CITR - BACSU - GREMLIN Contacts

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CITR - HTH-type transcriptional regulator CitR

UniProt:	P39127	Sequences: MDFKWLHTFVTAAKYENFRKTAETLFLSQPTVTVHIKQLEKEISCKLFERKGRQIQLTDEGRAYLPYALRLLDDYENSMAELHRVRQGYSQTLQLAVSPLIADTVLPSVMKRYTAMNTETEMAVTIFESAEIASLIKAGEADIGLSCLKVQSSSLSCHCLYKDPVVLVAPPDKRFIEDNEIDAKEVLEQYLLLTHNHPDYWDDLLRQVRMTFPFVRTMKVTQTHITKRFIKEGLGVSFLPLSTVKRELAEKQMIRIPYQSVQLPYAGAYAIALYENKKEKKFLDFLSHFHF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	291 (282)
Sequences:	79461 (57849)
Seq/√Len:	3444.8

ECOLI - OXYR CYNR YFER PGRR CYSB NAC YAFC LYSR YBHD AAER YNFL YDCI ILVY YFIE TTDR YCAN DMLR METR XAPR LEUO CBL YHJC ABGR HCAR ALLS YDHB DSDC YEEY YEIE GCVA YAHB NHAR TDCA YNEJ ICIA YBDO YBEF YHAJ YIAU YIDZ YGFI YJIE HDFR LRHA PERR
BACSU - CITR CYSL YWBI YCGK ALSR YTLI GLTC YYBE BSDA YWQM YVBU GLTR YOFA YUST YXJO YKUM YRAN CZCR YOAU

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_R	74_D	3.619	1.00
15_Y	24_T	3.418	1.00
158_H	287_S	2.676	1.00
96_A	141_A	2.618	1.00
67_Y	81_E	2.458	1.00
230_I	237_S	2.331	1.00
11_T	24_T	2.266	1.00
173_K	189_Q	2.238	1.00
164_P	241_L	2.220	1.00
159_C	162_K	2.205	1.00
162_K	264_P	2.195	1.00
92_T	123_A	2.195	1.00
20_K	23_E	2.128	1.00
92_T	121_E	2.107	1.00
14_K	69_L	2.091	1.00
159_C	264_P	2.080	1.00
182_D	185_E	2.061	1.00
45_C	60_E	2.057	1.00
8_T	35_H	2.045	1.00
227_K	247_E	2.014	1.00
10_V	65_L	2.011	1.00
162_K	262_Q	2.010	1.00
94_Q	123_A	1.987	1.00
67_Y	74_D	1.980	1.00
112_R	285_F	1.966	1.00
10_V	69_L	1.957	1.00
11_T	14_K	1.923	1.00
231_K	252_Q	1.921	1.00
8_T	32_V	1.904	1.00
10_V	14_K	1.903	1.00
11_T	15_Y	1.894	1.00
192_L	235_G	1.891	1.00
71_L	75_Y	1.882	1.00
13_A	57_L	1.881	1.00
166_V	241_L	1.865	1.00
18_F	36_I	1.836	1.00
65_L	69_L	1.822	1.00
169_A	256_I	1.776	1.00
49_E	56_Q	1.740	1.00
64_Y	78_S	1.737	1.00
231_K	247_E	1.736	1.00
190_Y	217_T	1.715	1.00
63_A	81_E	1.673	1.00
157_C	266_A	1.662	1.00
178_D	185_E	1.658	1.00
166_V	255_R	1.648	1.00
135_L	140_E	1.626	1.00
13_A	65_L	1.623	1.00
14_K	24_T	1.609	1.00
113_Y	282_F	1.592	1.00
15_Y	20_K	1.587	1.00
9_F	65_L	1.584	1.00
10_V	68_A	1.564	1.00
156_S	271_I	1.559	1.00
8_T	27_L	1.554	1.00
88_G	119_E	1.541	1.00
113_Y	120_T	1.519	1.00
201_W	205_L	1.516	1.00
5_W	35_H	1.512	1.00
19_R	29_Q	1.502	1.00
134_S	138_A	1.496	1.00
59_D	62_R	1.495	1.00
28_S	31_T	1.479	1.00
5_W	42_E	1.460	1.00
5_W	38_Q	1.458	1.00
17_N	20_K	1.451	1.00
158_H	269_Y	1.449	1.00
67_Y	70_R	1.443	1.00
46_K	49_E	1.440	1.00
11_T	25_L	1.423	1.00
10_V	72_L	1.422	1.00
275_E	279_E	1.400	1.00
71_L	78_S	1.389	1.00
146_S	268_A	1.386	1.00
156_S	269_Y	1.384	1.00
67_Y	77_N	1.384	1.00
148_L	266_A	1.379	1.00
103_D	224_H	1.357	1.00
171_P	252_Q	1.350	1.00
90_S	119_E	1.347	1.00
94_Q	125_T	1.337	1.00
137_K	154_S	1.331	1.00
143_I	279_E	1.327	1.00
267_G	283_L	1.324	1.00
136_I	144_G	1.312	1.00
64_Y	79_M	1.306	1.00
135_L	141_A	1.306	1.00
283_L	287_S	1.300	1.00
51_K	56_Q	1.296	1.00
163_D	242_S	1.293	1.00
281_K	284_D	1.283	1.00
42_E	79_M	1.282	1.00
74_D	77_N	1.277	1.00
189_Q	236_V	1.275	1.00
169_A	236_V	1.272	1.00
226_T	237_S	1.272	1.00
143_I	267_G	1.270	1.00
114_T	217_T	1.266	1.00
269_Y	283_L	1.264	1.00
3_F	75_Y	1.263	1.00
112_R	116_M	1.253	1.00
228_R	231_K	1.223	1.00
66_P	70_R	1.217	1.00
241_L	245_K	1.213	1.00
67_Y	78_S	1.209	1.00
37_K	41_K	1.206	1.00
62_R	66_P	1.203	1.00
114_T	190_Y	1.201	1.00
241_L	255_R	1.197	1.00
63_A	66_P	1.195	1.00
247_E	252_Q	1.189	1.00
159_C	266_A	1.182	1.00
9_F	48_F	1.179	1.00
179_N	254_I	1.176	1.00
111_K	115_A	1.175	1.00
174_R	189_Q	1.169	1.00
245_K	249_A	1.167	1.00
116_M	285_F	1.165	1.00
27_L	31_T	1.164	1.00
208_V	212_F	1.141	1.00
9_F	13_A	1.139	1.00
192_L	226_T	1.136	1.00
112_R	115_A	1.133	1.00
157_C	268_A	1.132	1.00
9_F	47_L	1.129	1.00
34_V	38_Q	1.126	1.00
93_L	282_F	1.126	1.00
34_V	37_K	1.115	1.00
111_K	232_E	1.107	1.00
123_A	219_K	1.106	1.00
33_T	37_K	1.099	1.00
18_F	55_I	1.098	1.00
127_F	135_L	1.093	1.00
190_Y	215_V	1.093	1.00
117_N	281_K	1.092	1.00
171_P	254_I	1.091	1.00
102_A	126_I	1.091	1.00
70_R	77_N	1.089	1.00
12_A	21_T	1.084	1.00
7_H	76_E	1.082	1.00
220_V	226_T	1.074	1.00
6_L	68_A	1.073	1.00
113_Y	285_F	1.071	1.00
11_T	21_T	1.060	1.00
71_L	74_D	1.058	1.00
181_I	185_E	1.055	1.00
57_L	61_G	1.049	1.00
202_D	205_L	1.043	1.00
63_A	67_Y	1.042	1.00
108_S	232_E	1.038	1.00
280_K	284_D	1.038	1.00
227_K	231_K	1.034	1.00
35_H	38_Q	1.032	1.00
284_D	287_S	1.031	1.00
170_P	233_G	1.030	1.00
4_K	7_H	1.023	1.00
228_R	232_E	1.017	1.00
137_K	152_S	1.010	1.00
158_H	283_L	1.005	1.00
109_V	286_L	1.004	1.00
79_M	83_H	0.998	1.00
8_T	25_L	0.995	1.00
168_V	255_R	0.987	1.00
27_L	32_V	0.982	1.00
246_R	250_E	0.981	1.00
76_E	80_A	0.981	1.00
76_E	79_M	0.975	1.00
113_Y	117_N	0.972	1.00
167_L	236_V	0.972	1.00
13_A	48_F	0.969	1.00
168_V	244_V	0.966	1.00
169_A	173_K	0.964	1.00
180_E	259_Q	0.961	1.00
64_Y	68_A	0.960	1.00
164_P	262_Q	0.955	1.00
12_A	18_F	0.954	1.00
73_D	77_N	0.954	1.00
9_F	57_L	0.941	1.00
220_V	229_F	0.938	1.00
135_L	138_A	0.934	1.00
276_N	279_E	0.930	1.00
21_T	32_V	0.924	1.00
193_L	216_R	0.923	1.00
125_T	135_L	0.920	1.00
48_F	55_I	0.917	1.00
38_Q	41_K	0.916	1.00
9_F	39_L	0.914	1.00
109_V	285_F	0.913	1.00
96_A	144_G	0.906	1.00
191_L	214_F	0.905	1.00
202_D	206_R	0.895	1.00
45_C	82_L	0.894	1.00
13_A	61_G	0.893	1.00
63_A	85_V	0.891	1.00
173_K	190_Y	0.888	1.00
141_A	144_G	0.887	1.00
20_K	24_T	0.884	1.00
244_V	247_E	0.883	1.00
121_E	215_V	0.882	1.00
169_A	174_R	0.880	1.00
96_A	146_S	0.879	1.00
154_S	271_I	0.872	1.00
173_K	176_I	0.871	1.00
66_P	69_L	0.870	1.00
99_P	222_Q	0.862	1.00
270_A	273_L	0.860	1.00
174_R	179_N	0.859	1.00
185_E	188_E	0.855	1.00
19_R	23_E	0.851	1.00
190_Y	216_R	0.851	1.00
70_R	73_D	0.851	1.00
120_T	278_K	0.848	1.00
133_A	137_K	0.847	1.00
177_E	190_Y	0.845	1.00
16_E	56_Q	0.845	1.00
148_L	264_P	0.839	1.00
155_L	268_A	0.837	1.00
95_L	143_I	0.836	1.00
25_L	32_V	0.834	1.00
51_K	54_Q	0.833	1.00
60_E	85_V	0.831	1.00
168_V	237_S	0.828	1.00
204_L	208_V	0.821	1.00
156_S	159_C	0.812	1.00
91_Q	278_K	0.809	1.00
16_E	62_R	0.807	1.00
257_P	260_S	0.807	1.00
275_E	280_K	0.807	1.00
9_F	64_Y	0.807	1.00
13_A	16_E	0.806	1.00
125_T	141_A	0.804	1.00
37_K	46_K	0.803	1.00
12_A	36_I	0.799	1.00
60_E	82_L	0.795	1.00
247_E	250_E	0.794	1.00
29_Q	33_T	0.793	1.00
248_L	251_K	0.787	1.00
111_K	234_L	0.785	1.00
184_K	187_L	0.782	1.00
89_Y	117_N	0.782	1.00
12_A	48_F	0.781	1.00
170_P	234_L	0.777	1.00
75_Y	78_S	0.774	1.00
182_D	259_Q	0.773	1.00
74_D	78_S	0.771	1.00
173_K	177_E	0.770	1.00
14_K	65_L	0.770	1.00
4_K	35_H	0.767	1.00
91_Q	120_T	0.766	1.00
175_F	189_Q	0.764	1.00
172_D	176_I	0.762	1.00
175_F	178_D	0.759	1.00
60_E	63_A	0.759	1.00
143_I	282_F	0.756	1.00
77_N	81_E	0.756	1.00
114_T	234_L	0.755	1.00
16_E	54_Q	0.754	1.00
75_Y	79_M	0.753	1.00
15_Y	21_T	0.752	1.00
3_F	72_L	0.748	1.00
229_F	234_L	0.745	1.00
5_W	8_T	0.745	1.00
83_H	86_R	0.734	1.00
68_A	71_L	0.730	1.00
187_L	212_F	0.727	1.00
168_V	239_L	0.726	1.00
137_K	155_L	0.723	1.00
78_S	82_L	0.721	1.00
7_H	11_T	0.719	1.00
240_P	243_T	0.718	1.00
277_K	281_K	0.717	1.00
94_Q	141_A	0.716	1.00
56_Q	62_R	0.715	1.00
49_E	58_T	0.715	1.00
57_L	62_R	0.712	1.00
31_T	35_H	0.711	1.00
113_Y	281_K	0.711	1.00
201_W	219_K	0.708	1.00
248_L	255_R	0.706	1.00
12_A	32_V	0.706	1.00
18_F	32_V	0.704	1.00
168_V	248_L	0.704	1.00
97_V	102_A	0.702	1.00
206_R	210_M	0.702	1.00
205_L	209_R	0.700	1.00
231_K	250_E	0.698	1.00
170_P	173_K	0.695	1.00
222_Q	225_I	0.691	1.00
244_V	248_L	0.690	1.00
60_E	64_Y	0.688	1.00
40_E	45_C	0.687	1.00
69_L	73_D	0.687	1.00
116_M	281_K	0.686	1.00
145_L	286_L	0.681	1.00
195_H	219_K	0.677	1.00
49_E	54_Q	0.676	1.00
94_Q	142_D	0.674	1.00
62_R	65_L	0.673	1.00
218_M	229_F	0.666	1.00
174_R	178_D	0.663	1.00
246_R	249_A	0.661	1.00
164_P	257_P	0.661	1.00
188_E	215_V	0.661	1.00
97_V	106_L	0.660	1.00
207_Q	210_M	0.658	1.00
169_A	175_F	0.656	1.00
59_D	63_A	0.654	1.00
169_A	254_I	0.653	1.00
203_D	207_Q	0.653	1.00
73_D	76_E	0.650	1.00
142_D	279_E	0.650	1.00
194_T	226_T	0.648	1.00
77_N	80_A	0.647	1.00
68_A	72_L	0.646	1.00
64_Y	82_L	0.645	1.00
40_E	50_R	0.644	1.00
18_F	54_Q	0.643	1.00
191_L	236_V	0.642	1.00
206_R	209_R	0.642	1.00
139_G	270_A	0.640	1.00
281_K	285_F	0.638	1.00
7_H	10_V	0.638	1.00
172_D	175_F	0.634	1.00
121_E	219_K	0.634	1.00
99_P	128_E	0.634	1.00
93_L	278_K	0.632	1.00
126_I	221_T	0.630	1.00
23_E	26_F	0.628	1.00
172_D	233_G	0.626	1.00
12_A	17_N	0.626	1.00
36_I	40_E	0.624	1.00
103_D	228_R	0.622	1.00
21_T	25_L	0.621	1.00
252_Q	255_R	0.618	1.00
67_Y	71_L	0.613	1.00
167_L	186_V	0.609	1.00
4_K	38_Q	0.608	1.00
176_I	254_I	0.608	1.00
277_K	280_K	0.604	1.00
136_I	268_A	0.604	1.00
273_L	276_N	0.603	1.00
80_A	84_R	0.602	1.00
167_L	238_F	0.601	1.00
63_A	82_L	0.601	1.00
203_D	206_R	0.600	1.00
90_S	121_E	0.600	1.00
180_E	185_E	0.599	1.00
93_L	143_I	0.598	1.00
106_L	109_V	0.594	1.00
143_I	283_L	0.594	1.00
167_L	191_L	0.593	1.00
171_P	251_K	0.593	1.00
172_D	254_I	0.588	1.00
175_F	181_I	0.586	1.00
126_I	222_Q	0.583	1.00
226_T	230_I	0.582	1.00
282_F	286_L	0.579	1.00
161_Y	265_Y	0.577	1.00
201_W	207_Q	0.576	1.00
165_V	238_F	0.574	1.00
195_H	221_T	0.574	1.00
204_L	207_Q	0.574	1.00
108_S	111_K	0.573	1.00
30_P	34_V	0.573	1.00
136_I	155_L	0.572	1.00
156_S	272_A	0.572	1.00
31_T	34_V	0.571	1.00
57_L	65_L	0.571	1.00
96_A	127_F	0.571	1.00
208_V	214_F	0.567	1.00
205_L	208_V	0.567	1.00
7_H	72_L	0.564	1.00
147_C	263_L	0.563	1.00
48_F	57_L	0.562	1.00
28_S	34_V	0.562	1.00
110_M	122_M	0.561	1.00
201_W	204_L	0.558	1.00
269_Y	280_K	0.558	1.00
43_I	64_Y	0.557	1.00
4_K	8_T	0.556	1.00
229_F	235_G	0.555	1.00
45_C	49_E	0.554	1.00
163_D	263_L	0.554	1.00
220_V	225_I	0.553	1.00
43_I	82_L	0.553	1.00
108_S	112_R	0.550	1.00
239_L	244_V	0.542	1.00
91_Q	119_E	0.540	1.00
196_N	219_K	0.538	1.00
173_K	236_V	0.538	1.00
96_A	125_T	0.538	1.00
8_T	36_I	0.537	1.00
66_P	81_E	0.537	1.00
72_L	76_E	0.536	1.00
43_I	46_K	0.535	1.00
160_L	267_G	0.533	1.00
101_I	105_V	0.533	1.00
174_R	177_E	0.526	1.00
117_N	120_T	0.524	1.00
9_F	61_G	0.522	1.00
223_T	240_P	0.521	1.00
72_L	75_Y	0.521	1.00
169_A	176_I	0.521	1.00
202_D	207_Q	0.520	1.00
148_L	157_C	0.519	1.00
8_T	21_T	0.519	1.00
279_E	283_L	0.518	1.00
36_I	48_F	0.517	1.00
46_K	60_E	0.516	1.00
18_F	29_Q	0.513	1.00
184_K	212_F	0.513	1.00
91_Q	117_N	0.511	1.00
18_F	50_R	0.510	1.00
84_R	89_Y	0.510	1.00
6_L	64_Y	0.510	1.00
108_S	228_R	0.508	1.00
68_A	75_Y	0.508	1.00
16_E	55_I	0.507	1.00
183_A	258_Y	0.506	1.00
67_Y	82_L	0.503	1.00
71_L	79_M	0.502	1.00
105_V	109_V	0.500	1.00
97_V	124_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
4x6gA	4	1	100	0.104	Contact Map
1uthA	2	0.7526	100	0.104	Contact Map
1ixcA	4	0.9897	100	0.104	Contact Map
2esnA	3	0.9931	100	0.105	Contact Map
3fxqA	3	0.9931	100	0.107	Contact Map
2h98A	2	0.6838	100	0.108	Contact Map
2h9bA	2	0.6907	100	0.111	Contact Map
1al3A	1	0.7045	100	0.111	Contact Map
3fzvA	4	0.9725	100	0.115	Contact Map
3szpA	3	0.9863	100	0.126	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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