CZCR - BACSU - GREMLIN Contacts

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CZCR - HTH-type transcriptional regulator CzcR

UniProt:	P71025	Sequences: MELRDLQIFKCVAHHKSITGAAKELNYVQSNVTARIKQLENELKTPLFNRHKKGVSLSPEGRKMIEYVNKILKDVEELEQVFLDTEIPSGILKIGTVETVRILPTIIASYYKKYPNVDLSLQAGLTEELIKKVMNHELDGAFISGPLKHSILEQYDVYTEKLTLVTSNKTFNIEDFSTTPILVFNQGCGYRSRLEQWLKDEGVLPNRMMEFNILETILNSVALGLGITVVPESAVMHLAVQGKVYCHPLPEKDSCISTIFIRHKDAYLTNSMRSLLKTIVEHKNMSMA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	288 (276)
Sequences:	79217 (57449)
Seq/√Len:	3458.0

ECOLI - NAC OXYR YFIE LEUO YEIE CYSB YBHD LYSR AAER YDCI TDCA YHJC ABGR YBDO YNEJ NHAR YIAU PGRR CYNR YAFC TTDR YBEF YGFI YFER DSDC DMLR CBL ILVY METR HCAR YNFL YDHB YIDZ YEEY ALLS YCAN YAHB XAPR GCVA ICIA YHAJ PERR LRHA YJIE HDFR
BACSU - CZCR YUST CYSL GLTR YOFA YWBI YCGK YYBE GLTC YWQM BSDA YRAN YTLI ALSR YVBU CITR YKUM 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_K	74_D	3.675	1.00
15_H	24_E	3.375	1.00
155_Y	280_V	2.616	1.00
11_C	24_E	2.546	1.00
67_Y	81_V	2.531	1.00
95_G	138_L	2.388	1.00
156_D	257_S	2.339	1.00
91_I	120_S	2.238	1.00
45_T	60_E	2.238	1.00
156_D	159_T	2.219	1.00
159_T	257_S	2.198	1.00
10_K	69_N	2.163	1.00
8_I	35_R	2.142	1.00
221_V	228_T	2.140	1.00
10_K	14_H	2.093	1.00
91_I	118_D	2.074	1.00
163_T	232_E	2.062	1.00
67_Y	74_D	2.056	1.00
109_S	278_T	2.025	1.00
11_C	15_H	2.015	1.00
159_T	255_C	1.987	1.00
222_A	243_K	1.985	1.00
161_K	232_E	1.982	1.00
93_K	120_S	1.948	1.00
11_C	14_H	1.923	1.00
20_G	23_K	1.915	1.00
13_A	57_L	1.896	1.00
10_K	65_I	1.868	1.00
71_I	75_V	1.854	1.00
172_N	175_D	1.854	1.00
8_I	32_V	1.852	1.00
166_T	247_H	1.851	1.00
218_L	238_L	1.847	1.00
182_L	226_G	1.835	1.00
65_I	69_N	1.821	1.00
222_A	238_L	1.815	1.00
14_H	69_N	1.808	1.00
163_T	246_C	1.801	1.00
13_A	65_I	1.748	1.00
180_P	208_M	1.744	1.00
154_Q	259_I	1.712	1.00
63_K	81_V	1.701	1.00
132_K	137_E	1.692	1.00
49_N	56_S	1.669	1.00
15_H	20_G	1.652	1.00
64_M	78_L	1.647	1.00
67_Y	70_K	1.618	1.00
153_E	264_K	1.569	1.00
129_L	141_A	1.565	1.00
17_S	20_G	1.545	1.00
10_K	68_V	1.544	1.00
155_Y	262_R	1.539	1.00
18_I	36_I	1.535	1.00
5_D	42_E	1.525	1.00
5_D	35_R	1.520	1.00
131_K	135_N	1.509	1.00
14_H	24_E	1.499	1.00
5_D	38_Q	1.495	1.00
262_R	276_L	1.467	1.00
28_V	31_N	1.461	1.00
51_H	56_S	1.456	1.00
67_Y	77_E	1.446	1.00
143_I	261_I	1.439	1.00
276_L	280_V	1.438	1.00
11_C	25_L	1.435	1.00
74_D	77_E	1.435	1.00
153_E	262_R	1.433	1.00
110_Y	275_L	1.427	1.00
46_P	49_N	1.419	1.00
9_F	65_I	1.406	1.00
145_G	259_I	1.405	1.00
113_K	278_T	1.403	1.00
132_K	138_L	1.399	1.00
8_I	27_Y	1.385	1.00
179_T	227_I	1.385	1.00
19_T	29_Q	1.369	1.00
71_I	78_L	1.358	1.00
110_Y	117_V	1.358	1.00
93_K	122_Q	1.356	1.00
274_S	277_K	1.347	1.00
87_I	116_N	1.345	1.00
133_V	141_A	1.344	1.00
66_E	70_K	1.336	1.00
89_S	116_N	1.334	1.00
64_M	79_E	1.333	1.00
268_L	272_M	1.312	1.00
191_R	195_E	1.311	1.00
217_I	228_T	1.310	1.00
10_K	72_L	1.309	1.00
260_F	276_L	1.305	1.00
59_P	62_R	1.302	1.00
67_Y	78_L	1.295	1.00
160_E	233_S	1.295	1.00
134_M	151_I	1.287	1.00
140_G	260_F	1.280	1.00
238_L	243_K	1.280	1.00
219_N	222_A	1.276	1.00
27_Y	31_N	1.271	1.00
156_D	259_I	1.268	1.00
109_S	113_K	1.239	1.00
168_N	245_Y	1.236	1.00
111_Y	208_M	1.235	1.00
168_N	243_K	1.222	1.00
63_K	66_E	1.221	1.00
34_A	38_Q	1.220	1.00
140_G	272_M	1.211	1.00
108_A	223_L	1.209	1.00
232_E	246_C	1.206	1.00
63_K	67_Y	1.203	1.00
42_E	79_E	1.193	1.00
111_Y	180_P	1.191	1.00
3_L	75_V	1.190	1.00
124_G	128_E	1.183	1.00
108_A	112_K	1.181	1.00
9_F	48_F	1.179	1.00
9_F	13_A	1.173	1.00
105_T	223_L	1.165	1.00
154_Q	261_I	1.140	1.00
232_E	236_M	1.133	1.00
246_C	249_L	1.121	1.00
70_K	77_E	1.121	1.00
124_G	132_K	1.120	1.00
166_T	227_I	1.120	1.00
171_F	175_D	1.117	1.00
170_T	250_P	1.114	1.00
6_L	68_V	1.111	1.00
34_A	37_K	1.109	1.00
236_M	240_V	1.103	1.00
62_R	66_E	1.103	1.00
180_P	206_N	1.101	1.00
155_Y	276_L	1.098	1.00
169_K	245_Y	1.097	1.00
114_Y	274_S	1.097	1.00
11_C	21_A	1.096	1.00
218_L	222_A	1.093	1.00
120_S	210_E	1.083	1.00
219_N	223_L	1.065	1.00
18_I	55_V	1.056	1.00
71_I	74_D	1.056	1.00
122_Q	132_K	1.055	1.00
37_K	41_N	1.054	1.00
167_S	224_G	1.053	1.00
277_K	280_V	1.042	1.00
35_R	38_Q	1.038	1.00
33_T	37_K	1.036	1.00
165_V	246_C	1.034	1.00
237_H	241_Q	1.033	1.00
134_M	149_H	1.024	1.00
79_E	83_L	1.022	1.00
183_V	207_R	1.021	1.00
273_R	277_K	1.015	1.00
9_F	47_L	1.014	1.00
73_K	77_E	1.011	1.00
161_K	255_C	1.009	1.00
110_Y	278_T	1.000	1.00
263_H	266_A	0.999	1.00
278_T	281_E	0.995	1.00
64_M	68_V	0.992	1.00
124_G	129_L	0.992	1.00
12_V	21_A	0.986	1.00
110_Y	114_Y	0.982	1.00
211_F	217_I	0.979	1.00
109_S	112_K	0.977	1.00
38_Q	41_N	0.972	1.00
4_R	7_Q	0.972	1.00
106_I	279_I	0.970	1.00
12_V	18_I	0.969	1.00
92_L	275_L	0.964	1.00
192_S	195_E	0.963	1.00
182_L	217_I	0.955	1.00
198_L	203_V	0.952	1.00
21_A	32_V	0.951	1.00
75_V	79_E	0.950	1.00
57_L	61_G	0.948	1.00
70_K	73_K	0.943	1.00
8_I	25_L	0.937	1.00
76_E	79_E	0.936	1.00
13_A	48_F	0.935	1.00
27_Y	32_V	0.934	1.00
20_G	24_E	0.933	1.00
165_V	235_V	0.923	1.00
7_Q	76_E	0.921	1.00
9_F	39_L	0.920	1.00
132_K	135_N	0.916	1.00
9_F	57_L	0.911	1.00
16_K	56_S	0.897	1.00
173_I	251_E	0.896	1.00
76_E	80_Q	0.895	1.00
269_T	272_M	0.895	1.00
211_F	220_S	0.895	1.00
164_L	227_I	0.889	1.00
197_W	201_E	0.887	1.00
98_E	213_I	0.884	1.00
60_E	63_K	0.882	1.00
106_I	278_T	0.880	1.00
145_G	257_S	0.878	1.00
45_T	82_F	0.877	1.00
108_A	225_L	0.872	1.00
66_E	69_N	0.872	1.00
153_E	156_D	0.869	1.00
192_S	196_Q	0.857	1.00
113_K	281_E	0.856	1.00
48_F	55_V	0.855	1.00
95_G	143_I	0.850	1.00
77_E	81_V	0.847	1.00
75_V	78_L	0.847	1.00
138_L	141_A	0.846	1.00
60_E	82_F	0.845	1.00
19_T	23_K	0.845	1.00
130_I	134_M	0.843	1.00
122_Q	138_L	0.842	1.00
180_P	207_R	0.841	1.00
238_L	241_Q	0.841	1.00
270_N	274_S	0.839	1.00
90_G	271_S	0.839	1.00
111_Y	225_L	0.838	1.00
51_H	54_G	0.835	1.00
166_T	245_Y	0.827	1.00
29_Q	33_T	0.827	1.00
15_H	21_A	0.825	1.00
14_H	65_I	0.824	1.00
7_Q	11_C	0.824	1.00
25_L	32_V	0.823	1.00
13_A	16_K	0.820	1.00
118_D	206_N	0.816	1.00
16_K	54_G	0.813	1.00
74_D	78_L	0.813	1.00
167_S	225_L	0.809	1.00
9_F	64_M	0.805	1.00
117_V	271_S	0.803	1.00
95_G	129_L	0.798	1.00
4_R	35_R	0.798	1.00
94_I	140_G	0.798	1.00
268_L	273_R	0.797	1.00
62_R	65_I	0.794	1.00
174_E	177_S	0.790	1.00
69_N	73_K	0.786	1.00
172_N	250_P	0.785	1.00
12_V	48_F	0.785	1.00
13_A	61_G	0.780	1.00
16_K	62_R	0.778	1.00
78_L	82_F	0.778	1.00
220_S	225_L	0.771	1.00
12_V	32_V	0.768	1.00
235_V	238_L	0.767	1.00
95_G	141_A	0.764	1.00
68_V	71_I	0.763	1.00
152_L	261_I	0.763	1.00
194_L	198_L	0.763	1.00
5_D	8_I	0.758	1.00
136_H	263_H	0.755	1.00
37_K	46_P	0.755	1.00
7_Q	10_K	0.753	1.00
3_L	72_L	0.751	1.00
49_N	58_S	0.751	1.00
18_I	32_V	0.750	1.00
165_V	228_T	0.747	1.00
274_S	278_T	0.744	1.00
197_W	200_D	0.744	1.00
181_I	205_P	0.744	1.00
193_R	197_W	0.736	1.00
235_V	239_A	0.733	1.00
196_Q	200_D	0.733	1.00
128_E	131_K	0.731	1.00
266_A	269_T	0.730	1.00
110_Y	274_S	0.729	1.00
12_V	36_I	0.729	1.00
277_K	281_E	0.724	1.00
213_I	216_T	0.724	1.00
161_K	248_P	0.723	1.00
140_G	275_L	0.723	1.00
90_G	117_V	0.721	1.00
134_M	152_L	0.717	1.00
165_V	230_V	0.716	1.00
59_P	63_K	0.716	1.00
177_S	203_V	0.715	1.00
49_N	54_G	0.708	1.00
139_D	272_M	0.707	1.00
165_V	239_A	0.707	1.00
185_N	210_E	0.702	1.00
113_K	274_S	0.700	1.00
60_E	64_M	0.696	1.00
231_P	234_A	0.694	1.00
67_Y	71_I	0.688	1.00
175_D	178_T	0.687	1.00
93_K	139_D	0.686	1.00
31_N	35_R	0.682	1.00
128_E	132_K	0.682	1.00
64_M	82_F	0.678	1.00
195_E	199_K	0.677	1.00
123_A	212_N	0.677	1.00
151_I	264_K	0.675	1.00
88_P	114_Y	0.675	1.00
239_A	242_G	0.674	1.00
239_A	246_C	0.672	1.00
93_K	138_L	0.665	1.00
57_L	62_R	0.665	1.00
222_A	241_Q	0.665	1.00
105_T	108_A	0.664	1.00
9_F	61_G	0.662	1.00
170_T	248_P	0.662	1.00
23_K	26_N	0.660	1.00
7_Q	72_L	0.658	1.00
56_S	62_R	0.656	1.00
184_F	217_I	0.650	1.00
40_E	50_R	0.649	1.00
103_L	106_I	0.647	1.00
181_I	227_I	0.643	1.00
77_E	80_Q	0.639	1.00
209_M	220_S	0.637	1.00
118_D	210_E	0.636	1.00
194_L	197_W	0.636	1.00
196_Q	199_K	0.633	1.00
237_H	240_V	0.631	1.00
172_N	251_E	0.631	1.00
144_S	256_I	0.629	1.00
270_N	273_R	0.628	1.00
164_L	229_V	0.624	1.00
174_E	201_E	0.623	1.00
192_S	197_W	0.621	1.00
4_R	38_Q	0.620	1.00
72_L	76_E	0.620	1.00
36_I	40_E	0.616	1.00
73_K	76_E	0.615	1.00
164_L	176_F	0.613	1.00
193_R	196_Q	0.612	1.00
13_A	62_R	0.611	1.00
40_E	45_T	0.610	1.00
140_G	276_L	0.604	1.00
43_L	64_M	0.602	1.00
161_K	252_K	0.601	1.00
211_F	216_T	0.601	1.00
109_S	281_E	0.600	1.00
92_L	140_G	0.600	1.00
12_V	17_S	0.599	1.00
105_T	109_S	0.596	1.00
80_Q	84_D	0.595	1.00
185_N	212_N	0.591	1.00
168_N	242_G	0.591	1.00
178_T	206_N	0.583	1.00
4_R	8_I	0.583	1.00
195_E	198_L	0.580	1.00
45_T	49_N	0.578	1.00
92_L	271_S	0.578	1.00
191_R	210_E	0.578	1.00
114_Y	117_V	0.577	1.00
160_E	256_I	0.575	1.00
68_V	72_L	0.575	1.00
21_A	25_L	0.574	1.00
48_F	57_L	0.572	1.00
133_V	152_L	0.571	1.00
63_K	82_F	0.569	1.00
43_L	82_F	0.569	1.00
190_Y	194_L	0.569	1.00
45_T	85_T	0.569	1.00
101_R	104_P	0.568	1.00
275_L	279_I	0.567	1.00
18_I	29_Q	0.561	1.00
105_T	219_N	0.559	1.00
262_R	273_R	0.557	1.00
89_S	118_D	0.556	1.00
157_V	260_F	0.555	1.00
31_N	34_A	0.554	1.00
43_L	46_P	0.549	1.00
96_T	103_L	0.549	1.00
230_V	235_V	0.547	1.00
81_V	84_D	0.547	1.00
271_S	274_S	0.545	1.00
134_M	137_E	0.545	1.00
104_P	108_A	0.545	1.00
80_Q	83_L	0.544	1.00
27_Y	35_R	0.543	1.00
28_V	34_A	0.542	1.00
162_L	229_V	0.542	1.00
198_L	205_P	0.541	1.00
90_G	116_N	0.541	1.00
46_P	60_E	0.540	1.00
30_S	34_A	0.540	1.00
95_G	122_Q	0.538	1.00
16_K	55_V	0.538	1.00
145_G	154_Q	0.536	1.00
102_I	106_I	0.533	1.00
214_L	231_P	0.532	1.00
123_A	213_I	0.531	1.00
96_T	121_L	0.531	1.00
97_V	100_V	0.529	1.00
217_I	221_V	0.528	1.00
133_V	261_I	0.527	1.00
78_L	81_V	0.526	1.00
38_Q	42_E	0.526	1.00
84_D	88_P	0.523	1.00
108_A	111_Y	0.523	1.00
174_E	203_V	0.523	1.00
101_R	215_E	0.523	1.00
186_Q	210_E	0.522	1.00
118_D	208_M	0.520	1.00
164_L	181_I	0.520	1.00
8_I	36_I	0.517	1.00
243_K	246_C	0.517	1.00
88_P	116_N	0.515	1.00
30_S	33_T	0.515	1.00
57_L	65_I	0.515	1.00
18_I	50_R	0.514	1.00
190_Y	193_R	0.513	1.00
158_Y	258_T	0.510	1.00
131_K	137_E	0.509	1.00
129_L	136_H	0.508	1.00
177_S	204_L	0.508	1.00
6_L	64_M	0.503	1.00
220_S	226_G	0.502	1.00
184_F	214_L	0.501	1.00
249_L	252_K	0.501	1.00
102_I	105_T	0.500	1.00
43_L	79_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
2esnA	3	0.9861	100	0.1	Contact Map
3fxqA	3	0.9861	100	0.105	Contact Map
1uthA	2	0.7535	100	0.105	Contact Map
1ixcA	4	0.9792	100	0.109	Contact Map
2h98A	2	0.684	100	0.11	Contact Map
1al3A	1	0.7014	100	0.115	Contact Map
3fzvA	4	0.9618	100	0.116	Contact Map
4x6gA	4	1	100	0.117	Contact Map
2h9bA	2	0.684	100	0.117	Contact Map
3szpA	3	0.9722	100	0.123	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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