ALLS - ECOLI - GREMLIN Contacts

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ALLS - HTH-type transcriptional activator AllS

UniProt:	P0ACR0	Sequences: MFDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSELQQVNDGVERQVNIVINNLLYNPQAVAQLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSLDPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGVGIGFLPKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRKFGSGKAVEDIVTLFTQRRPEISGFLEIFGNPRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13267
Length:	308 (282)
Sequences:	79731 (57877)
Seq/√Len:	3446.5

ECOLI - ALLS YDHB AAER YEEY YAHB OXYR DMLR YHJC TTDR CYSB YBHD METR CBL CYNR TDCA LEUO NAC LYSR ILVY HCAR GCVA PGRR YNEJ YHAJ YCAN YAFC YIAU YDCI YBDO XAPR YFER YFIE DSDC ABGR YEIE YNFL YBEF NHAR YIDZ ICIA YGFI LRHA YJIE HDFR PERR
BACSU - YWBI CYSL YCGK ALSR YVBU YTLI GLTR CITR GLTC YYBE BSDA YWQM YXJO YUST YOFA YKUM CZCR YRAN 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
71_D	75_W	3.609	1.00
16_T	25_R	3.334	1.00
162_D	290_T	2.616	1.00
68_Q	82_E	2.454	1.00
12_A	25_R	2.432	1.00
97_V	143_F	2.422	1.00
163_P	268_P	2.230	1.00
166_S	268_P	2.197	1.00
93_Q	125_H	2.195	1.00
163_P	166_S	2.191	1.00
46_V	61_A	2.146	1.00
232_H	239_G	2.144	1.00
114_W	292_R	2.128	1.00
11_I	70_R	2.101	1.00
9_T	36_R	2.094	1.00
93_Q	123_Q	2.030	1.00
168_Q	243_K	2.026	1.00
11_I	15_E	2.022	1.00
68_Q	75_W	2.013	1.00
166_S	266_P	2.000	1.00
170_R	243_K	1.986	1.00
233_L	254_Q	1.969	1.00
187_T	190_Q	1.965	1.00
12_A	16_T	1.956	1.00
114_W	288_L	1.956	1.00
21_K	24_E	1.940	1.00
95_N	125_H	1.937	1.00
12_A	15_E	1.903	1.00
229_I	249_M	1.883	1.00
14_A	58_L	1.869	1.00
11_I	66_L	1.862	1.00
15_E	70_R	1.862	1.00
9_T	33_I	1.839	1.00
72_W	76_L	1.832	1.00
173_M	258_R	1.812	1.00
66_L	70_R	1.812	1.00
178_P	194_F	1.783	1.00
197_V	237_G	1.760	1.00
170_R	257_S	1.752	1.00
233_L	249_M	1.701	1.00
195_P	219_E	1.701	1.00
161_L	270_S	1.691	1.00
14_A	66_L	1.681	1.00
64_H	82_E	1.678	1.00
50_F	57_T	1.669	1.00
65_L	79_M	1.666	1.00
137_S	142_G	1.639	1.00
16_T	21_K	1.610	1.00
134_V	146_A	1.603	1.00
68_Q	71_D	1.569	1.00
19_F	37_I	1.569	1.00
11_I	69_A	1.551	1.00
160_S	275_K	1.550	1.00
18_S	21_K	1.522	1.00
6_T	36_R	1.520	1.00
162_D	273_W	1.519	1.00
6_T	43_N	1.512	1.00
15_E	25_R	1.505	1.00
136_D	140_Y	1.477	1.00
6_T	39_L	1.477	1.00
183_E	190_Q	1.451	1.00
115_L	285_I	1.450	1.00
273_W	286_V	1.446	1.00
286_V	290_T	1.444	1.00
150_T	270_S	1.435	1.00
89_G	121_F	1.432	1.00
29_T	32_T	1.423	1.00
47_A	50_F	1.422	1.00
9_T	28_K	1.416	1.00
10_F	66_L	1.415	1.00
68_Q	78_S	1.414	1.00
12_A	26_L	1.407	1.00
105_P	226_E	1.406	1.00
148_G	272_A	1.404	1.00
160_S	273_W	1.404	1.00
52_T	57_T	1.401	1.00
20_S	30_T	1.398	1.00
115_L	122_T	1.390	1.00
137_S	143_F	1.382	1.00
206_L	210_V	1.380	1.00
75_W	78_S	1.376	1.00
138_L	146_A	1.357	1.00
72_W	79_M	1.349	1.00
284_D	287_T	1.344	1.00
118_R	288_L	1.343	1.00
95_N	127_S	1.342	1.00
91_E	121_F	1.321	1.00
65_L	80_P	1.315	1.00
11_I	73_L	1.314	1.00
3_D	6_T	1.310	1.00
60_A	63_E	1.308	1.00
67_S	71_D	1.304	1.00
167_V	244_S	1.299	1.00
145_L	282_V	1.297	1.00
271_L	286_V	1.293	1.00
145_L	271_L	1.291	1.00
114_W	118_R	1.288	1.00
194_F	238_I	1.285	1.00
139_L	158_T	1.283	1.00
228_K	239_G	1.276	1.00
4_P	76_L	1.275	1.00
68_Q	79_M	1.253	1.00
230_A	233_L	1.247	1.00
175_A	254_Q	1.238	1.00
175_A	256_V	1.234	1.00
116_N	219_E	1.230	1.00
163_P	270_S	1.230	1.00
28_K	32_T	1.226	1.00
64_H	67_S	1.205	1.00
116_N	195_P	1.205	1.00
243_K	257_S	1.205	1.00
249_M	254_Q	1.200	1.00
35_Y	39_L	1.194	1.00
10_F	49_F	1.190	1.00
43_N	80_P	1.184	1.00
113_A	234_A	1.184	1.00
113_A	117_E	1.181	1.00
243_K	247_Q	1.174	1.00
10_F	14_A	1.167	1.00
173_M	238_I	1.164	1.00
64_H	68_Q	1.146	1.00
161_L	272_A	1.139	1.00
185_P	261_P	1.137	1.00
110_Q	234_A	1.120	1.00
35_Y	38_K	1.111	1.00
71_D	78_S	1.110	1.00
186_L	190_Q	1.108	1.00
63_E	67_S	1.094	1.00
162_D	286_V	1.094	1.00
119_Y	284_D	1.090	1.00
38_K	42_E	1.089	1.00
184_E	256_V	1.083	1.00
7_L	69_A	1.082	1.00
257_S	260_I	1.081	1.00
12_A	22_A	1.080	1.00
288_L	292_R	1.078	1.00
195_P	217_Q	1.074	1.00
19_F	56_V	1.067	1.00
247_Q	251_D	1.067	1.00
125_H	221_I	1.066	1.00
172_V	257_S	1.063	1.00
5_E	8_R	1.061	1.00
230_A	234_A	1.055	1.00
72_W	75_W	1.055	1.00
114_W	117_E	1.054	1.00
36_R	39_L	1.051	1.00
139_L	156_A	1.050	1.00
287_T	290_T	1.049	1.00
10_F	48_L	1.040	1.00
229_I	233_L	1.037	1.00
34_S	38_K	1.037	1.00
111_L	289_F	1.035	1.00
283_E	287_T	1.029	1.00
127_S	137_S	1.029	1.00
206_L	209_R	1.029	1.00
274_R	277_G	1.023	1.00
115_L	288_L	1.016	1.00
80_P	84_Q	1.013	1.00
168_Q	266_P	1.011	1.00
248_S	252_N	1.008	1.00
174_A	235_G	1.005	1.00
13_V	22_A	1.002	1.00
288_L	291_Q	1.001	1.00
74_S	78_S	1.001	1.00
188_E	262_T	0.996	1.00
197_V	228_K	0.978	1.00
222_V	228_K	0.978	1.00
94_V	285_I	0.977	1.00
207_T	210_V	0.975	1.00
13_V	19_F	0.973	1.00
39_L	42_E	0.970	1.00
115_L	119_Y	0.958	1.00
65_L	69_A	0.957	1.00
8_R	77_E	0.951	1.00
77_E	80_P	0.950	1.00
28_K	33_I	0.947	1.00
172_V	246_C	0.947	1.00
58_L	62_G	0.945	1.00
9_T	26_L	0.943	1.00
279_G	282_V	0.942	1.00
22_A	33_I	0.941	1.00
198_N	218_K	0.941	1.00
14_A	49_F	0.938	1.00
10_F	40_L	0.920	1.00
21_K	25_R	0.918	1.00
10_F	58_L	0.918	1.00
71_D	74_S	0.916	1.00
137_S	140_Y	0.912	1.00
100_N	224_D	0.908	1.00
64_H	86_V	0.908	1.00
171_F	238_I	0.902	1.00
222_V	231_A	0.900	1.00
118_R	291_Q	0.896	1.00
5_E	36_R	0.895	1.00
76_L	80_P	0.893	1.00
77_E	81_S	0.890	1.00
17_G	57_T	0.884	1.00
173_M	179_L	0.878	1.00
49_F	56_V	0.875	1.00
67_S	70_R	0.875	1.00
143_F	146_A	0.869	1.00
46_V	83_L	0.865	1.00
150_T	268_P	0.863	1.00
111_L	288_L	0.861	1.00
180_A	256_V	0.861	1.00
61_A	64_H	0.860	1.00
97_V	148_G	0.860	1.00
209_R	214_L	0.860	1.00
208_K	212_W	0.858	1.00
160_S	163_P	0.857	1.00
20_S	24_E	0.854	1.00
113_A	236_V	0.854	1.00
97_V	134_V	0.849	1.00
246_C	249_M	0.837	1.00
135_W	139_L	0.833	1.00
111_L	292_R	0.829	1.00
61_A	86_V	0.829	1.00
179_L	194_F	0.828	1.00
14_A	62_G	0.826	1.00
78_S	82_E	0.825	1.00
92_R	281_A	0.824	1.00
26_L	33_I	0.823	1.00
127_S	143_F	0.823	1.00
123_Q	217_Q	0.821	1.00
195_P	218_K	0.820	1.00
207_T	211_A	0.820	1.00
52_T	55_S	0.820	1.00
75_W	79_M	0.820	1.00
96_I	145_L	0.819	1.00
30_T	34_S	0.818	1.00
122_T	281_A	0.817	1.00
15_E	66_L	0.814	1.00
116_N	236_V	0.813	1.00
61_A	83_L	0.812	1.00
17_G	55_S	0.810	1.00
8_R	12_A	0.809	1.00
76_L	79_M	0.809	1.00
97_V	146_A	0.807	1.00
16_T	22_A	0.805	1.00
159_F	272_A	0.803	1.00
233_L	252_N	0.800	1.00
280_K	284_D	0.800	1.00
10_F	65_L	0.798	1.00
14_A	17_G	0.795	1.00
249_M	252_N	0.792	1.00
190_Q	193_R	0.788	1.00
17_G	63_E	0.786	1.00
13_V	49_F	0.780	1.00
174_A	236_V	0.779	1.00
176_D	180_A	0.776	1.00
38_K	47_A	0.776	1.00
178_P	195_P	0.774	1.00
189_A	192_R	0.774	1.00
287_T	291_Q	0.771	1.00
4_P	73_L	0.768	1.00
70_R	74_S	0.767	1.00
19_F	33_I	0.767	1.00
172_V	239_G	0.766	1.00
79_M	83_L	0.766	1.00
6_T	9_T	0.764	1.00
187_T	261_P	0.764	1.00
208_K	211_A	0.761	1.00
144_S	282_V	0.759	1.00
231_A	236_V	0.756	1.00
13_V	33_I	0.754	1.00
69_A	72_W	0.751	1.00
63_E	66_L	0.750	1.00
98_I	104_N	0.748	1.00
168_Q	264_R	0.748	1.00
139_L	159_F	0.746	1.00
172_V	241_L	0.745	1.00
133_G	136_D	0.744	1.00
50_F	59_T	0.742	1.00
168_Q	259_V	0.741	1.00
145_L	285_I	0.734	1.00
92_R	122_T	0.734	1.00
13_V	37_I	0.732	1.00
284_D	288_L	0.727	1.00
246_C	250_I	0.726	1.00
141_E	274_R	0.719	1.00
173_M	256_V	0.718	1.00
8_R	11_I	0.718	1.00
118_R	284_D	0.717	1.00
250_I	253_Q	0.716	1.00
192_R	214_L	0.715	1.00
224_D	227_T	0.712	1.00
115_L	284_D	0.711	1.00
60_A	64_H	0.710	1.00
176_D	235_G	0.708	1.00
242_P	245_L	0.707	1.00
158_T	275_K	0.699	1.00
90_V	119_Y	0.698	1.00
196_A	216_G	0.698	1.00
172_V	250_I	0.695	1.00
114_W	291_Q	0.692	1.00
61_A	65_L	0.689	1.00
105_P	230_A	0.687	1.00
95_N	144_S	0.683	1.00
84_Q	87_N	0.682	1.00
68_Q	72_W	0.681	1.00
50_F	55_S	0.680	1.00
187_T	262_T	0.675	1.00
200_E	221_I	0.673	1.00
58_L	63_E	0.671	1.00
5_E	39_L	0.671	1.00
196_A	238_I	0.668	1.00
185_P	259_V	0.667	1.00
65_L	83_L	0.665	1.00
95_N	143_F	0.660	1.00
57_T	63_E	0.655	1.00
133_G	137_S	0.654	1.00
32_T	36_R	0.653	1.00
171_F	240_F	0.651	1.00
8_R	73_L	0.650	1.00
24_E	27_C	0.650	1.00
110_Q	113_A	0.649	1.00
179_L	184_E	0.648	1.00
78_S	81_S	0.641	1.00
199_I	228_K	0.639	1.00
280_K	283_E	0.638	1.00
10_F	62_G	0.638	1.00
123_Q	221_I	0.636	1.00
250_I	257_S	0.633	1.00
41_E	51_R	0.633	1.00
248_S	251_D	0.627	1.00
37_I	41_E	0.627	1.00
209_R	212_W	0.627	1.00
108_V	111_L	0.625	1.00
220_I	231_A	0.623	1.00
173_M	180_A	0.623	1.00
104_N	131_Y	0.622	1.00
149_V	267_S	0.621	1.00
110_Q	114_W	0.620	1.00
41_E	46_V	0.619	1.00
74_S	77_E	0.615	1.00
94_V	281_A	0.612	1.00
145_L	286_V	0.607	1.00
44_T	65_L	0.605	1.00
171_F	191_L	0.604	1.00
13_V	18_S	0.597	1.00
5_E	9_T	0.597	1.00
3_D	39_L	0.595	1.00
69_A	73_L	0.595	1.00
206_L	212_W	0.592	1.00
273_W	283_E	0.590	1.00
94_V	145_L	0.589	1.00
22_A	26_L	0.588	1.00
81_S	85_Q	0.586	1.00
73_L	77_E	0.585	1.00
98_I	108_V	0.585	1.00
222_V	227_T	0.584	1.00
44_T	83_L	0.582	1.00
14_A	63_E	0.581	1.00
46_V	50_F	0.577	1.00
64_H	83_L	0.576	1.00
193_R	217_Q	0.576	1.00
176_D	256_V	0.574	1.00
173_M	178_P	0.573	1.00
138_L	272_A	0.573	1.00
285_I	289_F	0.572	1.00
200_E	223_P	0.571	1.00
164_L	271_L	0.570	1.00
138_L	159_F	0.570	1.00
175_A	253_Q	0.570	1.00
91_E	123_Q	0.568	1.00
102_L	107_A	0.566	1.00
19_F	30_T	0.566	1.00
167_V	267_S	0.560	1.00
171_F	196_A	0.559	1.00
119_Y	122_T	0.559	1.00
31_A	35_Y	0.557	1.00
44_T	47_A	0.557	1.00
49_F	58_L	0.556	1.00
178_P	181_N	0.556	1.00
150_T	161_L	0.555	1.00
32_T	35_Y	0.554	1.00
29_T	35_Y	0.550	1.00
228_K	232_H	0.549	1.00
19_F	55_S	0.544	1.00
169_W	240_F	0.543	1.00
241_L	246_C	0.541	1.00
82_E	85_Q	0.541	1.00
28_K	36_R	0.540	1.00
92_R	121_F	0.538	1.00
107_A	111_L	0.538	1.00
97_V	127_S	0.536	1.00
225_M	242_P	0.536	1.00
58_L	66_L	0.533	1.00
165_G	269_L	0.532	1.00
282_V	286_V	0.531	1.00
139_L	142_G	0.529	1.00
179_L	183_E	0.529	1.00
231_A	237_G	0.529	1.00
17_G	56_V	0.525	1.00
85_Q	90_V	0.525	1.00
136_D	142_G	0.525	1.00
109_A	113_A	0.525	1.00
81_S	84_Q	0.525	1.00
9_T	37_I	0.524	1.00
183_E	186_L	0.524	1.00
19_F	51_R	0.520	1.00
98_I	126_I	0.519	1.00
105_P	224_D	0.518	1.00
160_S	276_F	0.516	1.00
110_Q	230_A	0.516	1.00
47_A	61_A	0.516	1.00
147_I	289_F	0.514	1.00
113_A	116_N	0.513	1.00
67_S	82_E	0.510	1.00
112_L	124_F	0.509	1.00
134_V	141_E	0.509	1.00
31_A	34_S	0.509	1.00
79_M	82_E	0.509	1.00
99_N	102_L	0.508	1.00
178_P	183_E	0.507	1.00
281_A	284_D	0.507	1.00
9_T	22_A	0.507	1.00
86_V	90_V	0.507	1.00
254_Q	257_S	0.502	1.00
3_D	8_R	0.502	1.00
167_V	242_P	0.501	1.00
11_I	77_E	0.500	1.00
68_Q	83_L	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
3fxqA	3	0.9416	100	0.102	Contact Map
3fzvA	4	0.9221	100	0.11	Contact Map
2esnA	3	0.9416	100	0.113	Contact Map
1ixcA	4	0.9351	100	0.115	Contact Map
1uthA	2	0.7208	100	0.12	Contact Map
2h98A	2	0.6721	100	0.129	Contact Map
1al3A	1	0.7078	100	0.131	Contact Map
2h9bA	2	0.6753	100	0.132	Contact Map
4x6gA	4	0.9675	100	0.134	Contact Map
3szpA	3	0.9253	100	0.14	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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