RPIR - ECOLI - GREMLIN Contacts

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RPIR - HTH-type transcriptional regulator RpiR

UniProt:	P0ACS7	Sequences: MSQSEFDSALPNGIGLAPYLRMKQEGMTENESRIVEWLLKPGNLSCAPAIKDVAEALAVSEAMIVKVSKLLGFSGFRNLRSALEDYFSQSEQVLPSELAFDEAPQDVVNKVFNITLRTIMEGQSIVNVDEIHRAARFFYQARQRDLYGAGGSNAICADVQHKFLRIGVRCQAYPDAHIMMMSASLLQEGDVVLVVTHSGRTSDVKAAVELAKKNGAKIICITHSYHSPIAKLADYIICSPAPETPLLGRNASARILQLTLLDAFFVSVAQLNIEQANINMQKTGAIVDFFSPGALK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12459
Length:	296 (261)
Sequences:	8698 (6112)
Seq/√Len:	378.3

ECOLI - RPIR YFHH MURR HEXR
BACSU - YBBH GLVR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_R	189_G	4.820	1.00
220_C	233_A	4.081	1.00
209_E	232_L	3.156	1.00
194_V	208_V	2.926	1.00
24_Q	36_E	2.855	1.00
137_F	217_K	2.757	1.00
200_R	228_P	2.721	1.00
51_K	70_L	2.649	1.00
142_R	187_Q	2.621	1.00
143_Q	169_R	2.610	1.00
117_R	121_E	2.524	1.00
208_V	218_I	2.490	1.00
212_K	234_D	2.445	1.00
134_A	219_I	2.364	1.00
134_A	235_Y	2.346	1.00
250_N	253_A	2.236	1.00
186_L	216_A	2.223	1.00
142_R	190_D	2.181	1.00
187_Q	190_D	2.134	1.00
41_P	44_L	2.130	1.00
210_L	213_K	2.128	1.00
192_V	211_A	2.079	1.00
135_A	267_S	2.039	1.00
136_R	271_L	2.035	1.00
116_L	120_M	2.014	1.00
73_F	82_A	1.944	1.00
36_E	40_K	1.936	1.00
195_V	261_L	1.881	1.00
159_V	163_F	1.873	1.00
191_V	219_I	1.870	1.00
217_K	234_D	1.850	1.00
137_F	235_Y	1.842	1.00
37_W	41_P	1.835	1.00
141_A	191_V	1.815	1.00
194_V	204_V	1.789	1.00
139_Y	271_L	1.787	1.00
208_V	229_I	1.772	1.00
23_K	26_G	1.761	1.00
196_T	229_I	1.712	1.00
237_I	260_L	1.707	1.00
195_V	221_I	1.698	1.00
211_A	216_A	1.694	1.00
72_G	75_G	1.691	1.00
146_L	193_L	1.674	1.00
217_K	235_Y	1.674	1.00
81_S	84_E	1.642	1.00
130_E	133_R	1.640	1.00
192_V	216_A	1.619	1.00
53_V	66_K	1.608	1.00
127_N	130_E	1.546	1.00
119_I	259_T	1.513	1.00
220_C	229_I	1.495	1.00
31_E	70_L	1.494	1.00
146_L	159_V	1.486	1.00
53_V	69_K	1.467	1.00
112_F	119_I	1.459	1.00
48_P	56_A	1.449	1.00
279_N	282_K	1.447	1.00
230_A	236_I	1.443	1.00
35_V	67_V	1.439	1.00
34_I	67_V	1.437	1.00
218_I	233_A	1.434	1.00
68_S	79_L	1.419	1.00
193_L	221_I	1.411	1.00
272_N	275_Q	1.402	1.00
267_S	271_L	1.398	1.00
76_F	80_R	1.394	1.00
53_V	70_L	1.394	1.00
74_S	78_N	1.370	1.00
139_Y	268_V	1.362	1.00
24_Q	32_S	1.359	1.00
133_R	235_Y	1.344	1.00
220_C	236_I	1.343	1.00
78_N	81_S	1.341	1.00
147_Y	192_V	1.328	1.00
122_G	240_P	1.328	1.00
80_R	84_E	1.319	1.00
146_L	156_C	1.312	1.00
194_V	218_I	1.307	1.00
202_S	206_A	1.294	1.00
22_M	26_G	1.282	1.00
78_N	88_S	1.272	1.00
30_N	33_R	1.271	1.00
239_S	257_Q	1.270	1.00
32_S	36_E	1.267	1.00
136_R	140_Q	1.258	1.00
20_L	23_K	1.247	1.00
270_Q	280_M	1.243	1.00
76_F	79_L	1.235	1.00
212_K	232_L	1.230	1.00
143_Q	190_D	1.229	1.00
151_G	250_N	1.225	1.00
139_Y	272_N	1.223	1.00
137_F	191_V	1.220	1.00
155_I	261_L	1.210	1.00
206_A	209_E	1.209	1.00
194_V	211_A	1.208	1.00
27_M	53_V	1.192	1.00
30_N	63_M	1.188	1.00
276_A	279_N	1.182	1.00
50_I	65_V	1.173	1.00
79_L	83_L	1.170	1.00
266_V	283_T	1.167	1.00
156_C	195_V	1.156	1.00
140_Q	217_K	1.140	1.00
138_F	191_V	1.135	1.00
73_F	76_F	1.133	1.00
22_M	25_E	1.125	1.00
73_F	79_L	1.122	1.00
102_E	110_K	1.120	1.00
37_W	57_L	1.110	1.00
122_G	239_S	1.110	1.00
118_T	256_L	1.107	1.00
19_Y	23_K	1.105	1.00
27_M	69_K	1.104	1.00
267_S	270_Q	1.101	1.00
103_A	106_D	1.100	1.00
138_F	268_V	1.093	1.00
24_Q	35_V	1.089	1.00
190_D	216_A	1.079	1.00
277_N	281_Q	1.076	1.00
157_A	174_P	1.057	1.00
186_L	190_D	1.057	1.00
82_A	86_Y	1.050	1.00
78_N	86_Y	1.047	1.00
133_R	137_F	1.047	1.00
44_L	56_A	1.040	1.00
145_D	190_D	1.040	1.00
158_D	162_K	1.032	1.00
130_E	235_Y	1.020	1.00
42_G	46_C	1.013	1.00
144_R	168_V	1.004	1.00
145_D	186_L	1.000	1.00
210_L	214_N	0.996	1.00
144_R	191_V	0.994	1.00
34_I	57_L	0.991	1.00
76_F	86_Y	0.986	1.00
159_V	262_D	0.986	1.00
134_A	137_F	0.983	1.00
20_L	25_E	0.982	1.00
85_D	88_S	0.979	1.00
82_A	85_D	0.975	1.00
165_R	185_L	0.971	1.00
68_S	86_Y	0.970	1.00
159_V	193_L	0.968	1.00
146_L	160_Q	0.958	1.00
33_R	65_V	0.958	1.00
135_A	271_L	0.957	1.00
279_N	283_T	0.957	1.00
44_L	48_P	0.955	1.00
209_E	213_K	0.951	1.00
109_N	113_N	0.941	1.00
162_K	183_A	0.940	1.00
137_F	140_Q	0.935	1.00
50_I	54_A	0.929	1.00
25_E	32_S	0.919	1.00
120_M	124_S	0.919	1.00
159_V	261_L	0.918	1.00
48_P	52_D	0.915	1.00
65_V	75_G	0.913	1.00
45_S	83_L	0.908	1.00
214_N	282_K	0.902	1.00
186_L	192_V	0.901	1.00
38_L	79_L	0.899	1.00
116_L	119_I	0.898	1.00
37_W	48_P	0.898	1.00
205_K	228_P	0.895	1.00
160_Q	171_Q	0.892	1.00
160_Q	164_L	0.892	1.00
109_N	123_Q	0.890	1.00
230_A	238_C	0.884	1.00
106_D	109_N	0.883	1.00
75_G	79_L	0.880	1.00
221_I	261_L	0.878	1.00
138_F	193_L	0.875	1.00
153_N	172_A	0.872	1.00
20_L	26_G	0.871	1.00
141_A	190_D	0.866	1.00
134_A	237_I	0.859	1.00
205_K	209_E	0.855	1.00
79_L	86_Y	0.854	1.00
129_D	132_H	0.853	1.00
222_T	230_A	0.851	1.00
138_F	144_R	0.843	1.00
160_Q	170_C	0.843	1.00
134_A	264_F	0.842	1.00
105_Q	109_N	0.838	1.00
121_E	124_S	0.838	1.00
78_N	82_A	0.837	1.00
117_R	120_M	0.830	1.00
30_N	69_K	0.829	1.00
37_W	56_A	0.826	1.00
155_I	195_V	0.816	1.00
133_R	136_R	0.813	1.00
144_R	193_L	0.813	1.00
158_D	254_R	0.810	1.00
160_Q	172_A	0.810	1.00
28_T	31_E	0.805	1.00
93_V	97_E	0.802	1.00
132_H	271_L	0.799	1.00
143_Q	171_Q	0.788	1.00
160_Q	265_F	0.786	1.00
37_W	44_L	0.782	1.00
130_E	134_A	0.781	1.00
79_L	87_F	0.779	1.00
171_Q	179_M	0.776	1.00
104_P	113_N	0.770	1.00
108_V	128_V	0.768	1.00
53_V	64_I	0.765	1.00
122_G	256_L	0.765	1.00
211_A	218_I	0.763	1.00
225_Y	238_C	0.763	1.00
136_R	139_Y	0.760	1.00
77_R	80_R	0.760	1.00
143_Q	187_Q	0.759	1.00
75_G	78_N	0.759	1.00
160_Q	268_V	0.758	1.00
27_M	70_L	0.754	1.00
84_E	88_S	0.750	1.00
46_C	49_A	0.747	1.00
93_V	96_S	0.743	1.00
159_V	162_K	0.742	1.00
46_C	84_E	0.739	1.00
132_H	267_S	0.736	1.00
115_T	259_T	0.735	1.00
275_Q	280_M	0.729	1.00
81_S	85_D	0.729	1.00
146_L	170_C	0.724	1.00
66_K	70_L	0.722	1.00
205_K	229_I	0.721	1.00
23_K	27_M	0.718	1.00
183_A	214_N	0.715	1.00
62_A	65_V	0.711	1.00
51_K	61_E	0.711	1.00
256_L	259_T	0.711	1.00
145_D	192_V	0.711	1.00
49_A	52_D	0.711	1.00
146_L	163_F	0.710	1.00
165_R	183_A	0.709	1.00
83_L	87_F	0.707	1.00
104_P	132_H	0.706	1.00
125_I	240_P	0.704	0.99
49_A	54_A	0.703	0.99
153_N	157_A	0.697	0.99
53_V	76_F	0.696	0.99
149_A	201_T	0.693	0.99
135_A	139_Y	0.689	0.99
157_A	160_Q	0.688	0.99
177_H	203_D	0.685	0.99
189_G	217_K	0.685	0.99
129_D	133_R	0.684	0.99
112_F	259_T	0.683	0.99
142_R	169_R	0.681	0.99
160_Q	168_V	0.680	0.99
138_F	141_A	0.679	0.99
34_I	64_I	0.679	0.99
38_L	67_V	0.679	0.99
245_P	248_G	0.678	0.99
278_I	282_K	0.678	0.99
200_R	223_H	0.675	0.99
235_Y	238_C	0.673	0.99
278_I	281_Q	0.672	0.99
34_I	63_M	0.672	0.99
67_V	71_L	0.671	0.99
47_A	50_I	0.670	0.99
128_V	132_H	0.669	0.99
222_T	227_S	0.668	0.99
154_A	157_A	0.668	0.99
155_I	257_Q	0.667	0.99
196_T	199_G	0.663	0.99
121_E	125_I	0.662	0.99
137_F	141_A	0.660	0.99
194_V	207_A	0.659	0.99
275_Q	279_N	0.659	0.99
63_M	66_K	0.658	0.99
265_F	269_A	0.657	0.99
208_V	232_L	0.656	0.99
191_V	217_K	0.653	0.99
33_R	58_A	0.652	0.99
66_K	69_K	0.652	0.99
105_Q	128_V	0.650	0.99
177_H	206_A	0.648	0.99
156_C	159_V	0.646	0.99
98_L	102_E	0.645	0.99
83_L	86_Y	0.644	0.99
72_G	79_L	0.644	0.99
247_L	250_N	0.644	0.99
251_A	254_R	0.642	0.99
152_S	257_Q	0.641	0.99
25_E	29_E	0.641	0.99
33_R	61_E	0.640	0.99
45_S	48_P	0.639	0.99
27_M	66_K	0.637	0.99
80_R	87_F	0.637	0.99
76_F	81_S	0.635	0.99
239_S	256_L	0.635	0.99
163_F	268_V	0.631	0.99
122_G	260_L	0.631	0.99
77_R	81_S	0.630	0.99
266_V	280_M	0.627	0.99
157_A	169_R	0.625	0.99
254_R	257_Q	0.624	0.99
20_L	67_V	0.623	0.99
27_M	54_A	0.621	0.99
132_H	135_A	0.619	0.99
19_Y	22_M	0.619	0.99
28_T	70_L	0.618	0.99
78_N	87_F	0.618	0.99
168_V	173_Y	0.618	0.99
277_N	280_M	0.615	0.99
193_L	219_I	0.612	0.99
115_T	255_I	0.609	0.99
270_Q	277_N	0.609	0.99
48_P	53_V	0.605	0.98
20_L	27_M	0.604	0.98
227_S	230_A	0.603	0.98
107_V	110_K	0.603	0.98
131_I	263_A	0.602	0.98
184_S	210_L	0.601	0.98
140_Q	189_G	0.597	0.98
233_A	236_I	0.596	0.98
52_D	55_E	0.595	0.98
38_L	45_S	0.589	0.98
111_V	115_T	0.588	0.98
135_A	268_V	0.585	0.98
228_P	232_L	0.585	0.98
179_M	183_A	0.584	0.98
33_R	64_I	0.584	0.98
121_E	240_P	0.583	0.98
157_A	161_H	0.580	0.98
147_Y	186_L	0.580	0.98
112_F	115_T	0.578	0.98
68_S	75_G	0.577	0.98
194_V	220_C	0.577	0.98
145_D	171_Q	0.574	0.98
80_R	83_L	0.573	0.98
183_A	216_A	0.569	0.98
148_G	152_S	0.567	0.98
220_C	227_S	0.563	0.98
206_A	210_L	0.562	0.98
165_R	184_S	0.560	0.98
254_R	258_L	0.559	0.97
94_L	99_A	0.559	0.97
161_H	164_L	0.556	0.97
146_L	195_V	0.554	0.97
212_K	218_I	0.554	0.97
237_I	264_F	0.553	0.97
43_N	47_A	0.549	0.97
169_R	173_Y	0.549	0.97
221_I	239_S	0.546	0.97
196_T	220_C	0.542	0.97
79_L	84_E	0.540	0.97
198_S	201_T	0.540	0.97
205_K	232_L	0.540	0.97
56_A	66_K	0.539	0.97
147_Y	194_V	0.538	0.97
111_V	259_T	0.537	0.97
183_A	210_L	0.536	0.97
61_E	65_V	0.536	0.97
259_T	262_D	0.536	0.97
230_A	233_A	0.533	0.97
149_A	203_D	0.533	0.97
222_T	236_I	0.532	0.97
174_P	178_I	0.532	0.97
27_M	35_V	0.531	0.97
94_L	97_E	0.531	0.97
221_I	260_L	0.531	0.97
239_S	260_L	0.528	0.96
148_G	203_D	0.527	0.96
188_E	215_G	0.527	0.96
112_F	122_G	0.527	0.96
147_Y	207_A	0.523	0.96
250_N	255_I	0.523	0.96
151_G	161_H	0.522	0.96
42_G	45_S	0.522	0.96
113_N	117_R	0.521	0.96
113_N	116_L	0.520	0.96
20_L	35_V	0.518	0.96
72_G	76_F	0.516	0.96
269_A	280_M	0.516	0.96
274_E	278_I	0.515	0.96
76_F	88_S	0.514	0.96
145_D	183_A	0.511	0.96
141_A	217_K	0.508	0.96
113_N	120_M	0.507	0.96
71_L	85_D	0.507	0.96
80_R	88_S	0.506	0.96
266_V	269_A	0.506	0.96
116_L	123_Q	0.506	0.96
273_I	276_A	0.505	0.95
219_I	235_Y	0.502	0.95
123_Q	263_A	0.500	0.95

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
4ivnA	2	0.8919	100	0.202	Contact Map
3shoA	4	0.6284	100	0.545	Contact Map
2xhzA	4	0.5777	100	0.561	Contact Map
3fxaA	4	0.6419	100	0.566	Contact Map
3etnA	4	0.6318	100	0.571	Contact Map
1m3sA	4	0.6014	100	0.583	Contact Map
1vimA	4	0.6182	100	0.586	Contact Map
2pocA	4	0.6486	100	0.59	Contact Map
1jeoA	4	0.5811	100	0.59	Contact Map
4s12A	2	0.7264	99.9	0.595	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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