XAPR - ECOLI - GREMLIN Contacts

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XAPR - HTH-type transcriptional regulator XapR

UniProt:	P23841	Sequences: MERVYRTDLKLLRYFLAVAEELHFGRAAARLNMSQPPLSIHIKELENQLGTQLFIRHSRSVVLTHAGKILMEESRRLLVNANNVLARIEQIGRGEAGRIELGVVGTAMWGRMRPVMRRFLRENPNVDVLFREKMPAMQMALLERRELDAGIWRMATEPPTGFTSLRLHESAFLVAMPEEHHLSSFSTVPLEALRDEYFVTMPPVYTDWDFLQRVCQQVGFSPVVIREVNEPQTVLAMVSMGIGITLIADSYAQMNWPGVIFRPLKQRIPADLYIVYETQQVTPAMVKLLAALTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11146
Length:	294 (281)
Sequences:	79214 (57518)
Seq/√Len:	3431.2

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_R	80_N	3.651	1.00
21_E	30_R	3.462	1.00
102_G	147_L	2.603	1.00
73_E	87_R	2.455	1.00
238_V	245_T	2.392	1.00
171_A	249_D	2.335	1.00
180_H	196_E	2.261	1.00
166_R	169_E	2.240	1.00
169_E	271_D	2.231	1.00
17_A	30_R	2.216	1.00
20_E	75_R	2.200	1.00
26_R	29_A	2.196	1.00
98_R	129_L	2.175	1.00
98_R	127_D	2.152	1.00
189_P	192_A	2.119	1.00
16_L	71_M	2.058	1.00
166_R	271_D	2.054	1.00
51_T	66_A	2.034	1.00
14_Y	41_H	2.031	1.00
100_E	129_L	2.031	1.00
169_E	269_P	1.977	1.00
73_E	80_N	1.975	1.00
17_A	20_E	1.947	1.00
14_Y	38_L	1.935	1.00
199_V	243_G	1.928	1.00
24_F	42_I	1.927	1.00
77_L	81_A	1.920	1.00
16_L	75_R	1.916	1.00
19_A	63_L	1.890	1.00
17_A	21_E	1.880	1.00
16_L	20_E	1.877	1.00
71_M	75_R	1.850	1.00
173_L	249_D	1.821	1.00
185_F	192_A	1.799	1.00
138_Q	150_G	1.797	1.00
118_R	291_A	1.790	1.00
55_I	62_V	1.783	1.00
70_L	84_V	1.765	1.00
256_W	259_V	1.745	1.00
197_Y	225_I	1.727	1.00
235_L	255_N	1.713	1.00
239_S	255_N	1.695	1.00
69_I	87_R	1.689	1.00
141_L	146_E	1.683	1.00
20_E	30_R	1.665	1.00
164_S	273_Y	1.658	1.00
15_F	71_M	1.638	1.00
119_F	288_L	1.637	1.00
16_L	74_S	1.600	1.00
19_A	71_M	1.600	1.00
14_Y	33_M	1.587	1.00
119_F	126_V	1.578	1.00
25_G	35_Q	1.569	1.00
94_G	125_N	1.563	1.00
65_H	68_K	1.559	1.00
208_W	212_Q	1.557	1.00
163_T	278_T	1.556	1.00
21_E	26_R	1.553	1.00
140_A	144_R	1.524	1.00
11_L	41_H	1.523	1.00
34_S	37_P	1.485	1.00
8_D	11_L	1.478	1.00
11_L	48_Q	1.472	1.00
16_L	78_L	1.466	1.00
281_V	285_M	1.464	1.00
52_Q	55_I	1.447	1.00
23_H	26_R	1.435	1.00
165_L	276_Y	1.432	1.00
11_L	44_E	1.422	1.00
17_A	31_L	1.419	1.00
73_E	76_R	1.414	1.00
77_L	84_V	1.395	1.00
73_E	83_N	1.393	1.00
163_T	276_Y	1.385	1.00
152_W	275_V	1.376	1.00
9_L	81_A	1.374	1.00
149_A	285_M	1.367	1.00
96_A	125_N	1.355	1.00
154_M	273_Y	1.351	1.00
274_I	289_L	1.349	1.00
109_W	232_Q	1.348	1.00
143_E	161_G	1.330	1.00
48_Q	85_L	1.326	1.00
100_E	131_R	1.316	1.00
176_M	244_I	1.303	1.00
196_E	244_I	1.298	1.00
70_L	85_L	1.295	1.00
120_L	225_I	1.282	1.00
118_R	122_E	1.280	1.00
141_L	147_L	1.274	1.00
149_A	274_I	1.272	1.00
170_S	250_S	1.271	1.00
234_V	245_T	1.267	1.00
57_H	62_V	1.263	1.00
43_K	47_N	1.263	1.00
276_Y	289_L	1.258	1.00
68_K	72_E	1.256	1.00
176_M	262_R	1.253	1.00
249_D	253_Q	1.235	1.00
215_C	220_F	1.234	1.00
80_N	83_N	1.231	1.00
236_A	239_S	1.212	1.00
287_K	290_A	1.212	1.00
72_E	76_R	1.209	1.00
181_H	196_E	1.196	1.00
118_R	121_R	1.195	1.00
120_L	197_Y	1.192	1.00
69_I	72_E	1.191	1.00
15_F	54_F	1.188	1.00
117_R	121_R	1.186	1.00
178_E	258_G	1.184	1.00
73_E	84_V	1.178	1.00
249_D	263_P	1.172	1.00
199_V	234_V	1.171	1.00
173_L	263_P	1.169	1.00
186_S	262_R	1.163	1.00
99_I	288_L	1.152	1.00
39_S	43_K	1.151	1.00
239_S	260_I	1.149	1.00
13_R	82_N	1.149	1.00
15_F	53_L	1.145	1.00
166_R	273_Y	1.143	1.00
40_I	43_K	1.140	1.00
277_E	280_Q	1.139	1.00
15_F	19_A	1.134	1.00
164_S	275_V	1.132	1.00
33_M	37_P	1.126	1.00
129_L	227_E	1.118	1.00
228_V	234_V	1.112	1.00
24_F	61_V	1.105	1.00
18_V	27_A	1.104	1.00
10_K	13_R	1.101	1.00
40_I	44_E	1.095	1.00
76_R	83_N	1.094	1.00
178_E	260_I	1.092	1.00
119_F	291_A	1.085	1.00
12_L	74_S	1.083	1.00
117_R	240_M	1.082	1.00
108_M	132_E	1.080	1.00
197_Y	223_V	1.076	1.00
123_N	287_K	1.076	1.00
253_Q	257_P	1.075	1.00
254_M	258_G	1.067	1.00
17_A	27_A	1.067	1.00
77_L	80_N	1.066	1.00
63_L	67_G	1.062	1.00
41_H	44_E	1.061	1.00
177_P	241_G	1.058	1.00
188_V	192_A	1.033	1.00
235_L	239_S	1.030	1.00
286_V	290_A	1.026	1.00
69_I	73_E	1.017	1.00
174_V	244_I	1.012	1.00
175_A	252_A	1.009	1.00
114_P	240_M	1.002	1.00
143_E	159_P	0.999	1.00
209_D	212_Q	0.999	1.00
82_N	86_A	0.999	1.00
187_T	265_K	0.996	1.00
85_L	89_E	0.994	1.00
236_A	240_M	0.991	1.00
82_N	85_L	0.990	1.00
19_A	54_F	0.984	1.00
14_Y	31_L	0.984	1.00
171_A	263_P	0.978	1.00
142_L	150_G	0.977	1.00
33_M	38_L	0.977	1.00
119_F	123_N	0.975	1.00
161_G	278_T	0.975	1.00
176_M	180_H	0.952	1.00
15_F	63_L	0.950	1.00
228_V	237_M	0.948	1.00
200_T	224_V	0.946	1.00
180_H	183_S	0.945	1.00
102_G	152_W	0.943	1.00
79_V	83_N	0.943	1.00
70_L	74_S	0.941	1.00
255_N	260_I	0.933	1.00
18_V	24_F	0.933	1.00
282_T	285_M	0.933	1.00
19_A	67_G	0.931	1.00
180_H	197_Y	0.930	1.00
51_T	88_I	0.929	1.00
156_T	159_P	0.922	1.00
122_E	291_A	0.921	1.00
115_V	291_A	0.921	1.00
263_P	266_Q	0.919	1.00
255_N	258_G	0.917	1.00
15_F	45_L	0.915	1.00
171_A	269_P	0.913	1.00
27_A	38_L	0.911	1.00
54_F	61_V	0.911	1.00
127_D	223_V	0.910	1.00
239_S	258_G	0.906	1.00
131_R	141_L	0.896	1.00
44_E	47_N	0.894	1.00
141_L	144_R	0.892	1.00
198_F	222_P	0.891	1.00
137_M	140_A	0.888	1.00
176_M	181_H	0.886	1.00
147_L	150_G	0.884	1.00
192_A	195_D	0.881	1.00
26_R	30_R	0.879	1.00
72_E	75_R	0.879	1.00
184_S	197_Y	0.869	1.00
22_L	62_V	0.863	1.00
162_F	275_V	0.862	1.00
25_G	29_A	0.861	1.00
102_G	138_Q	0.859	1.00
180_H	184_S	0.854	1.00
197_Y	224_V	0.851	1.00
105_G	230_E	0.849	1.00
126_V	284_A	0.849	1.00
175_A	245_T	0.846	1.00
154_M	271_D	0.846	1.00
9_L	78_L	0.843	1.00
101_L	149_A	0.840	1.00
31_L	38_L	0.836	1.00
102_G	150_G	0.833	1.00
57_H	60_S	0.832	1.00
165_L	289_L	0.830	1.00
181_H	186_S	0.829	1.00
10_K	41_H	0.827	1.00
18_V	42_I	0.826	1.00
139_M	143_E	0.822	1.00
163_T	166_R	0.819	1.00
209_D	213_R	0.816	1.00
76_R	79_V	0.816	1.00
43_K	52_Q	0.810	1.00
22_L	68_K	0.807	1.00
131_R	147_L	0.803	1.00
281_V	286_V	0.803	1.00
66_A	88_I	0.800	1.00
175_A	261_F	0.800	1.00
191_E	194_R	0.792	1.00
179_E	183_S	0.791	1.00
15_F	70_L	0.788	1.00
143_E	162_F	0.784	1.00
182_L	196_E	0.783	1.00
117_R	242_I	0.781	1.00
18_V	54_F	0.780	1.00
97_G	284_A	0.778	1.00
19_A	22_L	0.778	1.00
97_G	126_V	0.777	1.00
95_E	123_N	0.777	1.00
211_L	215_C	0.777	1.00
35_Q	39_S	0.776	1.00
89_E	92_G	0.774	1.00
214_V	218_V	0.772	1.00
177_P	242_I	0.772	1.00
20_E	71_M	0.769	1.00
208_W	227_E	0.769	1.00
149_A	288_L	0.768	1.00
69_I	91_I	0.760	1.00
254_M	257_P	0.759	1.00
80_N	84_V	0.758	1.00
237_M	242_I	0.754	1.00
21_E	27_A	0.753	1.00
81_A	84_V	0.749	1.00
62_V	68_K	0.746	1.00
63_L	68_K	0.746	1.00
259_V	263_P	0.746	1.00
11_L	14_Y	0.743	1.00
83_N	87_R	0.731	1.00
22_L	60_S	0.729	1.00
66_A	91_I	0.729	1.00
66_A	69_I	0.727	1.00
100_E	147_L	0.724	1.00
175_A	247_I	0.723	1.00
84_V	88_I	0.722	1.00
255_N	259_V	0.720	1.00
191_E	218_V	0.719	1.00
283_P	287_K	0.719	1.00
74_S	77_L	0.717	1.00
55_I	64_T	0.717	1.00
120_L	242_I	0.716	1.00
176_M	182_L	0.709	1.00
119_F	287_K	0.706	1.00
81_A	85_L	0.706	1.00
195_D	223_V	0.702	1.00
24_F	38_L	0.702	1.00
122_E	287_K	0.702	1.00
177_P	180_H	0.700	1.00
189_P	265_K	0.700	1.00
194_R	220_F	0.700	1.00
37_P	41_H	0.700	1.00
13_R	17_A	0.699	1.00
55_I	60_S	0.698	1.00
213_R	216_Q	0.696	1.00
103_V	108_M	0.695	1.00
18_V	38_L	0.692	1.00
46_E	51_T	0.688	1.00
74_S	78_L	0.686	1.00
99_I	284_A	0.683	1.00
66_A	70_L	0.682	1.00
214_V	217_Q	0.681	1.00
145_R	277_E	0.680	1.00
100_E	148_D	0.679	1.00
248_A	251_Y	0.678	1.00
230_E	233_T	0.674	1.00
103_V	112_M	0.671	1.00
226_R	237_M	0.667	1.00
24_F	60_S	0.667	1.00
208_W	214_V	0.666	1.00
79_V	82_N	0.661	1.00
213_R	217_Q	0.661	1.00
260_I	263_P	0.657	1.00
137_M	141_L	0.657	1.00
201_M	234_V	0.655	1.00
75_R	79_V	0.655	1.00
46_E	56_R	0.652	1.00
182_L	185_F	0.651	1.00
27_A	31_L	0.650	1.00
148_D	285_M	0.649	1.00
179_E	182_L	0.648	1.00
140_A	143_E	0.647	1.00
215_C	222_P	0.647	1.00
202_P	227_E	0.643	1.00
127_D	227_E	0.643	1.00
83_N	86_A	0.638	1.00
68_K	71_M	0.637	1.00
211_L	214_V	0.634	1.00
212_Q	216_Q	0.632	1.00
96_A	127_D	0.631	1.00
65_H	69_I	0.629	1.00
209_D	214_V	0.629	1.00
132_E	229_N	0.628	1.00
70_L	88_I	0.627	1.00
29_A	32_N	0.626	1.00
112_M	115_V	0.624	1.00
10_K	44_E	0.622	1.00
252_A	255_N	0.621	1.00
198_F	244_I	0.621	1.00
256_W	261_F	0.620	1.00
175_A	256_W	0.620	1.00
42_I	46_E	0.619	1.00
69_I	88_I	0.619	1.00
210_F	214_V	0.616	1.00
174_V	193_L	0.616	1.00
18_V	23_H	0.615	1.00
173_L	261_F	0.613	1.00
179_E	241_G	0.611	1.00
254_M	259_V	0.609	1.00
168_H	272_L	0.609	1.00
13_R	16_L	0.608	1.00
163_T	279_Q	0.607	1.00
73_E	77_L	0.605	1.00
109_W	236_A	0.599	1.00
63_L	71_M	0.598	1.00
182_L	188_V	0.595	1.00
181_H	185_F	0.595	1.00
174_V	198_F	0.594	1.00
234_V	238_V	0.594	1.00
237_M	243_G	0.594	1.00
283_P	286_V	0.594	1.00
259_V	266_Q	0.591	1.00
187_T	192_A	0.591	1.00
99_I	149_A	0.590	1.00
202_P	229_N	0.589	1.00
172_F	246_L	0.588	1.00
151_I	274_I	0.581	1.00
210_F	213_R	0.580	1.00
174_V	246_L	0.580	1.00
276_Y	286_V	0.578	1.00
86_A	90_Q	0.578	1.00
36_P	40_I	0.578	1.00
116_M	128_V	0.576	1.00
212_Q	215_C	0.574	1.00
132_E	230_E	0.572	1.00
149_A	289_L	0.572	1.00
51_T	55_I	0.570	1.00
8_D	48_Q	0.564	1.00
10_K	14_Y	0.561	1.00
34_S	40_I	0.558	1.00
256_W	263_P	0.557	1.00
37_P	40_I	0.556	1.00
54_F	63_L	0.556	1.00
78_L	81_A	0.555	1.00
72_E	87_R	0.555	1.00
49_L	70_L	0.551	1.00
42_I	54_F	0.550	1.00
49_L	88_I	0.550	1.00
74_S	81_A	0.548	1.00
114_P	117_R	0.548	1.00
228_V	233_T	0.547	1.00
285_M	289_L	0.547	1.00
287_K	291_A	0.546	1.00
107_A	111_R	0.546	1.00
142_L	275_V	0.545	1.00
97_G	125_N	0.542	1.00
259_V	262_R	0.542	1.00
109_W	230_E	0.541	1.00
203_P	227_E	0.541	1.00
114_P	118_R	0.541	1.00
140_A	146_E	0.540	1.00
208_W	211_L	0.539	1.00
49_L	52_Q	0.539	1.00
247_I	252_A	0.539	1.00
102_G	131_R	0.535	1.00
176_M	183_S	0.533	1.00
14_Y	42_I	0.527	1.00
90_Q	95_E	0.526	1.00
13_R	78_L	0.525	1.00
181_H	184_S	0.525	1.00
142_L	162_F	0.524	1.00
185_F	188_V	0.521	1.00
73_E	88_I	0.518	1.00
239_S	256_W	0.518	1.00
97_G	123_N	0.516	1.00
231_P	248_A	0.516	1.00
52_Q	66_A	0.515	1.00
24_F	35_Q	0.511	1.00
123_N	126_V	0.511	1.00
180_H	244_I	0.511	1.00
14_Y	27_A	0.510	1.00
78_L	82_N	0.510	1.00
145_R	280_Q	0.506	1.00
154_M	164_S	0.503	1.00
24_F	56_R	0.503	1.00
22_L	61_V	0.501	1.00
170_S	270_A	0.500	1.00
164_S	276_Y	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
2h98A	2	0.6735	100	0.095	Contact Map
1ixcA	4	0.9762	100	0.097	Contact Map
2h9bA	2	0.6735	100	0.1	Contact Map
2esnA	3	0.9898	100	0.102	Contact Map
1uthA	2	0.7313	100	0.109	Contact Map
3fzvA	4	0.9558	100	0.118	Contact Map
1al3A	1	0.6905	100	0.12	Contact Map
4x6gA	4	0.9898	100	0.125	Contact Map
3fxqA	3	0.9762	100	0.128	Contact Map
3szpA	3	0.9626	100	0.142	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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