ALSR - BACSU - GREMLIN Contacts

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ALSR - HTH-type transcriptional regulator AlsR

UniProt:	Q04778	Sequences: MELRHLQYFIAVAEELHFGKAARRLNMTQPPLSQQIKQLEEEVGVTLLKRTKRFVELTAAGEIFLNHCRMALMQIGQGIELAQRTARGEQGLLVIGFVGSATYEFLPPIVREYRKKFPSVKIELREISSSRQQEELLKGNIDIGILHPPLQHTALHIETAQSSPCVLALPKQHPLTSKESITIEDLRDEPIITVAKEAWPTLYMDFIQFCEQAGFRPNIVQEATEYQMVIGLVSAGIGMTFVPSSAKKLFNLDVTYRKMDQIQLNAEWVIAYRKDNHNPLIKHFIHISNCQQTRTKESDAGT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	302 (284)
Sequences:	79751 (58409)
Seq/√Len:	3465.9

ECOLI - OXYR CYNR LYSR CYSB YFER HCAR YBHD YNFL XAPR CBL NAC AAER YDHB YAFC TDCA TTDR DMLR YEEY ALLS YAHB LEUO YCAN PGRR ILVY ABGR YHJC YFIE METR YDCI YBDO ICIA YNEJ DSDC YEIE NHAR GCVA YHAJ YBEF YIAU LRHA YIDZ YJIE YGFI PERR HDFR
BACSU - ALSR YWBI YCGK YTLI CYSL GLTC YYBE CITR GLTR BSDA YVBU YUST YWQM YOFA YXJO YOAU 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
70_M	74_Q	3.635	1.00
15_E	24_R	3.407	1.00
158_E	289_N	2.723	1.00
96_G	141_I	2.516	1.00
67_H	81_L	2.455	1.00
11_A	24_R	2.330	1.00
233_V	240_T	2.295	1.00
112_E	291_Q	2.242	1.00
164_P	244_S	2.228	1.00
173_H	189_E	2.219	1.00
159_T	162_S	2.206	1.00
162_S	267_E	2.205	1.00
92_L	123_E	2.204	1.00
159_T	267_E	2.144	1.00
251_N	254_V	2.117	1.00
92_L	121_K	2.105	1.00
20_K	23_R	2.097	1.00
45_V	60_A	2.092	1.00
8_Y	35_Q	2.066	1.00
182_T	185_D	2.044	1.00
14_E	69_R	2.021	1.00
162_S	265_N	2.009	1.00
10_I	69_R	1.995	1.00
67_H	74_Q	1.989	1.00
112_E	287_I	1.983	1.00
94_V	123_E	1.981	1.00
10_I	65_L	1.971	1.00
10_I	14_E	1.952	1.00
230_I	250_F	1.936	1.00
11_A	14_E	1.935	1.00
166_V	244_S	1.914	1.00
192_I	238_G	1.912	1.00
11_A	15_E	1.908	1.00
8_Y	32_L	1.888	1.00
13_A	57_L	1.887	1.00
71_A	75_I	1.871	1.00
65_L	69_R	1.824	1.00
18_F	36_I	1.770	1.00
190_P	220_V	1.743	1.00
49_K	56_E	1.731	1.00
132_Q	144_G	1.725	1.00
64_F	78_G	1.721	1.00
157_I	269_V	1.690	1.00
63_I	81_L	1.685	1.00
234_S	250_F	1.652	1.00
135_E	140_N	1.649	1.00
13_A	65_L	1.637	1.00
113_Y	284_F	1.612	1.00
15_E	20_K	1.583	1.00
156_H	274_K	1.577	1.00
14_E	24_R	1.570	1.00
10_I	68_C	1.567	1.00
9_F	65_L	1.540	1.00
134_E	138_K	1.537	1.00
178_K	185_D	1.536	1.00
8_Y	27_M	1.525	1.00
5_H	35_Q	1.509	1.00
203_Y	207_I	1.500	1.00
88_G	119_S	1.494	1.00
158_E	272_Y	1.489	1.00
67_H	70_M	1.486	1.00
5_H	42_E	1.482	1.00
113_Y	120_V	1.481	1.00
17_H	20_K	1.479	1.00
19_G	29_Q	1.473	1.00
5_H	38_Q	1.461	1.00
28_T	31_P	1.455	1.00
46_T	49_K	1.452	1.00
285_I	289_N	1.433	1.00
146_L	271_A	1.432	1.00
11_A	25_L	1.427	1.00
59_A	62_E	1.423	1.00
10_I	72_L	1.398	1.00
67_H	77_Q	1.395	1.00
156_H	272_Y	1.393	1.00
103_Y	227_Q	1.372	1.00
272_Y	285_I	1.370	1.00
143_I	281_I	1.368	1.00
71_A	78_G	1.360	1.00
169_L	257_R	1.359	1.00
90_Q	119_S	1.341	1.00
51_T	56_E	1.335	1.00
135_E	141_I	1.335	1.00
112_E	116_K	1.331	1.00
94_V	125_R	1.328	1.00
283_H	286_H	1.323	1.00
137_L	154_A	1.318	1.00
136_L	144_G	1.312	1.00
163_S	245_S	1.307	1.00
64_F	79_I	1.305	1.00
74_Q	77_Q	1.305	1.00
270_I	285_I	1.300	1.00
169_L	239_M	1.284	1.00
116_K	287_I	1.279	1.00
148_P	269_V	1.278	1.00
42_E	79_I	1.275	1.00
3_L	75_I	1.272	1.00
229_V	240_T	1.268	1.00
143_I	270_I	1.268	1.00
189_E	239_M	1.265	1.00
114_R	220_V	1.260	1.00
66_N	70_M	1.253	1.00
114_R	190_P	1.221	1.00
67_H	78_G	1.221	1.00
231_G	234_S	1.213	1.00
171_K	253_D	1.208	1.00
63_I	66_N	1.199	1.00
111_R	115_K	1.189	1.00
9_F	48_L	1.188	1.00
159_T	269_V	1.185	1.00
27_M	31_P	1.182	1.00
62_E	66_N	1.176	1.00
166_V	258_K	1.172	1.00
171_K	255_T	1.167	1.00
37_K	41_E	1.167	1.00
244_S	248_K	1.159	1.00
157_I	271_A	1.143	1.00
9_F	13_A	1.142	1.00
34_Q	38_Q	1.141	1.00
111_R	235_A	1.132	1.00
174_P	189_E	1.130	1.00
112_E	115_K	1.128	1.00
210_C	215_F	1.126	1.00
34_Q	37_K	1.116	1.00
123_E	222_E	1.104	1.00
190_P	218_N	1.098	1.00
9_F	47_L	1.097	1.00
192_I	229_V	1.090	1.00
6_L	68_C	1.088	1.00
286_H	289_N	1.084	1.00
117_F	283_H	1.084	1.00
70_M	77_Q	1.083	1.00
33_S	37_K	1.080	1.00
18_F	55_V	1.079	1.00
63_I	67_H	1.078	1.00
287_I	291_Q	1.076	1.00
273_R	276_N	1.069	1.00
244_S	258_K	1.069	1.00
102_T	126_E	1.068	1.00
230_I	234_S	1.064	1.00
11_A	21_A	1.062	1.00
223_A	229_V	1.058	1.00
12_V	21_A	1.055	1.00
113_Y	287_I	1.051	1.00
158_E	285_I	1.050	1.00
108_P	235_A	1.048	1.00
93_L	284_F	1.047	1.00
71_A	74_Q	1.045	1.00
282_K	286_H	1.044	1.00
109_I	288_S	1.042	1.00
181_I	185_D	1.035	1.00
35_Q	38_Q	1.034	1.00
7_Q	76_G	1.032	1.00
180_S	260_D	1.029	1.00
234_S	253_D	1.025	1.00
170_P	236_G	1.024	1.00
137_L	152_H	1.024	1.00
231_G	235_A	1.017	1.00
4_R	7_Q	1.014	1.00
79_I	83_Q	1.006	1.00
179_E	257_R	1.004	1.00
234_S	255_T	1.002	1.00
57_L	61_G	0.999	1.00
167_L	239_M	0.989	1.00
164_P	265_N	0.988	1.00
168_A	247_K	0.986	1.00
73_M	77_Q	0.973	1.00
8_Y	25_L	0.971	1.00
278_N	281_I	0.968	1.00
193_T	219_I	0.967	1.00
27_M	32_L	0.965	1.00
76_G	79_I	0.965	1.00
64_F	68_C	0.964	1.00
13_A	48_L	0.960	1.00
287_I	290_C	0.955	1.00
113_Y	117_F	0.954	1.00
76_G	80_E	0.951	1.00
169_L	173_H	0.950	1.00
204_M	207_I	0.948	1.00
96_G	132_Q	0.947	1.00
12_V	18_F	0.946	1.00
223_A	232_L	0.945	1.00
9_F	57_L	0.944	1.00
125_R	135_E	0.943	1.00
173_H	176_T	0.936	1.00
164_P	258_K	0.931	1.00
248_K	252_L	0.931	1.00
116_K	290_C	0.929	1.00
135_E	138_K	0.928	1.00
38_Q	41_E	0.923	1.00
21_A	32_L	0.918	1.00
9_F	39_L	0.916	1.00
109_I	287_I	0.908	1.00
254_V	258_K	0.907	1.00
204_M	208_Q	0.894	1.00
20_K	24_R	0.887	1.00
48_L	55_V	0.884	1.00
45_V	82_A	0.881	1.00
121_K	218_N	0.877	1.00
13_A	61_G	0.874	1.00
120_V	280_L	0.868	1.00
141_I	144_G	0.867	1.00
66_N	69_R	0.867	1.00
177_S	190_P	0.865	1.00
96_G	146_L	0.865	1.00
99_G	225_E	0.863	1.00
169_L	174_P	0.857	1.00
249_L	253_D	0.856	1.00
70_M	73_M	0.856	1.00
16_L	56_E	0.852	1.00
191_I	217_P	0.848	1.00
174_P	179_E	0.846	1.00
19_G	23_R	0.845	1.00
173_H	190_P	0.845	1.00
190_P	219_I	0.841	1.00
51_T	54_F	0.837	1.00
156_H	159_T	0.836	1.00
95_I	143_I	0.835	1.00
185_D	188_D	0.827	1.00
168_A	256_Y	0.825	1.00
286_H	290_C	0.824	1.00
155_L	271_A	0.824	1.00
133_Q	137_L	0.823	1.00
25_L	32_L	0.822	1.00
154_A	274_K	0.820	1.00
175_L	189_E	0.818	1.00
247_K	250_F	0.813	1.00
125_R	141_I	0.808	1.00
168_A	240_T	0.808	1.00
148_P	267_E	0.807	1.00
111_R	237_I	0.803	1.00
96_G	144_G	0.800	1.00
250_F	255_T	0.800	1.00
60_A	82_A	0.798	1.00
91_G	280_L	0.797	1.00
75_I	79_I	0.794	1.00
184_E	187_R	0.792	1.00
209_F	213_A	0.792	1.00
37_K	46_T	0.792	1.00
13_A	16_L	0.784	1.00
16_L	62_E	0.783	1.00
4_R	35_Q	0.781	1.00
170_P	237_I	0.781	1.00
29_Q	33_S	0.780	1.00
63_I	85_T	0.779	1.00
9_F	64_F	0.778	1.00
75_I	78_G	0.775	1.00
3_L	72_L	0.774	1.00
206_F	210_C	0.773	1.00
74_Q	78_G	0.771	1.00
14_E	65_L	0.769	1.00
15_E	21_A	0.768	1.00
60_A	63_I	0.767	1.00
250_F	253_D	0.766	1.00
131_R	134_E	0.765	1.00
77_Q	81_L	0.762	1.00
166_V	256_Y	0.762	1.00
109_I	291_Q	0.761	1.00
83_Q	86_A	0.761	1.00
12_V	36_I	0.761	1.00
114_R	237_I	0.760	1.00
279_P	283_H	0.758	1.00
182_T	260_D	0.756	1.00
16_L	54_F	0.756	1.00
12_V	48_L	0.754	1.00
172_Q	176_T	0.754	1.00
91_G	120_V	0.752	1.00
232_L	237_I	0.742	1.00
143_I	284_F	0.742	1.00
5_H	8_Y	0.741	1.00
142_D	281_I	0.736	1.00
168_A	242_V	0.732	1.00
112_E	290_C	0.732	1.00
7_Q	11_A	0.730	1.00
18_F	32_L	0.725	1.00
113_Y	283_H	0.724	1.00
68_C	71_A	0.720	1.00
60_A	85_T	0.719	1.00
89_E	117_F	0.718	1.00
78_G	82_A	0.717	1.00
97_F	102_T	0.716	1.00
116_K	283_H	0.715	1.00
137_L	155_L	0.713	1.00
170_P	173_H	0.710	1.00
49_K	58_T	0.708	1.00
173_H	177_S	0.706	1.00
254_V	257_R	0.704	1.00
69_R	73_M	0.704	1.00
49_K	54_F	0.701	1.00
56_E	62_E	0.700	1.00
209_F	212_Q	0.698	1.00
31_P	35_Q	0.696	1.00
12_V	32_L	0.696	1.00
60_A	64_F	0.696	1.00
94_V	141_I	0.692	1.00
243_P	246_A	0.685	1.00
57_L	62_E	0.684	1.00
255_T	258_K	0.680	1.00
62_E	65_L	0.680	1.00
169_L	175_L	0.679	1.00
225_E	228_M	0.679	1.00
203_Y	222_E	0.676	1.00
94_V	142_D	0.674	1.00
195_A	222_E	0.673	1.00
208_Q	211_E	0.671	1.00
184_E	213_A	0.668	1.00
59_A	63_I	0.667	1.00
194_V	229_V	0.663	1.00
283_H	287_I	0.661	1.00
40_E	45_V	0.661	1.00
172_Q	175_L	0.658	1.00
208_Q	212_Q	0.658	1.00
187_R	215_F	0.657	1.00
139_G	273_R	0.655	1.00
7_Q	10_I	0.651	1.00
103_Y	231_G	0.649	1.00
221_Q	232_L	0.648	1.00
172_Q	236_G	0.647	1.00
205_D	209_F	0.647	1.00
77_Q	80_E	0.642	1.00
93_L	280_L	0.640	1.00
36_I	40_E	0.640	1.00
64_F	82_A	0.636	1.00
251_N	256_Y	0.636	1.00
207_I	211_E	0.636	1.00
73_M	76_G	0.636	1.00
191_I	239_M	0.635	1.00
40_E	50_R	0.634	1.00
188_D	218_N	0.634	1.00
126_E	224_T	0.631	1.00
121_K	222_E	0.628	1.00
23_R	26_N	0.626	1.00
145_I	288_S	0.620	1.00
67_H	71_A	0.620	1.00
279_P	282_K	0.619	1.00
97_F	106_L	0.614	1.00
68_C	72_L	0.610	1.00
164_P	263_Q	0.604	1.00
167_L	186_L	0.604	1.00
167_L	241_F	0.603	1.00
21_A	25_L	0.603	1.00
12_V	17_H	0.602	1.00
90_Q	121_K	0.600	1.00
195_A	224_T	0.595	1.00
18_F	54_F	0.594	1.00
206_F	209_F	0.591	1.00
143_I	285_I	0.589	1.00
108_P	111_R	0.589	1.00
63_I	82_A	0.589	1.00
4_R	38_Q	0.588	1.00
131_R	135_E	0.588	1.00
272_Y	282_K	0.584	1.00
210_C	217_P	0.579	1.00
108_P	112_E	0.578	1.00
106_L	109_I	0.578	1.00
126_E	225_E	0.578	1.00
93_L	143_I	0.577	1.00
163_S	266_A	0.577	1.00
80_E	84_R	0.576	1.00
30_P	34_Q	0.574	1.00
147_H	266_A	0.574	1.00
167_L	191_I	0.573	1.00
4_R	8_Y	0.573	1.00
136_L	271_A	0.572	1.00
229_V	233_V	0.571	1.00
161_Q	268_W	0.570	1.00
205_D	208_Q	0.568	1.00
7_Q	72_L	0.567	1.00
284_F	288_S	0.567	1.00
43_V	64_F	0.563	1.00
203_Y	209_F	0.563	1.00
57_L	65_L	0.560	1.00
204_M	209_F	0.559	1.00
249_L	252_L	0.559	1.00
31_P	34_Q	0.559	1.00
43_V	82_A	0.558	1.00
48_L	57_L	0.557	1.00
165_C	241_F	0.556	1.00
156_H	275_D	0.555	1.00
28_T	34_Q	0.555	1.00
223_A	228_M	0.553	1.00
175_L	181_I	0.553	1.00
45_V	49_K	0.553	1.00
168_A	251_N	0.553	1.00
136_L	155_L	0.552	1.00
9_F	61_G	0.548	1.00
72_L	76_G	0.547	1.00
207_I	210_C	0.546	1.00
232_L	238_G	0.546	1.00
132_Q	139_G	0.545	1.00
203_Y	206_F	0.541	1.00
101_A	105_F	0.535	1.00
110_V	122_I	0.534	1.00
91_G	119_S	0.532	1.00
72_L	75_I	0.532	1.00
117_F	120_V	0.532	1.00
234_S	251_N	0.532	1.00
173_H	239_M	0.531	1.00
242_V	247_K	0.531	1.00
175_L	178_K	0.531	1.00
196_K	222_E	0.525	1.00
66_N	81_L	0.524	1.00
8_Y	36_I	0.524	1.00
18_F	29_Q	0.524	1.00
103_Y	225_E	0.522	1.00
43_V	46_T	0.521	1.00
202_L	205_D	0.518	1.00
169_L	176_T	0.518	1.00
134_E	140_N	0.517	1.00
258_K	261_Q	0.515	1.00
226_Y	243_P	0.515	1.00
180_S	185_D	0.513	1.00
96_G	125_R	0.511	1.00
174_P	178_K	0.511	1.00
187_R	216_R	0.511	1.00
202_L	206_F	0.510	1.00
84_R	89_E	0.510	1.00
67_H	82_A	0.509	1.00
160_A	270_I	0.509	1.00
8_Y	21_A	0.506	1.00
13_A	62_E	0.506	1.00
46_T	60_A	0.505	1.00
27_M	35_Q	0.503	1.00
182_T	261_Q	0.503	1.00
16_L	55_V	0.502	1.00
178_K	181_I	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
2h9bA	2	0.7053	100	0.075	Contact Map
1ixcA	4	0.9735	100	0.075	Contact Map
2h98A	2	0.7053	100	0.078	Contact Map
2esnA	3	0.9636	100	0.099	Contact Map
4x6gA	4	0.9934	100	0.101	Contact Map
1al3A	1	0.7119	100	0.102	Contact Map
1uthA	2	0.7417	100	0.103	Contact Map
3fzvA	4	0.9404	100	0.107	Contact Map
3fxqA	3	0.957	100	0.111	Contact Map
3szpA	3	0.9503	100	0.126	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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