CYSL - BACSU - GREMLIN Contacts

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CYSL - HTH-type transcriptional regulator CysL

UniProt:	P39647	Sequences: MYYDVLKTFIAVVEEKNFTKAAEKLMISQPSVSLHIKNLEKEFQTALLNRSPKHFTTTPTGDILYQRAKQMVFLYEQAKAEIYAHHHYVKGELKIAASFTIGEYILPPLLAQLQKLYPELNLDVMIGNTEEVSERVRMLQADIGLIEGHTNENELEIEPFMEDEMCIAAPNQHPLAGRKEISISDLQNEAWVTREKGSGTREYLDHVLSSNGLRPKSMFTISSNQGVKEAVINGMGLSVLSRSVLRKDLIHREISILHINNFSLKRKLSYIHSPLMENTKNKEIFITMLKSNYQSQLLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	299 (285)
Sequences:	79819 (58373)
Seq/√Len:	3457.7

ECOLI - OXYR CYNR CYSB AAER YBHD NAC CBL LYSR PGRR YAFC LEUO YFER YHJC DSDC NHAR YFIE YNFL TTDR TDCA YDHB YEIE YDCI ILVY YCAN YBDO HCAR DMLR ABGR YEEY YAHB ALLS METR XAPR YNEJ YBEF YIDZ YIAU YHAJ ICIA GCVA YGFI YJIE PERR LRHA HDFR
BACSU - CYSL YWBI YCGK YYBE BSDA ALSR CITR YVBU GLTC YWQM GLTR YTLI YUST YOFA YXJO CZCR YRAN YKUM 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_Q	74_L	3.605	1.00
15_E	24_K	3.419	1.00
158_E	290_K	2.733	1.00
96_A	141_A	2.635	1.00
67_R	81_E	2.445	1.00
231_V	238_S	2.347	1.00
164_E	242_R	2.235	1.00
11_A	24_K	2.233	1.00
173_H	189_E	2.226	1.00
162_E	267_K	2.211	1.00
159_P	162_E	2.210	1.00
92_E	123_D	2.190	1.00
20_K	23_E	2.160	1.00
92_E	121_N	2.127	1.00
14_E	69_K	2.116	1.00
159_P	267_K	2.112	1.00
182_S	185_D	2.073	1.00
8_T	35_H	2.050	1.00
45_T	60_T	2.038	1.00
10_I	65_Y	2.017	1.00
112_Q	288_M	2.006	1.00
162_E	265_K	1.996	1.00
94_K	123_D	1.996	1.00
67_R	74_L	1.973	1.00
10_I	69_K	1.936	1.00
169_A	257_L	1.933	1.00
11_A	14_E	1.919	1.00
8_T	32_V	1.914	1.00
71_M	75_Y	1.907	1.00
10_I	14_E	1.889	1.00
232_I	253_E	1.889	1.00
13_V	57_T	1.888	1.00
192_V	236_G	1.884	1.00
11_A	15_E	1.884	1.00
18_F	36_I	1.858	1.00
166_C	242_R	1.850	1.00
65_Y	69_K	1.831	1.00
49_N	56_T	1.748	1.00
64_L	78_A	1.726	1.00
190_A	218_M	1.710	1.00
63_I	81_E	1.693	1.00
166_C	256_I	1.673	1.00
178_R	185_D	1.668	1.00
157_I	269_S	1.659	1.00
113_L	285_F	1.653	1.00
135_R	140_Q	1.637	1.00
14_E	24_K	1.621	1.00
13_V	65_Y	1.601	1.00
9_F	65_Y	1.597	1.00
15_E	20_K	1.587	1.00
156_E	274_P	1.583	1.00
10_I	68_A	1.582	1.00
8_T	27_I	1.568	1.00
113_L	120_L	1.546	1.00
19_T	29_Q	1.542	1.00
88_Y	119_E	1.535	1.00
134_E	138_M	1.511	1.00
59_P	62_D	1.509	1.00
5_V	35_H	1.502	1.00
158_E	272_H	1.469	1.00
28_S	31_S	1.468	1.00
46_A	49_N	1.462	1.00
5_V	42_E	1.461	1.00
5_V	38_N	1.448	1.00
278_N	282_K	1.448	1.00
17_N	20_K	1.444	1.00
10_I	72_V	1.443	1.00
11_A	25_L	1.439	1.00
67_R	70_Q	1.434	1.00
201_R	205_D	1.417	1.00
286_I	290_K	1.403	1.00
146_I	271_I	1.400	1.00
156_E	272_H	1.392	1.00
71_M	78_A	1.390	1.00
148_G	269_S	1.388	1.00
171_N	253_E	1.387	1.00
67_R	77_Q	1.385	1.00
103_E	225_Q	1.359	1.00
90_K	119_E	1.350	1.00
137_R	154_E	1.350	1.00
94_K	125_M	1.345	1.00
270_Y	286_I	1.337	1.00
272_H	286_I	1.337	1.00
112_Q	116_L	1.336	1.00
143_I	282_K	1.329	1.00
284_I	287_T	1.325	1.00
135_R	141_A	1.316	1.00
136_V	144_G	1.315	1.00
42_E	79_K	1.296	1.00
163_D	243_S	1.295	1.00
64_L	79_K	1.291	1.00
51_S	56_T	1.284	1.00
114_Q	218_M	1.282	1.00
169_A	237_L	1.282	1.00
189_E	237_L	1.274	1.00
3_Y	75_Y	1.271	1.00
227_V	238_S	1.269	1.00
143_I	270_Y	1.266	1.00
74_L	77_Q	1.252	1.00
242_R	246_R	1.249	1.00
116_L	288_M	1.248	1.00
62_D	66_Q	1.223	1.00
37_K	41_K	1.222	1.00
66_Q	70_Q	1.221	1.00
229_E	232_I	1.220	1.00
242_R	256_I	1.216	1.00
67_R	78_A	1.202	1.00
114_Q	190_A	1.200	1.00
63_I	66_Q	1.198	1.00
171_N	255_S	1.198	1.00
9_F	48_L	1.191	1.00
159_P	269_S	1.191	1.00
246_R	250_I	1.190	1.00
111_A	115_K	1.178	1.00
179_K	255_S	1.177	1.00
157_I	271_I	1.173	1.00
208_L	213_L	1.173	1.00
174_P	189_E	1.172	1.00
112_Q	115_K	1.166	1.00
27_I	31_S	1.149	1.00
192_V	227_V	1.143	1.00
9_F	47_L	1.134	1.00
9_F	13_V	1.129	1.00
123_D	220_T	1.126	1.00
93_L	285_F	1.121	1.00
34_L	38_N	1.120	1.00
33_S	37_K	1.118	1.00
34_L	37_K	1.118	1.00
111_A	233_N	1.112	1.00
287_T	290_K	1.112	1.00
113_L	288_M	1.109	1.00
7_K	76_E	1.101	1.00
168_A	256_I	1.097	1.00
190_A	216_K	1.096	1.00
117_Y	284_I	1.094	1.00
221_I	227_V	1.093	1.00
12_V	21_A	1.092	1.00
18_F	55_F	1.090	1.00
127_G	135_R	1.089	1.00
70_Q	77_Q	1.086	1.00
6_L	68_A	1.083	1.00
11_A	21_A	1.076	1.00
102_G	126_I	1.073	1.00
180_E	260_N	1.069	1.00
71_M	74_L	1.068	1.00
283_E	287_T	1.066	1.00
256_I	259_I	1.060	1.00
109_L	289_L	1.057	1.00
57_T	61_G	1.057	1.00
170_P	234_G	1.054	1.00
63_I	67_R	1.046	1.00
181_I	185_D	1.036	1.00
108_P	233_N	1.035	1.00
35_H	38_N	1.034	1.00
4_D	7_K	1.033	1.00
158_E	286_I	1.025	1.00
183_I	261_N	1.022	1.00
137_R	152_E	1.017	1.00
229_E	233_N	1.015	1.00
79_K	83_Y	1.001	1.00
8_T	25_L	1.000	1.00
167_I	237_L	0.997	1.00
247_K	251_H	0.997	1.00
168_A	245_L	0.997	1.00
76_E	80_A	0.994	1.00
27_I	32_V	0.990	1.00
76_E	79_K	0.987	1.00
228_K	232_I	0.981	1.00
13_V	48_L	0.980	1.00
164_E	265_K	0.980	1.00
202_E	205_D	0.972	1.00
73_F	77_Q	0.966	1.00
116_L	291_S	0.964	1.00
64_L	68_A	0.964	1.00
12_V	18_F	0.959	1.00
113_L	117_Y	0.955	1.00
169_A	173_H	0.954	1.00
193_T	217_S	0.949	1.00
9_F	57_T	0.947	1.00
279_T	282_K	0.941	1.00
135_R	138_M	0.938	1.00
109_L	288_M	0.937	1.00
221_I	230_A	0.936	1.00
288_M	291_S	0.936	1.00
45_T	82_I	0.925	1.00
125_M	135_R	0.923	1.00
48_L	55_F	0.922	1.00
173_H	190_A	0.921	1.00
96_A	144_G	0.920	1.00
21_A	32_V	0.920	1.00
9_F	39_L	0.916	1.00
249_L	252_R	0.915	1.00
154_E	274_P	0.915	1.00
13_V	61_G	0.911	1.00
173_H	176_A	0.907	1.00
38_N	41_K	0.900	1.00
141_A	144_G	0.896	1.00
191_W	215_P	0.893	1.00
202_E	206_H	0.891	1.00
121_N	216_K	0.888	1.00
96_A	146_I	0.888	1.00
20_K	24_K	0.886	1.00
66_Q	69_K	0.877	1.00
155_L	271_I	0.874	1.00
185_D	188_N	0.869	1.00
177_G	190_A	0.866	1.00
99_F	223_S	0.864	1.00
120_L	281_N	0.864	1.00
19_T	23_E	0.861	1.00
16_K	56_T	0.861	1.00
148_G	267_K	0.860	1.00
190_A	217_S	0.860	1.00
287_T	291_S	0.858	1.00
51_S	54_H	0.856	1.00
169_A	174_P	0.855	1.00
273_S	276_M	0.853	1.00
168_A	238_S	0.851	1.00
95_I	143_I	0.850	1.00
70_Q	73_F	0.844	1.00
174_P	179_K	0.840	1.00
25_L	32_V	0.832	1.00
156_E	159_P	0.831	1.00
125_M	141_A	0.820	1.00
133_S	137_R	0.817	1.00
278_N	283_E	0.815	1.00
60_T	82_I	0.812	1.00
37_K	46_A	0.812	1.00
12_V	36_I	0.810	1.00
16_K	62_D	0.803	1.00
204_L	208_L	0.801	1.00
207_V	211_N	0.800	1.00
9_F	64_L	0.798	1.00
184_S	187_Q	0.797	1.00
29_Q	33_S	0.793	1.00
13_V	16_K	0.793	1.00
111_A	235_M	0.791	1.00
91_G	281_N	0.789	1.00
74_L	78_A	0.786	1.00
170_P	235_M	0.786	1.00
89_V	117_Y	0.785	1.00
91_G	120_L	0.785	1.00
164_E	258_H	0.785	1.00
12_V	48_L	0.783	1.00
75_Y	78_A	0.779	1.00
14_E	65_Y	0.776	1.00
4_D	35_H	0.768	1.00
280_K	284_I	0.765	1.00
15_E	21_A	0.761	1.00
3_Y	72_V	0.761	1.00
230_A	235_M	0.759	1.00
143_I	285_F	0.757	1.00
63_I	85_H	0.755	1.00
83_Y	86_H	0.754	1.00
77_Q	81_E	0.754	1.00
164_E	263_S	0.753	1.00
201_R	220_T	0.753	1.00
114_Q	235_M	0.751	1.00
16_K	54_H	0.750	1.00
60_T	63_I	0.746	1.00
182_S	260_N	0.746	1.00
75_Y	79_K	0.745	1.00
5_V	8_T	0.742	1.00
116_L	284_I	0.741	1.00
172_Q	176_A	0.741	1.00
57_T	62_D	0.740	1.00
60_T	85_H	0.738	1.00
168_A	240_L	0.736	1.00
137_R	155_L	0.735	1.00
56_T	62_D	0.734	1.00
94_K	141_A	0.734	1.00
245_L	249_L	0.732	1.00
31_S	35_H	0.731	1.00
113_L	284_I	0.727	1.00
68_A	71_M	0.725	1.00
7_K	11_A	0.725	1.00
78_A	82_I	0.718	1.00
169_A	255_S	0.713	1.00
18_F	32_V	0.712	1.00
241_S	244_V	0.712	1.00
12_V	32_V	0.711	1.00
49_N	58_T	0.711	1.00
145_L	289_L	0.709	1.00
97_A	102_G	0.708	1.00
170_P	173_H	0.707	1.00
232_I	251_H	0.706	1.00
176_A	255_S	0.705	1.00
206_H	210_S	0.704	1.00
223_S	226_G	0.696	1.00
60_T	64_L	0.694	1.00
112_Q	291_S	0.692	1.00
180_E	258_H	0.689	1.00
69_K	73_F	0.688	1.00
40_E	45_T	0.687	1.00
94_K	142_D	0.687	1.00
187_Q	213_L	0.686	1.00
247_K	250_I	0.685	1.00
249_L	256_I	0.682	1.00
173_H	177_G	0.681	1.00
49_N	54_H	0.679	1.00
18_F	54_H	0.678	1.00
188_N	216_K	0.678	1.00
168_A	249_L	0.677	1.00
142_D	282_K	0.676	1.00
195_E	220_T	0.676	1.00
97_A	106_L	0.675	1.00
68_A	72_V	0.674	1.00
206_H	209_S	0.673	1.00
73_F	76_E	0.672	1.00
62_D	65_Y	0.671	1.00
219_F	230_A	0.668	1.00
59_P	63_I	0.664	1.00
207_V	210_S	0.660	1.00
175_L	178_R	0.658	1.00
77_Q	80_A	0.658	1.00
93_L	281_N	0.657	1.00
64_L	82_I	0.655	1.00
194_R	227_V	0.654	1.00
175_L	189_E	0.654	1.00
167_I	186_L	0.654	1.00
139_L	273_S	0.654	1.00
184_S	211_N	0.652	1.00
284_I	288_M	0.651	1.00
169_A	175_L	0.650	1.00
203_Y	207_V	0.649	1.00
171_N	252_R	0.649	1.00
172_Q	175_L	0.648	1.00
172_Q	255_S	0.647	1.00
40_E	50_R	0.645	1.00
208_L	215_P	0.645	1.00
204_L	207_V	0.641	1.00
121_N	220_T	0.640	1.00
191_W	237_L	0.640	1.00
205_D	209_S	0.637	1.00
23_E	26_M	0.635	1.00
21_A	25_L	0.635	1.00
36_I	40_E	0.634	1.00
182_S	261_N	0.633	1.00
136_V	271_I	0.633	1.00
172_Q	234_G	0.631	1.00
7_K	10_I	0.631	1.00
161_M	268_L	0.630	1.00
103_E	229_E	0.625	1.00
99_F	128_N	0.623	1.00
90_K	121_N	0.621	1.00
126_I	222_S	0.621	1.00
67_R	71_M	0.620	1.00
12_V	17_N	0.620	1.00
63_I	82_I	0.610	1.00
4_D	38_N	0.608	1.00
276_M	279_T	0.607	1.00
175_L	181_I	0.606	1.00
80_A	84_A	0.605	1.00
156_E	275_L	0.603	1.00
280_K	283_E	0.601	1.00
93_L	143_I	0.601	1.00
285_F	289_L	0.600	1.00
167_I	191_W	0.598	1.00
143_I	286_I	0.597	1.00
106_L	109_L	0.597	1.00
167_I	239_V	0.595	1.00
57_T	65_Y	0.590	1.00
96_A	127_G	0.589	1.00
30_P	34_L	0.587	1.00
227_V	231_V	0.585	1.00
230_A	236_G	0.584	1.00
126_I	223_S	0.584	1.00
31_S	34_L	0.583	1.00
136_V	155_L	0.579	1.00
174_P	178_R	0.572	1.00
43_F	64_L	0.572	1.00
43_F	82_I	0.572	1.00
28_S	34_L	0.571	1.00
195_E	222_S	0.571	1.00
202_E	207_V	0.570	1.00
165_M	239_V	0.567	1.00
110_L	122_L	0.567	1.00
203_Y	206_H	0.565	1.00
48_L	57_T	0.565	1.00
221_I	226_G	0.562	1.00
180_E	185_D	0.561	1.00
163_D	266_R	0.561	1.00
101_I	105_I	0.561	1.00
108_P	111_A	0.561	1.00
7_K	72_V	0.560	1.00
45_T	49_N	0.560	1.00
4_D	8_T	0.560	1.00
147_E	266_R	0.560	1.00
196_K	220_T	0.559	1.00
66_Q	81_E	0.553	1.00
108_P	112_Q	0.553	1.00
96_A	125_M	0.548	1.00
272_H	283_E	0.547	1.00
43_F	46_A	0.545	1.00
91_G	119_E	0.545	1.00
8_T	36_I	0.544	1.00
72_V	75_Y	0.544	1.00
36_I	48_L	0.543	1.00
259_I	262_F	0.542	1.00
228_K	245_L	0.540	1.00
72_V	76_E	0.538	1.00
240_L	245_L	0.536	1.00
160_F	270_Y	0.536	1.00
67_R	82_I	0.532	1.00
68_A	75_Y	0.528	1.00
9_F	61_G	0.527	1.00
117_Y	120_L	0.527	1.00
145_L	270_Y	0.527	1.00
205_D	208_L	0.525	1.00
148_G	157_I	0.524	1.00
224_N	241_S	0.523	1.00
173_H	237_L	0.519	1.00
282_K	286_I	0.518	1.00
91_G	117_Y	0.516	1.00
46_A	60_T	0.516	1.00
103_E	223_S	0.516	1.00
8_T	21_A	0.514	1.00
18_F	29_Q	0.513	1.00
6_L	64_L	0.512	1.00
27_I	35_H	0.512	1.00
18_F	50_R	0.509	1.00
80_A	83_Y	0.509	1.00
84_A	89_V	0.509	1.00
272_H	278_N	0.505	1.00
201_R	207_V	0.505	1.00
105_I	109_L	0.504	1.00
16_K	55_F	0.501	1.00
150_T	153_N	0.501	1.00
97_A	124_V	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
1al3A	1	0.7124	100	0.079	Contact Map
2esnA	3	0.9799	100	0.079	Contact Map
1ixcA	4	0.9766	100	0.079	Contact Map
1uthA	2	0.7592	100	0.08	Contact Map
2h98A	2	0.6923	100	0.082	Contact Map
3fzvA	4	0.9599	100	0.086	Contact Map
4x6gA	4	1	100	0.086	Contact Map
3fxqA	3	0.9766	100	0.086	Contact Map
2h9bA	2	0.6923	100	0.09	Contact Map
3szpA	3	0.9699	100	0.099	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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