YRAN - BACSU - GREMLIN Contacts

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YRAN - Uncharacterized HTH-type transcriptional regulator YraN

UniProt:	O07906	Sequences: MDEKDWILLKILHEEQSVTKTAERLFTSQPSITYRLKKIEEIFGIELFTKRHKGITFTAEGEHLVAYARRMLQELQDTKDHISNLSKEVQGHLRLGVSSNFAQYKLPKLLREFSTMYPNVQYSVQTGWSTDVMKLLDAGIVQVGILRGSHRWKGVEERLTREKLHIISKKPITIEQLPFLPFIKYKTDASLKTIIEDWMHTNLKQAPIIAMEVDRQETCKEMVKHGLGYSIAPEICLQESDHLYTMELYNAKGKPLMRDTWLMYDQKSLGIKLVKAFIDFLKGEQMVTI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	289 (276)
Sequences:	78917 (57090)
Seq/√Len:	3436.4

ECOLI - OXYR NAC LEUO YFIE CYNR ABGR YDCI CYSB ILVY YBHD TDCA YNEJ YBDO NHAR YHJC PGRR LYSR YEIE CBL AAER YNFL YIAU TTDR HCAR YBEF YFER YAFC DMLR YEEY YDHB ALLS YIDZ DSDC YCAN YAHB XAPR METR YGFI ICIA LRHA YHAJ YJIE GCVA HDFR PERR
BACSU - YRAN CYSL YOFA YKUM YWBI GLTR CZCR YUST YYBE YCGK CITR GLTC YVBU YTLI BSDA YWQM ALSR YXJO 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_E	3.734	1.00
15_E	24_R	3.435	1.00
157_E	282_K	2.635	1.00
67_Y	81_H	2.569	1.00
11_I	24_R	2.561	1.00
96_G	141_V	2.475	1.00
158_R	259_D	2.334	1.00
92_H	123_S	2.256	1.00
45_I	60_E	2.234	1.00
158_R	161_R	2.229	1.00
161_R	259_D	2.227	1.00
223_V	230_S	2.201	1.00
8_L	35_R	2.175	1.00
10_K	69_R	2.171	1.00
10_K	14_E	2.114	1.00
92_H	121_Q	2.092	1.00
67_Y	74_E	2.089	1.00
165_H	234_E	2.073	1.00
163_K	234_E	2.048	1.00
161_R	257_M	2.037	1.00
11_I	15_E	2.034	1.00
112_E	280_F	2.029	1.00
224_K	245_T	1.992	1.00
94_R	123_S	1.985	1.00
20_K	23_E	1.968	1.00
11_I	14_E	1.959	1.00
168_S	249_Y	1.938	1.00
13_H	57_F	1.930	1.00
10_K	65_V	1.912	1.00
220_K	240_S	1.909	1.00
8_L	32_I	1.889	1.00
71_M	75_L	1.886	1.00
14_E	69_R	1.881	1.00
224_K	240_S	1.873	1.00
65_V	69_R	1.863	1.00
173_T	176_Q	1.859	1.00
183_I	228_G	1.844	1.00
165_H	248_L	1.816	1.00
13_H	65_V	1.763	1.00
181_P	210_A	1.759	1.00
63_H	81_H	1.721	1.00
49_T	56_T	1.701	1.00
64_L	78_T	1.683	1.00
15_E	20_K	1.675	1.00
67_Y	70_R	1.637	1.00
134_K	138_A	1.630	1.00
18_V	36_L	1.590	1.00
10_K	68_A	1.573	1.00
17_S	20_K	1.567	1.00
157_E	264_Y	1.560	1.00
156_E	266_Q	1.557	1.00
5_D	35_R	1.544	1.00
5_D	42_I	1.540	1.00
14_E	24_R	1.534	1.00
5_D	38_K	1.532	1.00
132_V	144_G	1.520	1.00
103_Q	217_E	1.501	1.00
264_Y	278_I	1.486	1.00
28_S	31_S	1.476	1.00
146_L	263_M	1.470	1.00
113_F	277_F	1.468	1.00
67_Y	77_D	1.467	1.00
127_G	131_D	1.463	1.00
51_R	56_T	1.456	1.00
11_I	25_L	1.449	1.00
156_E	264_Y	1.446	1.00
46_E	49_T	1.444	1.00
9_L	65_V	1.440	1.00
278_I	282_K	1.439	1.00
74_E	77_D	1.434	1.00
8_L	27_T	1.424	1.00
192_K	196_E	1.421	1.00
180_L	229_Y	1.405	1.00
19_T	29_Q	1.404	1.00
88_E	119_N	1.403	1.00
116_M	280_F	1.403	1.00
148_G	261_W	1.399	1.00
113_F	120_V	1.399	1.00
71_M	78_T	1.398	1.00
94_R	125_Q	1.393	1.00
136_L	144_G	1.365	1.00
64_L	79_K	1.354	1.00
59_A	62_E	1.351	1.00
66_A	70_R	1.344	1.00
276_A	279_D	1.342	1.00
10_K	72_L	1.333	1.00
158_R	261_W	1.333	1.00
219_C	230_S	1.331	1.00
90_Q	119_N	1.330	1.00
270_G	274_V	1.330	1.00
162_E	235_I	1.324	1.00
262_L	278_I	1.305	1.00
240_S	245_T	1.305	1.00
143_V	262_L	1.302	1.00
221_E	224_K	1.299	1.00
67_Y	78_T	1.296	1.00
27_T	31_S	1.276	1.00
112_E	116_M	1.271	1.00
170_K	245_T	1.257	1.00
170_K	247_E	1.249	1.00
137_D	154_G	1.247	1.00
34_Y	38_K	1.245	1.00
63_H	66_A	1.243	1.00
143_V	274_V	1.242	1.00
114_S	210_A	1.231	1.00
9_L	48_F	1.229	1.00
234_E	248_L	1.226	1.00
3_E	75_L	1.222	1.00
111_R	225_H	1.215	1.00
9_L	13_H	1.196	1.00
63_H	67_Y	1.191	1.00
42_I	79_K	1.186	1.00
111_R	115_T	1.180	1.00
114_S	181_P	1.171	1.00
234_E	238_Q	1.161	1.00
108_K	225_H	1.143	1.00
172_I	176_Q	1.143	1.00
34_Y	37_K	1.141	1.00
70_R	77_D	1.125	1.00
62_E	66_A	1.125	1.00
248_L	251_A	1.121	1.00
117_Y	276_A	1.119	1.00
238_Q	242_H	1.116	1.00
168_S	229_Y	1.111	1.00
6_W	68_A	1.109	1.00
157_E	278_I	1.103	1.00
11_I	21_T	1.102	1.00
123_S	212_E	1.099	1.00
220_K	224_K	1.098	1.00
193_T	196_E	1.098	1.00
102_A	126_T	1.089	1.00
167_I	248_L	1.075	1.00
37_K	41_E	1.074	1.00
18_V	55_I	1.071	1.00
221_E	225_H	1.067	1.00
239_E	243_L	1.060	1.00
71_M	74_E	1.056	1.00
181_P	208_I	1.053	1.00
33_T	37_K	1.051	1.00
35_R	38_K	1.049	1.00
169_K	226_G	1.049	1.00
275_K	279_D	1.043	1.00
279_D	282_K	1.040	1.00
79_K	83_S	1.039	1.00
9_L	47_L	1.035	1.00
113_F	280_F	1.025	1.00
163_K	257_M	1.024	1.00
73_Q	77_D	1.017	1.00
265_D	268_S	1.015	1.00
12_L	21_T	1.009	1.00
137_D	152_W	1.009	1.00
93_L	277_F	1.004	1.00
109_L	281_L	0.997	1.00
184_K	209_I	0.996	1.00
64_L	68_A	0.996	1.00
112_E	115_T	0.995	1.00
12_L	18_V	0.995	1.00
4_K	7_I	0.992	1.00
213_V	219_C	0.985	1.00
57_F	61_G	0.979	1.00
113_F	117_Y	0.979	1.00
280_F	283_G	0.976	1.00
38_K	41_E	0.974	1.00
199_M	205_Q	0.971	1.00
183_I	219_C	0.960	1.00
21_T	32_I	0.956	1.00
8_L	25_L	0.951	1.00
13_H	48_F	0.946	1.00
27_T	32_I	0.944	1.00
7_I	76_Q	0.944	1.00
70_R	73_Q	0.943	1.00
76_Q	79_K	0.943	1.00
167_I	237_L	0.940	1.00
20_K	24_R	0.937	1.00
75_L	79_K	0.935	1.00
96_G	146_L	0.933	1.00
63_H	85_L	0.930	1.00
9_L	39_I	0.928	1.00
213_V	222_M	0.926	1.00
9_L	57_F	0.923	1.00
193_T	197_D	0.920	1.00
174_I	253_G	0.911	1.00
109_L	280_F	0.903	1.00
271_I	274_V	0.894	1.00
99_S	215_R	0.894	1.00
166_I	229_Y	0.893	1.00
76_Q	80_D	0.893	1.00
60_E	63_H	0.890	1.00
171_P	252_K	0.890	1.00
16_Q	56_T	0.888	1.00
181_P	209_I	0.886	1.00
141_V	144_G	0.882	1.00
116_M	283_G	0.880	1.00
66_A	69_R	0.872	1.00
45_I	82_I	0.869	1.00
148_G	259_D	0.867	1.00
19_T	23_E	0.867	1.00
111_R	227_L	0.865	1.00
91_G	273_L	0.862	1.00
48_F	55_I	0.862	1.00
168_S	247_E	0.855	1.00
77_D	81_H	0.851	1.00
51_R	54_G	0.850	1.00
75_L	78_T	0.848	1.00
25_L	32_I	0.846	1.00
125_Q	141_V	0.839	1.00
29_Q	33_T	0.838	1.00
60_E	85_L	0.833	1.00
74_E	78_T	0.831	1.00
14_E	65_V	0.827	1.00
240_S	243_L	0.825	1.00
15_E	21_T	0.823	1.00
272_K	276_A	0.822	1.00
131_D	134_K	0.822	1.00
114_S	227_L	0.821	1.00
13_H	16_Q	0.821	1.00
9_L	64_L	0.820	1.00
7_I	11_I	0.819	1.00
60_E	82_I	0.818	1.00
169_K	227_L	0.817	1.00
16_Q	54_G	0.815	1.00
195_I	199_M	0.815	1.00
270_G	275_K	0.806	1.00
175_E	178_P	0.806	1.00
95_L	143_V	0.805	1.00
96_G	144_G	0.801	1.00
4_K	35_R	0.799	1.00
13_H	61_G	0.798	1.00
120_V	273_L	0.797	1.00
12_L	48_F	0.792	1.00
16_Q	62_E	0.787	1.00
222_M	227_L	0.783	1.00
155_V	263_M	0.783	1.00
62_E	65_V	0.783	1.00
69_R	73_Q	0.781	1.00
121_Q	208_I	0.771	1.00
12_L	32_I	0.771	1.00
5_D	8_L	0.770	1.00
78_T	82_I	0.769	1.00
37_K	46_E	0.768	1.00
163_K	250_N	0.766	1.00
194_I	198_W	0.766	1.00
68_A	71_M	0.764	1.00
178_P	205_Q	0.763	1.00
167_I	230_S	0.762	1.00
113_F	276_A	0.758	1.00
49_T	58_T	0.758	1.00
18_V	32_I	0.758	1.00
237_L	240_S	0.756	1.00
3_E	72_L	0.755	1.00
139_G	265_D	0.755	1.00
97_V	102_A	0.751	1.00
215_R	218_T	0.749	1.00
7_I	10_K	0.749	1.00
83_S	86_S	0.748	1.00
182_F	207_P	0.748	1.00
197_D	201_T	0.748	1.00
279_D	283_G	0.747	1.00
276_A	280_F	0.745	1.00
196_E	200_H	0.744	1.00
173_T	253_G	0.744	1.00
163_K	255_P	0.741	1.00
12_L	36_L	0.741	1.00
167_I	232_A	0.735	1.00
91_G	120_V	0.727	1.00
198_W	201_T	0.727	1.00
59_A	63_H	0.722	1.00
268_S	271_I	0.721	1.00
194_I	197_D	0.720	1.00
143_V	277_F	0.719	1.00
241_D	244_Y	0.716	1.00
137_D	155_V	0.715	1.00
142_Q	274_V	0.714	1.00
60_E	64_L	0.713	1.00
195_I	198_W	0.711	1.00
186_K	212_E	0.707	1.00
116_M	276_A	0.705	1.00
103_Q	221_E	0.703	1.00
31_S	35_R	0.702	1.00
67_Y	71_M	0.697	1.00
94_R	142_Q	0.692	1.00
233_P	236_C	0.691	1.00
133_M	137_D	0.680	1.00
192_K	198_W	0.679	1.00
89_V	117_Y	0.674	1.00
64_L	82_I	0.673	1.00
108_K	111_R	0.669	1.00
167_I	241_D	0.668	1.00
171_P	250_N	0.667	1.00
49_T	54_G	0.667	1.00
57_F	62_E	0.666	1.00
94_R	141_V	0.665	1.00
126_T	214_D	0.664	1.00
7_I	72_L	0.663	1.00
191_L	195_I	0.663	1.00
176_Q	179_F	0.661	1.00
56_T	62_E	0.660	1.00
154_G	266_Q	0.659	1.00
9_L	61_G	0.657	1.00
121_Q	212_E	0.657	1.00
40_E	50_K	0.656	1.00
96_G	132_V	0.655	1.00
127_G	132_V	0.655	1.00
23_E	26_F	0.654	1.00
166_I	231_I	0.652	1.00
237_L	241_D	0.649	1.00
185_Y	219_C	0.646	1.00
77_D	80_D	0.639	1.00
241_D	248_L	0.637	1.00
272_K	275_K	0.636	1.00
182_F	229_Y	0.635	1.00
4_K	38_K	0.628	1.00
211_M	222_M	0.624	1.00
73_Q	76_Q	0.619	1.00
147_R	258_R	0.617	1.00
166_I	177_L	0.616	1.00
224_K	243_L	0.616	1.00
72_L	76_Q	0.614	1.00
190_S	193_T	0.612	1.00
197_D	200_H	0.611	1.00
40_E	45_I	0.610	1.00
36_L	40_E	0.609	1.00
143_V	278_I	0.607	1.00
106_L	109_L	0.606	1.00
13_H	62_E	0.606	1.00
12_L	17_S	0.601	1.00
43_F	64_L	0.599	1.00
186_K	214_D	0.597	1.00
239_E	242_H	0.597	1.00
112_E	283_G	0.591	1.00
213_V	218_T	0.591	1.00
97_V	106_L	0.590	1.00
68_A	72_L	0.587	1.00
173_T	252_K	0.584	1.00
191_L	194_I	0.583	1.00
170_K	244_Y	0.583	1.00
21_T	25_L	0.581	1.00
80_D	84_N	0.581	1.00
4_K	8_L	0.579	1.00
171_P	176_Q	0.579	1.00
108_K	112_E	0.578	1.00
193_T	198_W	0.577	1.00
45_I	49_T	0.574	1.00
117_Y	120_V	0.573	1.00
93_L	143_V	0.573	1.00
134_K	137_D	0.572	1.00
90_Q	121_Q	0.572	1.00
105_K	109_L	0.572	1.00
93_L	273_L	0.570	1.00
277_F	281_L	0.569	1.00
196_E	199_M	0.567	1.00
63_H	82_I	0.563	1.00
96_G	125_Q	0.563	1.00
18_V	29_Q	0.559	1.00
179_F	208_I	0.558	1.00
192_K	212_E	0.556	1.00
48_F	57_F	0.556	1.00
30_P	34_Y	0.556	1.00
43_F	82_I	0.555	1.00
28_S	34_Y	0.554	1.00
136_L	155_V	0.553	1.00
126_T	215_R	0.550	1.00
219_C	223_V	0.549	1.00
162_E	258_R	0.548	1.00
43_F	46_E	0.547	1.00
91_G	119_N	0.544	1.00
31_S	34_Y	0.543	1.00
264_Y	275_K	0.542	1.00
81_H	84_N	0.540	1.00
107_P	111_R	0.540	1.00
166_I	182_F	0.538	1.00
177_L	180_L	0.537	1.00
164_L	231_I	0.537	1.00
199_M	207_P	0.537	1.00
84_N	89_V	0.537	1.00
16_Q	55_I	0.536	1.00
111_R	114_S	0.535	1.00
27_T	35_R	0.533	1.00
216_Q	233_P	0.532	1.00
46_E	60_E	0.531	1.00
136_L	263_M	0.531	1.00
232_A	237_L	0.529	1.00
222_M	228_G	0.527	1.00
159_L	262_L	0.526	1.00
101_F	105_K	0.526	1.00
80_D	83_S	0.526	1.00
57_F	65_V	0.524	1.00
97_V	124_V	0.524	1.00
273_L	276_A	0.524	1.00
192_K	195_I	0.524	1.00
96_G	127_G	0.523	1.00
8_L	36_L	0.522	1.00
137_D	140_I	0.521	1.00
103_Q	215_R	0.521	1.00
178_P	206_A	0.520	1.00
108_K	221_E	0.519	1.00
38_K	42_I	0.515	1.00
217_E	221_E	0.512	1.00
18_V	50_K	0.511	1.00
18_V	54_G	0.509	1.00
274_V	278_I	0.508	1.00
8_L	21_T	0.508	1.00
156_E	267_K	0.508	1.00
245_T	248_L	0.506	1.00
187_T	212_E	0.505	1.00
121_Q	210_A	0.505	1.00
71_M	79_K	0.504	1.00
6_W	64_L	0.503	1.00
160_T	260_T	0.503	1.00
275_K	278_I	0.501	1.00
85_L	89_V	0.500	1.00
30_P	33_T	0.500	1.00
43_F	79_K	0.500	1.00
175_E	205_Q	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
2esnA	3	0.9862	100	0.092	Contact Map
3fxqA	3	0.9862	100	0.097	Contact Map
1uthA	2	0.7509	100	0.103	Contact Map
3fzvA	4	0.9619	100	0.107	Contact Map
1al3A	1	0.699	100	0.107	Contact Map
1ixcA	4	0.9792	100	0.107	Contact Map
4x6gA	4	1	100	0.11	Contact Map
2h98A	2	0.6782	100	0.113	Contact Map
2h9bA	2	0.6782	100	0.12	Contact Map
3szpA	3	0.9723	100	0.125	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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