.228	1.00
140_R	192_E	2.189	1.00
87_V	242_Q	2.125	1.00
18_F	53_L	2.099	1.00
146_L	150_E	2.068	1.00
97_E	223_R	2.050	1.00
89_E	115_I	2.043	1.00
13_A	50_M	2.009	1.00
145_F	205_F	1.922	1.00
104_R	133_L	1.886	1.00
202_A	236_V	1.857	1.00
87_V	246_K	1.846	1.00
202_A	240_A	1.840	1.00
189_S	199_A	1.834	1.00
190_Y	198_A	1.822	1.00
90_E	242_Q	1.799	1.00
198_A	221_E	1.797	1.00
54_S	62_S	1.783	1.00
233_T	237_K	1.773	1.00
14_L	29_L	1.755	1.00
90_E	94_E	1.717	1.00
17_L	24_L	1.703	1.00
92_C	99_V	1.702	1.00
17_L	32_L	1.695	1.00
84_A	243_I	1.687	1.00
16_N	50_M	1.684	1.00
17_L	33_T	1.684	1.00
170_D	173_K	1.681	1.00
44_V	53_L	1.663	1.00
171_P	175_L	1.658	1.00
17_L	29_L	1.658	1.00
202_A	237_K	1.654	1.00
191_S	221_E	1.635	1.00
219_G	224_F	1.601	1.00
24_L	32_L	1.599	1.00
25_T	28_E	1.588	1.00
44_V	61_Y	1.557	1.00
228_R	231_Y	1.546	1.00
186_Y	233_T	1.539	1.00
217_I	232_L	1.528	1.00
177_E	180_A	1.524	1.00
95_V	235_K	1.519	1.00
164_G	167_T	1.517	1.00
29_L	40_V	1.516	1.00
23_S	62_S	1.507	1.00
87_V	90_E	1.506	1.00
191_S	196_Y	1.501	1.00
151_I	175_L	1.486	1.00
35_M	40_V	1.481	1.00
147_P	150_E	1.480	1.00
181_S	187_T	1.480	1.00
23_S	60_A	1.473	1.00
235_K	238_D	1.471	1.00
109_A	142_I	1.422	1.00
66_V	69_E	1.412	1.00
48_E	53_L	1.405	1.00
116_E	122_R	1.403	1.00
18_F	23_S	1.403	1.00
205_F	244_S	1.393	1.00
152_E	171_P	1.380	1.00
48_E	55_R	1.376	1.00
109_A	133_L	1.350	1.00
84_A	101_L	1.349	1.00
12_M	50_M	1.342	1.00
56_D	62_S	1.340	1.00
92_C	115_I	1.329	1.00
16_N	52_F	1.322	1.00
81_R	113_E	1.320	1.00
107_N	157_Q	1.305	1.00
240_A	244_S	1.296	1.00
18_F	24_L	1.295	1.00
91_L	235_K	1.290	1.00
156_K	171_P	1.267	1.00
88_M	101_L	1.255	1.00
178_I	181_S	1.247	1.00
168_I	177_E	1.245	1.00
30_V	40_V	1.245	1.00
85_K	89_E	1.245	1.00
41_H	45_S	1.242	1.00
91_L	239_A	1.229	1.00
148_R	175_L	1.223	1.00
238_D	242_Q	1.221	1.00
36_P	39_S	1.212	1.00
29_L	44_V	1.209	1.00
205_F	211_V	1.167	1.00
144_S	181_S	1.165	1.00
148_R	152_E	1.149	1.00
26_L	41_H	1.130	1.00
104_R	146_L	1.113	1.00
145_F	203_P	1.111	1.00
202_A	233_T	1.109	1.00
166_G	191_S	1.109	1.00
27_S	31_S	1.106	1.00
145_F	211_V	1.102	1.00
9_V	46_S	1.097	1.00
95_V	232_L	1.094	1.00
237_K	241_L	1.093	1.00
151_I	182_V	1.090	1.00
135_A	167_T	1.085	1.00
104_R	107_N	1.084	1.00
102_I	109_A	1.082	1.00
135_A	163_I	1.077	1.00
21_K	32_L	1.076	1.00
138_C	214_G	1.071	1.00
25_T	60_A	1.063	1.00
148_R	151_I	1.059	1.00
101_L	213_A	1.058	1.00
67_F	74_V	1.058	1.00
9_V	49_E	1.054	1.00
105_D	130_R	1.053	1.00
242_Q	246_K	1.052	1.00
90_E	239_A	1.041	1.00
89_E	93_R	1.041	1.00
5_N	46_S	1.040	1.00
101_L	204_I	1.033	1.00
148_R	179_D	1.031	1.00
103_M	213_A	1.025	1.00
155_I	171_P	1.018	1.00
95_V	217_I	1.018	1.00
134_Y	167_T	1.017	1.00
26_L	30_V	1.014	1.00
136_G	139_A	1.013	1.00
88_M	99_V	1.012	1.00
234_E	238_D	1.012	1.00
52_F	70_F	1.009	1.00
206_N	210_Q	1.007	1.00
215_I	243_I	1.001	1.00
28_E	31_S	0.989	1.00
150_E	153_A	0.989	1.00
94_E	238_D	0.985	1.00
241_L	245_R	0.980	1.00
225_T	228_R	0.975	1.00
162_S	169_T	0.974	1.00
152_E	156_K	0.970	1.00
85_K	115_I	0.970	1.00
23_S	56_D	0.958	1.00
27_S	37_K	0.948	1.00
165_S	195_N	0.945	1.00
181_S	184_N	0.937	1.00
141_S	145_F	0.935	1.00
102_I	111_Y	0.933	1.00
83_I	246_K	0.928	1.00
137_A	199_A	0.928	1.00
179_D	183_Q	0.913	1.00
150_E	154_Y	0.912	1.00
6_K	10_K	0.910	1.00
28_E	32_L	0.909	1.00
203_P	211_V	0.908	1.00
14_L	33_T	0.905	1.00
110_I	130_R	0.903	1.00
151_I	178_I	0.902	1.00
176_Q	180_A	0.899	1.00
200_I	233_T	0.895	1.00
173_K	177_E	0.885	1.00
153_A	157_Q	0.885	1.00
175_L	179_D	0.884	1.00
143_L	174_L	0.882	1.00
230_P	234_E	0.878	1.00
80_I	213_A	0.875	1.00
176_Q	179_D	0.873	1.00
163_I	167_T	0.872	1.00
99_V	217_I	0.872	1.00
163_I	193_L	0.870	1.00
206_N	212_A	0.865	1.00
88_M	113_E	0.865	1.00
191_S	195_N	0.860	1.00
15_L	67_F	0.858	1.00
141_S	211_V	0.848	1.00
88_M	215_I	0.845	1.00
20_H	32_L	0.841	1.00
239_A	242_Q	0.835	1.00
190_Y	221_E	0.834	1.00
38_T	41_H	0.832	1.00
100_Q	218_A	0.831	1.00
201_G	216_S	0.826	1.00
141_S	181_S	0.824	1.00
231_Y	235_K	0.823	1.00
81_R	85_K	0.814	1.00
10_K	39_S	0.812	1.00
138_C	216_S	0.811	1.00
137_A	201_G	0.805	1.00
184_N	233_T	0.802	1.00
105_D	110_I	0.801	1.00
48_E	61_Y	0.801	1.00
220_F	223_R	0.800	1.00
97_E	119_Q	0.794	1.00
33_T	40_V	0.794	1.00
144_S	178_I	0.793	1.00
173_K	176_Q	0.792	1.00
168_I	173_K	0.789	1.00
177_E	181_S	0.785	1.00
180_A	183_Q	0.783	1.00
104_R	150_E	0.781	1.00
14_L	43_M	0.775	1.00
236_V	240_A	0.769	1.00
35_M	39_S	0.761	1.00
7_T	11_S	0.754	1.00
55_R	59_G	0.753	1.00
177_E	184_N	0.751	1.00
87_V	243_I	0.746	1.00
142_I	214_G	0.743	1.00
15_L	52_F	0.741	1.00
205_F	212_A	0.738	1.00
45_S	49_E	0.738	1.00
45_S	48_E	0.735	1.00
26_L	40_V	0.733	1.00
67_F	71_G	0.733	1.00
67_F	70_F	0.731	1.00
151_I	154_Y	0.731	1.00
26_L	44_V	0.728	1.00
234_E	237_K	0.728	1.00
119_Q	223_R	0.728	1.00
24_L	29_L	0.728	1.00
100_Q	114_K	0.727	1.00
80_I	84_A	0.726	1.00
88_M	115_I	0.726	1.00
54_S	64_G	0.719	1.00
30_V	33_T	0.717	1.00
146_L	151_I	0.716	1.00
55_R	58_S	0.713	1.00
199_A	216_S	0.711	1.00
200_I	229_L	0.710	1.00
199_A	218_A	0.706	1.00
135_A	193_L	0.703	1.00
100_Q	125_T	0.702	1.00
107_N	154_Y	0.700	1.00
21_K	24_L	0.696	1.00
140_R	181_S	0.695	1.00
8_V	43_M	0.692	1.00
238_D	241_L	0.687	1.00
154_Y	158_T	0.686	1.00
231_Y	234_E	0.686	1.00
188_V	229_L	0.685	1.00
190_Y	226_E	0.678	1.00
229_L	234_E	0.678	1.00
5_N	43_M	0.678	1.00
63_L	67_F	0.678	1.00
103_M	112_V	0.678	1.00
14_L	40_V	0.673	1.00
26_L	37_K	0.673	1.00
168_I	174_L	0.669	1.00
83_I	86_P	0.664	1.00
71_G	74_V	0.663	1.00
151_I	179_D	0.660	1.00
54_S	65_L	0.660	1.00
104_R	142_I	0.660	1.00
91_L	217_I	0.659	1.00
90_E	93_R	0.658	1.00
79_D	82_K	0.657	1.00
237_K	240_A	0.654	1.00
148_R	182_V	0.654	1.00
241_L	244_S	0.654	1.00
91_L	95_V	0.651	1.00
26_L	61_Y	0.650	1.00
142_I	146_L	0.649	1.00
92_C	117_G	0.647	1.00
239_A	243_I	0.645	1.00
151_I	155_I	0.644	1.00
229_L	233_T	0.644	1.00
215_I	240_A	0.643	1.00
169_T	173_K	0.641	1.00
100_Q	199_A	0.640	1.00
179_D	182_V	0.638	1.00
185_G	205_F	0.637	1.00
202_A	244_S	0.628	1.00
143_L	178_I	0.627	1.00
134_Y	160_L	0.626	1.00
13_A	16_N	0.623	1.00
155_I	159_E	0.620	1.00
16_N	69_E	0.618	1.00
91_L	99_V	0.614	1.00
132_P	135_A	0.614	1.00
228_R	232_L	0.612	1.00
215_I	239_A	0.609	1.00
164_G	168_I	0.607	1.00
10_K	35_M	0.604	1.00
96_D	118_T	0.603	1.00
191_S	198_A	0.602	1.00
126_A	129_R	0.598	1.00
97_E	219_G	0.597	1.00
52_F	66_V	0.597	1.00
8_V	12_M	0.596	1.00
19_L	70_F	0.595	1.00
45_S	55_R	0.594	1.00
7_T	43_M	0.593	1.00
89_E	113_E	0.591	1.00
23_S	58_S	0.590	1.00
30_V	37_K	0.589	1.00
19_L	63_L	0.588	1.00
13_A	17_L	0.587	1.00
56_D	60_A	0.587	1.00
143_L	151_I	0.586	1.00
166_G	195_N	0.586	1.00
11_S	43_M	0.582	1.00
116_E	126_A	0.580	1.00
242_Q	245_R	0.578	1.00
114_K	127_I	0.576	1.00
93_R	118_T	0.575	1.00
86_P	246_K	0.573	1.00
55_R	61_Y	0.568	1.00
232_L	235_K	0.567	1.00
172_E	175_L	0.564	1.00
28_E	60_A	0.564	1.00
142_I	213_A	0.564	1.00
99_V	115_I	0.563	1.00
186_Y	237_K	0.561	1.00
97_E	217_I	0.560	1.00
111_Y	138_C	0.560	1.00
141_S	201_G	0.559	1.00
235_K	239_A	0.558	1.00
8_V	46_S	0.557	1.00
51_G	66_V	0.556	1.00
136_G	199_A	0.554	0.99
15_L	70_F	0.553	0.99
202_A	215_I	0.548	0.99
83_I	243_I	0.545	0.99
114_K	125_T	0.543	0.99
111_Y	125_T	0.541	0.99
109_A	131_S	0.540	0.99
141_S	203_P	0.539	0.99
204_I	213_A	0.538	0.99
174_L	178_I	0.537	0.99
17_L	20_H	0.535	0.99
113_E	127_I	0.534	0.99
84_A	88_M	0.534	0.99
109_A	138_C	0.530	0.99
121_V	222_A	0.530	0.99
111_Y	136_G	0.526	0.99
196_Y	221_E	0.525	0.99
16_N	70_F	0.525	0.99
140_R	189_S	0.524	0.99
141_S	214_G	0.518	0.99
107_N	158_T	0.518	0.99
41_H	55_R	0.517	0.99
72_Q	75_A	0.517	0.99
141_S	187_T	0.513	0.99
215_I	236_V	0.510	0.99
98_A	114_K	0.510	0.99
68_L	75_A	0.509	0.99
86_P	90_E	0.509	0.99
172_E	176_Q	0.508	0.99
111_Y	114_K	0.506	0.99
145_F	182_V	0.506	0.99
11_S	47_L	0.505	0.99
201_G	214_G	0.504	0.99
109_A	136_G	0.504	0.99
207_H	244_S	0.503	0.99
125_T	129_R	0.502	0.99
25_T	37_K	0.502	0.99
100_Q	216_S	0.502	0.99
10_K	43_M	0.502	0.99
138_C	199_A	0.500	0.99

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
3mq0A	2	0.988	100	0.084	Contact Map
1mkmA	4	0.984	100	0.088	Contact Map
2g7uA	6	0.996	100	0.088	Contact Map
2ia2A	4	0.984	100	0.089	Contact Map
3r4kA	2	0.984	100	0.097	Contact Map
2xrnA	3	0.956	100	0.122	Contact Map
2o0yA	4	0.968	100	0.136	Contact Map
1ysqA	1	0.696	100	0.395	Contact Map
1tf1A	1	0.732	100	0.395	Contact Map
1yspA	1	0.656	100	0.402	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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