LICT - BACSU - GREMLIN Contacts

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LICT - Transcription antiterminator LicT

UniProt:	P39805	Sequences: MKIAKVINNNVISVVNEQGKELVVMGRGLAFQKKSGDDVDEARIEKVFTLDNKDVSEKFKTLLYDIPIECMEVSEEIISYAKLQLGKKLNDSIYVSLTDHINFAIQRNQKGLDIKNALLWETKRLYKDEFAIGKEALVMVKNKTGVSLPEDEAGFIALHIVNAELNEEMPNIINITKVMQEILSIVKYHFKIEFNEESLHYYRFVTHLKFFAQRLFNGTHMESQDDFLLDTVKEKYHRAYECTKKIQTYIEREYEHKLTSDELLYLTIHIERVVKQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	277 (264)
Sequences:	3683 (3195)
Seq/√Len:	196.6

ECOLI - BGLG CSIE FRVR
BACSU - LICT SACT GLCT SACY MANR MTLR LICR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
141_K	147_S	4.499	1.00
84_Q	135_E	4.176	1.00
251_E	257_K	3.071	1.00
229_L	264_L	3.006	1.00
189_H	245_K	2.986	1.00
187_K	193_E	2.908	1.00
233_K	240_Y	2.904	1.00
106_Q	110_K	2.818	1.00
233_K	260_S	2.804	1.00
239_A	271_E	2.786	1.00
181_E	253_E	2.586	1.00
76_E	143_K	2.564	1.00
243_T	267_T	2.382	1.00
41_E	47_V	2.326	1.00
134_K	153_A	2.315	1.00
100_H	159_H	2.176	1.00
185_I	249_Y	2.167	1.00
186_V	204_F	2.159	1.00
14_V	22_L	2.101	1.00
43_R	47_V	2.070	1.00
214_R	262_E	2.062	1.00
8_N	16_N	2.058	1.00
77_I	136_A	2.051	1.00
21_E	33_K	1.976	1.00
12_I	15_V	1.973	1.00
218_G	256_H	1.935	1.00
247_Q	263_L	1.923	1.00
80_Y	139_M	1.915	1.00
243_T	263_L	1.910	1.00
180_Q	201_Y	1.850	1.00
244_K	260_S	1.807	1.00
12_I	16_N	1.801	1.00
239_A	243_T	1.795	1.00
80_Y	135_E	1.776	1.00
131_A	134_K	1.722	1.00
186_V	270_I	1.693	1.00
81_A	136_A	1.685	1.00
119_L	154_G	1.626	1.00
9_N	12_I	1.623	1.00
134_K	150_E	1.619	1.00
190_F	242_C	1.605	1.00
40_D	43_R	1.594	1.00
8_N	15_V	1.587	1.00
197_E	273_V	1.586	1.00
182_I	246_I	1.571	1.00
8_N	12_I	1.553	1.00
244_K	263_L	1.552	1.00
108_N	149_P	1.538	1.00
186_V	242_C	1.535	1.00
239_A	270_I	1.534	1.00
27_R	31_F	1.528	1.00
108_N	148_L	1.528	1.00
184_S	188_Y	1.525	1.00
231_T	235_K	1.522	1.00
207_H	269_H	1.516	1.00
137_L	141_K	1.492	1.00
241_E	244_K	1.492	1.00
248_T	251_E	1.489	1.00
247_Q	266_L	1.467	1.00
43_R	107_R	1.436	1.00
16_N	20_K	1.429	1.00
96_S	159_H	1.417	1.00
67_P	70_C	1.417	1.00
28_G	45_E	1.414	1.00
226_D	264_L	1.399	1.00
81_A	132_I	1.383	1.00
200_H	273_V	1.379	1.00
11_V	16_N	1.371	1.00
183_L	201_Y	1.368	1.00
211_F	215_L	1.362	1.00
222_E	261_D	1.358	1.00
212_A	216_F	1.351	1.00
38_D	41_E	1.342	1.00
24_V	27_R	1.338	1.00
70_C	74_S	1.325	1.00
133_G	153_A	1.320	1.00
243_T	247_Q	1.316	1.00
29_L	41_E	1.312	1.00
9_N	16_N	1.305	1.00
194_F	270_I	1.305	1.00
78_I	98_T	1.289	1.00
105_I	109_Q	1.275	1.00
129_E	157_A	1.272	1.00
20_K	31_F	1.264	1.00
13_S	16_N	1.264	1.00
82_K	89_L	1.256	1.00
92_S	96_S	1.253	1.00
96_S	100_H	1.253	1.00
77_I	81_A	1.251	1.00
229_L	260_S	1.246	1.00
232_V	267_T	1.242	1.00
44_I	47_V	1.240	1.00
137_L	153_A	1.236	1.00
73_V	144_T	1.226	1.00
11_V	15_V	1.222	1.00
73_V	143_K	1.199	1.00
194_F	273_V	1.198	1.00
221_M	265_Y	1.190	1.00
186_V	243_T	1.189	1.00
149_P	152_E	1.169	1.00
227_F	261_D	1.157	1.00
42_A	45_E	1.156	1.00
18_Q	22_L	1.154	1.00
240_Y	267_T	1.138	1.00
230_D	234_E	1.137	1.00
130_F	153_A	1.131	1.00
208_L	211_F	1.116	1.00
244_K	248_T	1.109	1.00
70_C	102_N	1.102	1.00
32_Q	40_D	1.100	1.00
201_Y	205_V	1.096	1.00
211_F	259_T	1.086	1.00
20_K	24_V	1.086	1.00
41_E	45_E	1.075	1.00
12_I	17_E	1.071	1.00
211_F	258_L	1.071	1.00
33_K	37_D	1.069	1.00
94_Y	98_T	1.065	1.00
135_E	138_V	1.060	1.00
175_I	212_A	1.058	1.00
185_I	188_Y	1.055	1.00
80_Y	84_Q	1.051	1.00
74_S	78_I	1.047	1.00
37_D	43_R	1.043	1.00
8_N	11_V	1.038	1.00
105_I	148_L	1.037	1.00
130_F	157_A	1.030	1.00
261_D	264_L	1.029	1.00
243_T	270_I	1.022	1.00
240_Y	260_S	1.015	1.00
243_T	266_L	1.003	1.00
37_D	41_E	1.002	1.00
102_N	106_Q	0.999	1.00
70_C	105_I	0.998	1.00
179_M	182_I	0.997	1.00
38_D	43_R	0.996	1.00
127_K	130_F	0.995	1.00
179_M	205_V	0.986	1.00
243_T	246_I	0.983	0.99
38_D	42_A	0.982	0.99
141_K	144_T	0.980	0.99
240_Y	244_K	0.975	0.99
93_I	163_A	0.972	0.99
75_E	95_V	0.967	0.99
85_L	135_E	0.966	0.99
138_V	147_S	0.965	0.99
82_K	85_L	0.965	0.99
101_I	156_I	0.965	0.99
24_V	31_F	0.962	0.99
137_L	156_I	0.960	0.99
229_L	240_Y	0.960	0.99
81_A	160_I	0.953	0.99
72_E	75_E	0.951	0.99
70_C	73_V	0.946	0.99
182_I	249_Y	0.946	0.99
133_G	157_A	0.944	0.99
226_D	261_D	0.937	0.99
113_D	149_P	0.934	0.99
232_V	264_L	0.934	0.99
187_K	194_F	0.932	0.99
133_G	136_A	0.924	0.99
264_L	267_T	0.923	0.99
246_I	249_Y	0.916	0.99
9_N	15_V	0.916	0.99
130_F	134_K	0.916	0.99
73_V	139_M	0.912	0.99
242_C	246_I	0.910	0.99
134_K	138_V	0.905	0.99
135_E	139_M	0.897	0.99
211_F	214_R	0.897	0.99
119_L	155_F	0.893	0.99
140_V	148_L	0.892	0.99
181_E	249_Y	0.892	0.99
130_F	154_G	0.890	0.99
17_E	20_K	0.884	0.99
77_I	139_M	0.883	0.99
249_Y	253_E	0.880	0.99
72_E	76_E	0.878	0.99
181_E	184_S	0.873	0.99
182_I	270_I	0.865	0.99
203_R	272_R	0.864	0.99
240_Y	243_T	0.861	0.99
247_Q	258_L	0.859	0.99
101_I	140_V	0.859	0.99
89_L	160_I	0.858	0.99
125_L	150_E	0.854	0.99
206_T	210_F	0.853	0.99
128_D	131_A	0.853	0.99
204_F	266_L	0.851	0.99
186_V	190_F	0.851	0.99
75_E	94_Y	0.846	0.98
265_Y	269_H	0.844	0.98
163_A	211_F	0.843	0.98
74_S	101_I	0.842	0.98
185_I	189_H	0.839	0.98
269_H	272_R	0.834	0.98
187_K	197_E	0.832	0.98
157_A	161_V	0.831	0.98
185_I	246_I	0.831	0.98
87_K	268_I	0.831	0.98
178_V	182_I	0.830	0.98
246_I	270_I	0.830	0.98
136_A	139_M	0.826	0.98
8_N	13_S	0.819	0.98
28_G	31_F	0.818	0.98
141_K	148_L	0.815	0.98
39_V	43_R	0.813	0.98
212_A	254_Y	0.813	0.98
177_K	253_E	0.813	0.98
100_H	104_A	0.811	0.98
253_E	256_H	0.809	0.98
160_I	164_E	0.808	0.98
73_V	77_I	0.807	0.98
179_M	183_L	0.807	0.98
57_E	60_K	0.805	0.98
199_L	203_R	0.800	0.98
41_E	46_K	0.799	0.98
79_S	94_Y	0.796	0.98
189_H	242_C	0.794	0.98
8_N	17_E	0.790	0.98
227_F	231_T	0.788	0.98
116_N	122_T	0.786	0.98
115_K	151_D	0.783	0.98
239_A	267_T	0.774	0.97
238_R	241_E	0.771	0.97
12_I	39_V	0.769	0.97
81_A	139_M	0.767	0.97
116_N	154_G	0.766	0.97
152_E	265_Y	0.765	0.97
179_M	208_L	0.763	0.97
23_V	27_R	0.760	0.97
250_I	254_Y	0.758	0.97
11_V	155_F	0.754	0.97
172_I	176_T	0.751	0.97
109_Q	145_G	0.748	0.97
171_N	174_N	0.746	0.97
203_R	273_V	0.742	0.97
137_L	140_V	0.737	0.96
215_L	256_H	0.736	0.96
133_G	160_I	0.729	0.96
87_K	164_E	0.729	0.96
238_R	243_T	0.727	0.96
31_F	34_K	0.724	0.96
43_R	46_K	0.722	0.96
75_E	79_S	0.721	0.96
231_T	234_E	0.721	0.96
210_F	213_Q	0.720	0.96
106_Q	109_Q	0.712	0.96
248_T	252_R	0.712	0.96
90_N	164_E	0.710	0.96
122_T	154_G	0.709	0.96
85_L	132_I	0.707	0.95
104_A	108_N	0.703	0.95
35_S	38_D	0.703	0.95
176_T	205_V	0.701	0.95
271_E	274_V	0.700	0.95
25_M	31_F	0.700	0.95
66_I	102_N	0.698	0.95
109_Q	138_V	0.697	0.95
227_F	235_K	0.697	0.95
227_F	264_L	0.691	0.95
178_V	208_L	0.690	0.95
50_L	55_V	0.690	0.95
240_Y	263_L	0.684	0.95
169_M	172_I	0.681	0.94
83_L	86_G	0.680	0.94
39_V	47_V	0.677	0.94
81_A	135_E	0.677	0.94
200_H	204_F	0.677	0.94
20_K	27_R	0.677	0.94
74_S	98_T	0.675	0.94
41_E	44_I	0.672	0.94
136_A	160_I	0.672	0.94
239_A	274_V	0.670	0.94
79_S	82_K	0.667	0.94
139_M	142_N	0.657	0.93
78_I	136_A	0.657	0.93
209_K	213_Q	0.654	0.93
229_L	233_K	0.653	0.93
241_E	245_K	0.651	0.93
207_H	265_Y	0.648	0.93
236_Y	271_E	0.647	0.93
190_F	194_F	0.645	0.93
174_N	177_K	0.644	0.93
117_A	158_L	0.644	0.93
108_N	113_D	0.643	0.93
194_F	200_H	0.641	0.92
203_R	269_H	0.640	0.92
221_M	261_D	0.640	0.92
12_I	30_A	0.639	0.92
53_K	56_S	0.639	0.92
114_I	152_E	0.639	0.92
62_L	69_E	0.639	0.92
197_E	200_H	0.634	0.92
79_S	83_L	0.633	0.92
52_N	55_V	0.632	0.92
180_Q	184_S	0.629	0.92
74_S	77_I	0.627	0.92
9_N	13_S	0.627	0.92
10_N	13_S	0.627	0.92
231_T	236_Y	0.622	0.91
116_N	121_E	0.620	0.91
108_N	152_E	0.620	0.91
233_K	264_L	0.619	0.91
190_F	193_E	0.617	0.91
107_R	155_F	0.616	0.91
250_I	256_H	0.613	0.91
176_T	201_Y	0.613	0.91
100_H	152_E	0.610	0.91
244_K	247_Q	0.604	0.90
184_S	195_N	0.603	0.90
105_I	140_V	0.601	0.90
140_V	144_T	0.600	0.90
212_A	256_H	0.596	0.90
226_D	263_L	0.596	0.90
250_I	258_L	0.595	0.89
242_C	270_I	0.594	0.89
226_D	230_D	0.594	0.89
184_S	187_K	0.593	0.89
77_I	80_Y	0.592	0.89
229_L	261_D	0.590	0.89
80_Y	132_I	0.589	0.89
183_L	187_K	0.589	0.89
237_H	267_T	0.588	0.89
183_L	270_I	0.584	0.89
213_Q	217_N	0.582	0.88
116_N	151_D	0.582	0.88
59_F	95_V	0.580	0.88
175_I	205_V	0.580	0.88
89_L	93_I	0.579	0.88
92_S	163_A	0.579	0.88
62_L	66_I	0.578	0.88
134_K	147_S	0.577	0.88
25_M	30_A	0.576	0.88
19_G	22_L	0.575	0.88
81_A	85_L	0.575	0.88
183_L	186_V	0.574	0.88
197_E	269_H	0.573	0.88
100_H	203_R	0.572	0.88
151_D	154_G	0.570	0.87
67_P	118_L	0.569	0.87
162_N	210_F	0.568	0.87
190_F	246_I	0.566	0.87
34_K	38_D	0.566	0.87
138_V	142_N	0.564	0.87
17_E	24_V	0.563	0.87
183_L	200_H	0.563	0.87
199_L	210_F	0.563	0.87
85_L	129_E	0.560	0.86
211_F	269_H	0.558	0.86
185_I	245_K	0.557	0.86
36_G	40_D	0.556	0.86
130_F	150_E	0.556	0.86
139_M	143_K	0.551	0.86
182_I	243_T	0.548	0.85
103_F	107_R	0.547	0.85
167_E	234_E	0.547	0.85
107_R	152_E	0.546	0.85
121_E	154_G	0.546	0.85
85_L	89_L	0.545	0.85
127_K	157_A	0.544	0.85
230_D	233_K	0.544	0.85
77_I	140_V	0.543	0.85
178_V	254_Y	0.541	0.85
116_N	156_I	0.540	0.84
24_V	39_V	0.540	0.84
15_V	19_G	0.538	0.84
232_V	268_I	0.537	0.84
199_L	204_F	0.534	0.84
12_I	24_V	0.533	0.84
129_E	161_V	0.532	0.84
18_Q	23_V	0.532	0.84
49_T	92_S	0.529	0.83
133_G	156_I	0.529	0.83
130_F	161_V	0.527	0.83
30_A	126_Y	0.525	0.83
130_F	133_G	0.524	0.83
76_E	80_Y	0.523	0.83
10_N	17_E	0.522	0.82
93_I	211_F	0.522	0.82
206_T	261_D	0.522	0.82
243_T	256_H	0.514	0.81
155_F	227_F	0.514	0.81
162_N	211_F	0.512	0.81
24_V	29_L	0.511	0.81
241_E	248_T	0.511	0.81
69_E	143_K	0.510	0.81
240_Y	271_E	0.510	0.81
70_C	109_Q	0.508	0.81
105_I	146_V	0.507	0.81
89_L	92_S	0.505	0.80
178_V	249_Y	0.503	0.80
27_R	180_Q	0.502	0.80
102_N	271_E	0.501	0.80
49_T	64_Y	0.501	0.80
198_S	202_Y	0.500	0.80

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
4r6iA	2	0.9675	100	0.335	Contact Map
1h99A	2	0.7942	100	0.382	Contact Map
3sqnA	2	0.9278	100	0.457	Contact Map
3rioA	1	0.5993	99.9	0.577	Contact Map
3ufeA	2	0.3863	99.8	0.681	Contact Map
1auuA	2	0.1986	93.6	0.903	Contact Map
1l1cA	2	0.1986	93.4	0.904	Contact Map
3nufA	2	0.426	89.6	0.913	Contact Map
1wtyA	4	0.2238	12	0.954	Contact Map
1wwpA	2	0.2238	9	0.957	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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