BSDA - BACSU - GREMLIN Contacts

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BSDA - HTH-type transcriptional regulator BsdA

UniProt:	P94403	Sequences: MDIRQLRYFITIAQEQKITSAAKKLHMAQPPLSRQLKQLEDELGVVLFDRNKKKQMTLTYEGAVFLKRAKEILHRFEDAVIEVQELKEEVAGTLAVGSTIYCAALMLEKVTQIKERYPHLTFNIWENEPATLLELLESRQIDAAVTTTLIKSDTVQFKQLDDIPCVLVLSDEAGYPCGDTIKMVDIPSFPLILLRPVNGKGVYNQVMNEFHRLNLEPRIVCECHDSATLLSLVSSGFGASILPVTMIPVHMRNHVHTVHIENNPFIMTPAVMWRTDSYLPKPAQQFLDLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (279)
Sequences:	79116 (57800)
Seq/√Len:	3460.4

ECOLI - OXYR CYSB YBHD ILVY LYSR CYNR CBL YNFL YFER AAER NAC PGRR TDCA YDCI XAPR LEUO YAFC YGFI HCAR YCAN YDHB YHJC TTDR YAHB YFIE DSDC ABGR YIAU DMLR YBDO ALLS YEIE YEEY METR NHAR YBEF YNEJ YIDZ GCVA YHAJ ICIA HDFR LRHA YJIE PERR
BACSU - BSDA YWBI CYSL GLTC YCGK YYBE CITR ALSR YTLI YWQM GLTR YVBU YOFA YUST CZCR YKUM YXJO YOAU 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
71_E	75_R	3.749	1.00
15_E	24_K	3.412	1.00
11_T	24_K	2.770	1.00
68_R	82_E	2.616	1.00
159_Q	268_T	2.530	1.00
45_V	61_E	2.386	1.00
10_I	70_K	2.381	1.00
97_G	141_I	2.340	1.00
166_V	244_V	2.302	1.00
10_I	14_Q	2.245	1.00
93_T	123_N	2.239	1.00
159_Q	162_D	2.232	1.00
162_D	268_T	2.220	1.00
68_R	75_R	2.189	1.00
8_Y	35_Q	2.185	1.00
11_T	15_E	2.176	1.00
93_T	121_T	2.080	1.00
166_V	257_T	2.058	1.00
173_A	189_F	2.046	1.00
95_A	123_N	2.024	1.00
234_S	254_H	1.978	1.00
13_A	58_L	1.972	1.00
162_D	266_I	1.968	1.00
233_V	240_S	1.957	1.00
164_P	244_V	1.945	1.00
72_I	76_F	1.918	1.00
66_L	70_K	1.908	1.00
11_T	14_Q	1.893	1.00
13_A	66_L	1.890	1.00
182_K	185_D	1.883	1.00
230_L	250_H	1.873	1.00
8_Y	32_L	1.870	1.00
20_S	23_K	1.804	1.00
10_I	66_L	1.801	1.00
68_R	71_E	1.792	1.00
234_S	250_H	1.783	1.00
190_P	220_V	1.783	1.00
14_Q	70_K	1.779	1.00
157_F	270_A	1.757	1.00
64_V	82_E	1.751	1.00
15_E	20_S	1.717	1.00
192_I	238_G	1.687	1.00
169_L	258_V	1.684	1.00
17_K	20_S	1.664	1.00
135_L	140_Q	1.640	1.00
49_D	57_T	1.630	1.00
158_K	273_W	1.581	1.00
65_F	79_A	1.568	1.00
156_Q	275_T	1.565	1.00
75_R	78_D	1.548	1.00
51_N	57_T	1.544	1.00
10_I	69_A	1.531	1.00
5_Q	42_E	1.522	1.00
68_R	78_D	1.515	1.00
5_Q	38_Q	1.513	1.00
135_L	141_I	1.483	1.00
11_T	25_L	1.470	1.00
14_Q	24_K	1.463	1.00
28_A	31_P	1.462	1.00
156_Q	273_W	1.447	1.00
5_Q	35_Q	1.432	1.00
18_I	36_L	1.431	1.00
273_W	287_L	1.422	1.00
67_K	71_E	1.415	1.00
95_A	125_W	1.413	1.00
134_E	138_S	1.401	1.00
146_T	272_M	1.397	1.00
148_T	270_A	1.391	1.00
203_Y	207_M	1.386	1.00
46_V	49_D	1.381	1.00
72_I	79_A	1.381	1.00
159_Q	270_A	1.376	1.00
113_I	120_L	1.373	1.00
163_I	245_T	1.369	1.00
136_L	144_A	1.360	1.00
68_R	79_A	1.346	1.00
231_S	234_S	1.339	1.00
89_E	119_H	1.335	1.00
171_D	256_H	1.332	1.00
65_F	80_V	1.324	1.00
250_H	254_H	1.323	1.00
229_L	240_S	1.322	1.00
19_T	29_Q	1.318	1.00
91_A	119_H	1.317	1.00
143_A	271_V	1.316	1.00
27_M	31_P	1.310	1.00
111_T	235_S	1.309	1.00
271_V	287_L	1.309	1.00
64_V	68_R	1.308	1.00
178_G	185_D	1.298	1.00
9_F	66_L	1.295	1.00
3_I	76_F	1.294	1.00
10_I	73_L	1.283	1.00
113_I	286_F	1.280	1.00
60_Y	63_A	1.270	1.00
34_R	38_Q	1.269	1.00
143_A	283_A	1.256	1.00
114_K	220_V	1.253	1.00
180_T	261_E	1.250	1.00
189_F	239_A	1.249	1.00
108_E	235_S	1.248	1.00
137_E	154_T	1.243	1.00
64_V	67_K	1.239	1.00
114_K	190_P	1.237	1.00
112_Q	116_R	1.231	1.00
169_L	239_A	1.231	1.00
8_Y	27_M	1.231	1.00
52_K	55_Q	1.230	1.00
285_Q	288_D	1.227	1.00
279_L	283_A	1.215	1.00
71_E	78_D	1.209	1.00
111_T	115_E	1.206	1.00
127_N	135_L	1.206	1.00
174_G	189_F	1.201	1.00
257_T	260_I	1.199	1.00
244_V	257_T	1.192	1.00
6_L	69_A	1.189	1.00
171_D	254_H	1.187	1.00
157_F	272_M	1.168	1.00
9_F	13_A	1.167	1.00
42_E	80_V	1.160	1.00
181_I	185_D	1.157	1.00
231_S	235_S	1.146	1.00
190_P	218_R	1.142	1.00
11_T	21_A	1.137	1.00
63_A	67_K	1.136	1.00
34_R	37_K	1.132	1.00
125_W	135_L	1.126	1.00
244_V	248_P	1.121	1.00
72_I	75_R	1.120	1.00
117_Y	285_Q	1.117	1.00
9_F	48_F	1.114	1.00
76_F	80_V	1.085	1.00
193_L	219_I	1.074	1.00
164_P	266_I	1.063	1.00
137_E	152_S	1.061	1.00
168_V	257_T	1.060	1.00
249_V	252_R	1.058	1.00
170_S	236_G	1.049	1.00
18_I	56_M	1.048	1.00
37_K	41_D	1.046	1.00
230_L	234_S	1.046	1.00
179_D	256_H	1.045	1.00
35_Q	38_Q	1.044	1.00
74_H	78_D	1.039	1.00
61_E	64_V	1.035	1.00
80_V	84_Q	1.032	1.00
103_A	126_E	1.031	1.00
33_S	37_K	1.023	1.00
113_I	117_Y	1.018	1.00
65_F	69_A	1.006	1.00
71_E	74_H	1.003	1.00
94_L	286_F	1.003	1.00
123_N	222_E	0.981	1.00
284_Q	288_D	0.981	1.00
204_N	208_N	0.977	1.00
248_P	251_M	0.970	1.00
274_R	277_S	0.965	1.00
168_V	247_I	0.962	1.00
12_I	21_A	0.961	1.00
21_A	32_L	0.959	1.00
64_V	86_L	0.958	1.00
111_T	237_F	0.957	1.00
112_Q	115_E	0.956	1.00
16_Q	57_T	0.955	1.00
38_Q	41_D	0.952	1.00
12_I	18_I	0.951	1.00
192_I	229_L	0.949	1.00
7_R	77_E	0.949	1.00
20_S	24_K	0.948	1.00
58_L	62_G	0.942	1.00
156_Q	159_Q	0.935	1.00
234_S	252_R	0.935	1.00
76_F	79_A	0.933	1.00
78_D	82_E	0.931	1.00
13_A	48_F	0.925	1.00
7_R	11_T	0.924	1.00
9_F	47_L	0.924	1.00
204_N	207_M	0.923	1.00
158_K	287_L	0.918	1.00
77_E	80_V	0.915	1.00
223_C	229_L	0.910	1.00
9_F	39_L	0.910	1.00
51_N	55_Q	0.905	1.00
4_R	7_R	0.904	1.00
15_E	21_A	0.902	1.00
167_L	239_A	0.901	1.00
8_Y	25_L	0.900	1.00
281_K	285_Q	0.894	1.00
7_R	10_I	0.891	1.00
280_P	283_A	0.891	1.00
75_R	79_A	0.889	1.00
135_L	138_S	0.886	1.00
114_K	237_F	0.885	1.00
67_K	70_K	0.881	1.00
27_M	32_L	0.880	1.00
19_T	23_K	0.877	1.00
63_A	66_L	0.877	1.00
61_E	86_L	0.872	1.00
209_E	213_L	0.870	1.00
223_C	232_L	0.870	1.00
169_L	173_A	0.868	1.00
16_Q	55_Q	0.867	1.00
100_I	225_D	0.867	1.00
13_A	16_Q	0.866	1.00
45_V	83_V	0.864	1.00
14_Q	66_L	0.860	1.00
133_L	137_E	0.855	1.00
92_G	282_P	0.854	1.00
148_T	268_T	0.852	1.00
12_I	48_F	0.851	1.00
183_M	262_N	0.845	1.00
172_E	236_G	0.844	1.00
9_F	58_L	0.844	1.00
175_Y	189_F	0.839	1.00
61_E	83_V	0.831	1.00
79_A	83_V	0.831	1.00
125_W	141_I	0.830	1.00
96_V	143_A	0.827	1.00
232_L	237_F	0.825	1.00
173_A	176_P	0.824	1.00
225_D	228_T	0.822	1.00
77_E	81_I	0.821	1.00
48_F	56_M	0.820	1.00
70_K	74_H	0.820	1.00
176_P	256_H	0.814	1.00
4_R	35_Q	0.812	1.00
97_G	144_A	0.811	1.00
190_P	219_I	0.809	1.00
29_Q	33_S	0.809	1.00
98_S	103_A	0.806	1.00
141_I	144_A	0.806	1.00
12_I	36_L	0.804	1.00
184_V	187_P	0.803	1.00
177_C	190_P	0.803	1.00
7_R	73_L	0.794	1.00
25_L	32_L	0.794	1.00
210_F	215_L	0.793	1.00
69_A	72_I	0.792	1.00
97_G	146_T	0.789	1.00
12_I	32_L	0.786	1.00
139_R	274_R	0.782	1.00
209_E	212_R	0.780	1.00
18_I	32_L	0.778	1.00
277_S	280_P	0.775	1.00
164_P	264_P	0.775	1.00
113_I	285_Q	0.774	1.00
60_Y	64_V	0.774	1.00
169_L	174_G	0.772	1.00
170_S	173_A	0.771	1.00
182_K	261_E	0.767	1.00
120_L	282_P	0.762	1.00
191_L	217_P	0.760	1.00
174_G	179_D	0.760	1.00
247_I	250_H	0.758	1.00
205_Q	209_E	0.758	1.00
108_E	111_T	0.755	1.00
170_S	237_F	0.751	1.00
155_V	272_M	0.750	1.00
9_F	62_G	0.750	1.00
168_V	242_L	0.749	1.00
206_V	210_F	0.749	1.00
37_K	46_V	0.747	1.00
185_D	188_S	0.745	1.00
121_T	218_R	0.741	1.00
5_Q	8_Y	0.739	1.00
142_D	283_A	0.738	1.00
169_L	256_H	0.736	1.00
58_L	63_A	0.736	1.00
49_D	59_T	0.735	1.00
279_L	284_Q	0.735	1.00
195_R	222_E	0.734	1.00
13_A	63_A	0.734	1.00
3_I	73_L	0.733	1.00
9_F	65_F	0.731	1.00
16_Q	63_A	0.731	1.00
143_A	286_F	0.730	1.00
68_R	72_I	0.727	1.00
187_P	215_L	0.723	1.00
164_P	259_H	0.723	1.00
95_A	142_D	0.722	1.00
106_M	109_K	0.721	1.00
167_L	241_I	0.718	1.00
137_E	155_V	0.713	1.00
172_E	176_P	0.711	1.00
173_A	177_C	0.710	1.00
51_N	54_K	0.704	1.00
13_A	62_G	0.701	1.00
180_T	259_H	0.700	1.00
208_N	212_R	0.699	1.00
90_V	117_Y	0.694	1.00
205_Q	208_N	0.692	1.00
23_K	26_H	0.692	1.00
203_Y	209_E	0.690	1.00
84_Q	87_K	0.687	1.00
31_P	35_Q	0.683	1.00
49_D	55_Q	0.679	1.00
73_L	77_E	0.678	1.00
207_M	211_H	0.675	1.00
147_T	267_M	0.673	1.00
168_V	240_S	0.672	1.00
206_V	209_E	0.671	1.00
281_K	284_Q	0.670	1.00
202_V	206_V	0.668	1.00
126_E	224_H	0.666	1.00
191_L	239_A	0.663	1.00
243_P	246_M	0.660	1.00
194_L	229_L	0.660	1.00
57_T	63_A	0.660	1.00
61_E	65_F	0.659	1.00
92_G	120_L	0.655	1.00
154_T	275_T	0.654	1.00
107_L	111_T	0.650	1.00
65_F	83_V	0.648	1.00
43_L	65_F	0.645	1.00
182_K	262_N	0.639	1.00
121_T	222_E	0.638	1.00
116_R	285_Q	0.635	1.00
223_C	228_T	0.633	1.00
78_D	81_I	0.632	1.00
195_R	224_H	0.631	1.00
172_E	175_Y	0.631	1.00
202_V	205_Q	0.627	1.00
221_C	232_L	0.625	1.00
171_D	253_N	0.623	1.00
95_A	141_I	0.618	1.00
136_L	155_V	0.614	1.00
184_V	213_L	0.612	1.00
94_L	143_A	0.607	1.00
111_T	114_K	0.605	1.00
4_R	38_Q	0.602	1.00
117_Y	120_L	0.601	1.00
82_E	85_E	0.600	1.00
137_E	140_Q	0.599	1.00
148_T	157_F	0.596	1.00
169_L	175_Y	0.595	1.00
64_V	83_V	0.595	1.00
108_E	112_Q	0.594	1.00
105_L	109_K	0.594	1.00
43_L	46_V	0.593	1.00
4_R	8_Y	0.590	1.00
175_Y	178_G	0.589	1.00
40_E	50_R	0.588	1.00
143_A	287_L	0.586	1.00
21_A	25_L	0.586	1.00
100_I	128_E	0.586	1.00
160_L	271_V	0.578	1.00
97_G	127_N	0.578	1.00
12_I	17_K	0.576	1.00
45_V	49_D	0.576	1.00
173_A	239_A	0.576	1.00
18_I	29_Q	0.575	1.00
74_H	77_E	0.573	1.00
165_C	241_I	0.572	1.00
98_S	124_I	0.571	1.00
38_Q	42_E	0.563	1.00
97_G	125_W	0.563	1.00
91_A	121_T	0.562	1.00
210_F	217_P	0.561	1.00
254_H	257_T	0.559	1.00
81_I	85_E	0.558	1.00
16_Q	56_M	0.555	1.00
136_L	272_M	0.554	1.00
81_I	84_Q	0.553	1.00
108_E	231_S	0.552	1.00
167_L	186_I	0.552	1.00
31_P	34_R	0.552	1.00
175_Y	181_I	0.550	1.00
174_G	178_G	0.549	1.00
79_A	82_E	0.548	1.00
208_N	211_H	0.546	1.00
92_G	119_H	0.546	1.00
282_P	285_Q	0.545	1.00
46_V	61_E	0.545	1.00
6_L	65_F	0.545	1.00
10_I	77_E	0.543	1.00
163_I	267_M	0.543	1.00
48_F	58_L	0.542	1.00
273_W	284_Q	0.541	1.00
229_L	233_V	0.538	1.00
283_A	287_L	0.538	1.00
194_L	226_S	0.538	1.00
98_S	106_M	0.538	1.00
207_M	210_F	0.537	1.00
43_L	83_V	0.536	1.00
45_V	87_K	0.535	1.00
173_A	190_P	0.534	1.00
30_P	33_S	0.533	1.00
273_W	279_L	0.531	1.00
30_P	34_R	0.529	1.00
121_T	220_V	0.529	1.00
203_Y	222_E	0.528	1.00
69_A	73_L	0.527	1.00
99_T	102_C	0.526	1.00
115_E	237_F	0.526	1.00
43_L	80_V	0.525	1.00
172_E	256_H	0.525	1.00
97_G	135_L	0.525	1.00
102_C	105_L	0.524	1.00
85_E	90_V	0.521	1.00
168_V	255_V	0.521	1.00
36_L	40_E	0.519	1.00
204_N	209_E	0.518	1.00
27_M	35_Q	0.518	1.00
90_V	119_H	0.517	1.00
104_A	227_A	0.514	1.00
242_L	247_I	0.513	1.00
251_M	254_H	0.513	1.00
13_A	70_K	0.511	1.00
133_L	152_S	0.510	1.00
121_T	219_I	0.510	1.00
226_S	243_P	0.510	1.00
163_I	243_P	0.510	1.00
184_V	215_L	0.509	1.00
72_I	80_V	0.508	1.00
109_K	112_Q	0.505	1.00
203_Y	206_V	0.503	1.00
104_A	231_S	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
1ixcA	4	0.9897	100	0.081	Contact Map
1al3A	1	0.6966	100	0.085	Contact Map
2h98A	2	0.6828	100	0.086	Contact Map
4x6gA	4	0.9897	100	0.091	Contact Map
2h9bA	2	0.6828	100	0.092	Contact Map
2esnA	3	0.9828	100	0.093	Contact Map
3fxqA	3	0.9828	100	0.095	Contact Map
1uthA	2	0.7414	100	0.096	Contact Map
3fzvA	4	0.9621	100	0.098	Contact Map
3szpA	3	0.9759	100	0.121	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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