YCGK - BACSU - GREMLIN Contacts

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YCGK - Uncharacterized HTH-type transcriptional regulator YcgK

UniProt:	P94387	Sequences: MDIKVMEYAAEIARRQSFTKAAEHLHIAQPSLSQQIKKLEAELGLTLFHRSHGSVTLTPHGRRFIEKAEDIIRSRDDLLREMQERSQGIGHKLSIGIPAVTGRYLFPPLLKQFLARYPHVEVQLVEKDPVSLEKMTAKGEVDLSVLSLPIEDERLSITPLLTEPVVLAVPKEKQRWMPPELVALIEKALEEDEGRQPCVPIDMVRNVPFILLKEGFGFRRTVLDLCAESGFKPNAAFKTSHIETAQSLVANGLGVTMAPNMVRRDKDPGVIYLSIQSAPSRTLVFVFLKNRYVSLTAQAFMELSRESLKQTFDEGCLGNKDENI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	324 (286)
Sequences:	79283 (57302)
Seq/√Len:	3388.3

ECOLI - LYSR OXYR CYSB CYNR CBL YBHD DMLR AAER YFER NAC TDCA YAFC YNFL TTDR YDHB XAPR HCAR YEEY METR PGRR LEUO ABGR YAHB YCAN YDCI NHAR YEIE YFIE ALLS YHJC ICIA YBDO ILVY GCVA DSDC YIAU YBEF YIDZ YNEJ YHAJ YGFI LRHA PERR HDFR YJIE
BACSU - YCGK YWBI CYSL ALSR YTLI GLTC YYBE CITR BSDA YWQM GLTR YVBU YUST 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_D	74_S	3.682	1.00
15_R	24_H	3.452	1.00
158_T	305_R	2.736	1.00
67_K	81_E	2.504	1.00
96_G	141_V	2.501	1.00
11_E	24_H	2.395	1.00
249_V	256_T	2.299	1.00
162_T	282_T	2.267	1.00
173_K	207_V	2.248	1.00
92_K	123_Q	2.241	1.00
159_P	162_T	2.237	1.00
112_Q	307_S	2.217	1.00
159_P	282_T	2.213	1.00
164_P	260_N	2.142	1.00
45_L	60_H	2.131	1.00
8_Y	35_Q	2.102	1.00
92_K	121_E	2.100	1.00
20_K	23_E	2.077	1.00
162_T	280_S	2.067	1.00
10_A	69_E	2.053	1.00
67_K	74_S	2.019	1.00
14_R	69_E	2.019	1.00
10_A	14_R	2.017	1.00
200_P	203_M	2.015	1.00
112_Q	303_L	2.005	1.00
94_S	123_Q	1.987	1.00
10_A	65_I	1.975	1.00
166_V	260_N	1.968	1.00
11_E	15_R	1.965	1.00
11_E	14_R	1.949	1.00
13_A	57_L	1.932	1.00
210_I	254_G	1.925	1.00
8_Y	32_L	1.925	1.00
132_L	144_S	1.917	1.00
71_I	75_R	1.892	1.00
65_I	69_E	1.847	1.00
208_P	236_A	1.768	1.00
18_F	36_I	1.755	1.00
64_F	78_L	1.730	1.00
49_H	56_T	1.728	1.00
157_I	284_V	1.715	1.00
63_R	81_E	1.700	1.00
13_A	65_I	1.681	1.00
135_M	140_E	1.655	1.00
15_R	20_K	1.628	1.00
156_S	289_K	1.593	1.00
14_R	24_H	1.590	1.00
10_A	68_A	1.580	1.00
113_F	300_F	1.561	1.00
169_V	273_L	1.548	1.00
5_V	35_Q	1.543	1.00
9_A	65_I	1.536	1.00
67_K	70_D	1.528	1.00
158_T	287_F	1.522	1.00
134_K	138_K	1.515	1.00
8_Y	27_I	1.512	1.00
17_S	20_K	1.511	1.00
113_F	120_V	1.488	1.00
5_V	42_E	1.488	1.00
5_V	38_K	1.485	1.00
28_A	31_S	1.484	1.00
196_Q	203_M	1.466	1.00
19_T	29_Q	1.465	1.00
88_G	119_H	1.449	1.00
46_T	49_H	1.449	1.00
301_M	305_R	1.439	1.00
146_L	286_V	1.436	1.00
59_P	62_R	1.431	1.00
11_E	25_L	1.430	1.00
219_R	223_L	1.424	1.00
103_R	243_E	1.417	1.00
156_S	287_F	1.416	1.00
293_V	297_A	1.411	1.00
67_K	77_D	1.404	1.00
10_A	72_I	1.396	1.00
71_I	78_L	1.385	1.00
148_L	284_V	1.381	1.00
287_F	301_M	1.379	1.00
51_S	56_T	1.373	1.00
94_S	125_V	1.357	1.00
250_A	269_G	1.345	1.00
299_A	302_E	1.345	1.00
90_G	119_H	1.341	1.00
136_T	144_S	1.340	1.00
112_Q	116_R	1.331	1.00
64_F	79_L	1.330	1.00
135_M	141_V	1.330	1.00
127_K	131_S	1.329	1.00
74_S	77_D	1.325	1.00
116_R	303_L	1.319	1.00
285_F	301_M	1.314	1.00
163_E	261_M	1.311	1.00
137_A	154_R	1.308	1.00
169_V	255_V	1.293	1.00
245_A	256_T	1.289	1.00
3_I	75_R	1.284	1.00
143_L	297_A	1.280	1.00
66_E	70_D	1.277	1.00
143_L	285_F	1.268	1.00
207_V	255_V	1.266	1.00
42_E	79_L	1.264	1.00
114_L	236_A	1.262	1.00
67_K	78_L	1.254	1.00
159_P	284_V	1.232	1.00
114_L	208_P	1.227	1.00
247_S	250_A	1.226	1.00
27_I	31_S	1.215	1.00
63_R	66_E	1.204	1.00
111_K	115_A	1.200	1.00
9_A	48_F	1.194	1.00
174_Q	207_V	1.188	1.00
34_Q	38_K	1.178	1.00
171_K	269_G	1.175	1.00
273_L	276_Q	1.169	1.00
62_R	66_E	1.169	1.00
111_K	251_N	1.162	1.00
9_A	13_A	1.157	1.00
37_K	41_A	1.152	1.00
271_I	274_S	1.146	1.00
157_I	286_V	1.142	1.00
260_N	264_R	1.135	1.00
123_Q	238_K	1.126	1.00
198_C	276_Q	1.117	1.00
112_Q	115_A	1.114	1.00
9_A	47_L	1.111	1.00
34_Q	37_K	1.110	1.00
117_Y	299_A	1.110	1.00
63_R	67_K	1.107	1.00
226_C	231_F	1.105	1.00
208_P	234_N	1.103	1.00
171_K	271_I	1.100	1.00
210_I	245_A	1.098	1.00
70_D	77_D	1.097	1.00
266_K	269_G	1.095	1.00
102_G	126_E	1.082	1.00
303_L	307_S	1.079	1.00
12_I	21_A	1.079	1.00
127_K	135_M	1.078	1.00
108_P	251_N	1.078	1.00
18_F	55_V	1.076	1.00
11_E	21_A	1.074	1.00
6_M	68_A	1.072	1.00
199_V	203_M	1.071	1.00
93_L	300_F	1.071	1.00
33_S	37_K	1.068	1.00
71_I	74_S	1.066	1.00
158_T	301_M	1.065	1.00
113_F	303_L	1.064	1.00
302_E	305_R	1.063	1.00
298_Q	302_E	1.047	1.00
247_S	251_N	1.043	1.00
35_Q	38_K	1.040	1.00
170_P	252_G	1.039	1.00
239_T	245_A	1.029	1.00
109_L	304_S	1.026	1.00
7_E	76_D	1.024	1.00
4_K	7_E	1.016	1.00
246_Q	250_A	1.015	1.00
79_L	83_Q	1.011	1.00
168_A	263_R	0.998	1.00
164_P	280_S	0.996	1.00
57_L	61_G	0.995	1.00
73_R	77_D	0.991	1.00
137_A	152_D	0.988	1.00
211_L	235_A	0.987	1.00
303_L	306_E	0.983	1.00
8_Y	25_L	0.980	1.00
166_V	272_Y	0.979	1.00
13_A	48_F	0.975	1.00
169_V	173_K	0.973	1.00
125_V	135_M	0.972	1.00
167_L	255_V	0.971	1.00
250_A	270_V	0.969	1.00
12_I	18_F	0.968	1.00
64_F	68_A	0.966	1.00
27_I	32_L	0.961	1.00
113_F	117_Y	0.961	1.00
220_R	223_L	0.957	1.00
239_T	248_L	0.949	1.00
76_D	79_L	0.941	1.00
76_D	80_R	0.939	1.00
9_A	57_L	0.934	1.00
38_K	41_A	0.931	1.00
21_A	32_L	0.930	1.00
116_R	306_E	0.930	1.00
9_A	39_L	0.928	1.00
135_M	138_K	0.917	1.00
63_R	85_R	0.913	1.00
48_F	55_V	0.907	1.00
294_S	297_A	0.898	1.00
96_G	132_L	0.895	1.00
20_K	24_H	0.894	1.00
109_L	303_L	0.893	1.00
70_D	73_R	0.882	1.00
45_L	82_M	0.878	1.00
99_A	241_H	0.876	1.00
168_A	272_Y	0.876	1.00
141_V	144_S	0.874	1.00
16_Q	56_T	0.867	1.00
66_E	69_E	0.866	1.00
13_A	61_G	0.863	1.00
173_K	208_P	0.856	1.00
121_E	234_N	0.849	1.00
19_T	23_E	0.848	1.00
148_L	282_T	0.847	1.00
208_P	235_A	0.846	1.00
95_I	143_L	0.844	1.00
96_G	146_L	0.836	1.00
203_M	206_N	0.835	1.00
120_V	296_T	0.834	1.00
25_L	32_L	0.833	1.00
169_V	174_Q	0.833	1.00
156_S	159_P	0.831	1.00
288_L	291_R	0.830	1.00
51_S	54_S	0.829	1.00
111_K	253_L	0.829	1.00
175_R	207_V	0.827	1.00
60_H	85_R	0.826	1.00
133_E	137_A	0.824	1.00
91_H	296_T	0.822	1.00
164_P	274_S	0.820	1.00
155_L	286_V	0.819	1.00
75_R	79_L	0.819	1.00
174_Q	197_P	0.815	1.00
222_V	226_C	0.815	1.00
220_R	224_D	0.811	1.00
125_V	141_V	0.809	1.00
96_G	144_S	0.808	1.00
202_D	205_R	0.807	1.00
13_A	16_Q	0.806	1.00
168_A	256_T	0.805	1.00
60_H	82_M	0.803	1.00
293_V	298_Q	0.802	1.00
75_R	78_L	0.801	1.00
60_H	63_R	0.801	1.00
9_A	64_F	0.800	1.00
109_L	307_S	0.799	1.00
127_K	132_L	0.797	1.00
74_S	78_L	0.796	1.00
176_W	195_R	0.793	1.00
77_D	81_E	0.791	1.00
37_K	46_T	0.788	1.00
265_D	268_P	0.788	1.00
16_Q	62_R	0.788	1.00
12_I	48_F	0.786	1.00
4_K	35_Q	0.785	1.00
195_R	208_P	0.785	1.00
225_L	229_S	0.784	1.00
14_R	65_I	0.784	1.00
302_E	306_E	0.783	1.00
12_I	36_I	0.782	1.00
114_L	253_L	0.782	1.00
170_P	253_L	0.781	1.00
131_S	134_K	0.777	1.00
16_Q	54_S	0.776	1.00
29_Q	33_S	0.775	1.00
15_R	21_A	0.775	1.00
154_R	289_K	0.773	1.00
264_R	267_D	0.773	1.00
3_I	72_I	0.772	1.00
295_L	299_A	0.772	1.00
164_P	278_A	0.765	1.00
200_P	276_Q	0.765	1.00
7_E	11_E	0.761	1.00
91_H	120_V	0.760	1.00
5_V	8_Y	0.746	1.00
143_L	300_F	0.741	1.00
18_F	32_L	0.741	1.00
78_L	82_M	0.741	1.00
248_L	253_L	0.737	1.00
113_F	299_A	0.732	1.00
69_E	73_R	0.729	1.00
266_K	270_V	0.729	1.00
260_N	272_Y	0.727	1.00
224_D	228_E	0.725	1.00
89_I	117_Y	0.725	1.00
12_I	32_L	0.725	1.00
168_A	258_A	0.722	1.00
68_A	71_I	0.722	1.00
197_P	272_Y	0.722	1.00
49_H	54_S	0.722	1.00
116_R	299_A	0.721	1.00
225_L	228_E	0.720	1.00
137_A	155_L	0.720	1.00
170_P	173_K	0.716	1.00
97_I	102_G	0.716	1.00
270_V	274_S	0.716	1.00
241_H	244_T	0.714	1.00
83_Q	86_S	0.713	1.00
49_H	58_T	0.709	1.00
166_V	273_L	0.706	1.00
176_W	271_I	0.704	1.00
112_Q	306_E	0.703	1.00
62_R	65_I	0.702	1.00
60_H	64_F	0.697	1.00
246_Q	265_D	0.697	1.00
205_R	231_F	0.691	1.00
142_D	297_A	0.690	1.00
31_S	35_Q	0.689	1.00
56_T	62_R	0.689	1.00
259_P	262_V	0.688	1.00
57_L	62_R	0.688	1.00
131_S	135_M	0.687	1.00
202_D	229_S	0.687	1.00
209_F	233_P	0.685	1.00
213_K	238_K	0.684	1.00
221_T	225_L	0.683	1.00
169_V	175_R	0.682	1.00
299_A	303_L	0.681	1.00
139_G	288_L	0.680	1.00
94_S	141_V	0.679	1.00
172_E	252_G	0.677	1.00
103_R	247_S	0.677	1.00
7_E	10_A	0.676	1.00
219_R	238_K	0.675	1.00
59_P	63_R	0.675	1.00
94_S	142_D	0.673	1.00
223_L	227_A	0.668	1.00
224_D	227_A	0.663	1.00
212_L	245_A	0.658	1.00
209_F	255_V	0.655	1.00
237_F	248_L	0.654	1.00
64_F	82_M	0.651	1.00
172_E	175_R	0.650	1.00
222_V	225_L	0.647	1.00
121_E	238_K	0.646	1.00
77_D	80_R	0.642	1.00
40_E	45_L	0.640	1.00
23_E	26_H	0.634	1.00
167_L	257_M	0.634	1.00
40_E	50_R	0.630	1.00
97_I	106_F	0.628	1.00
67_K	71_I	0.627	1.00
291_R	294_S	0.625	1.00
73_R	76_D	0.625	1.00
173_K	176_W	0.623	1.00
167_L	204_V	0.622	1.00
68_A	72_I	0.619	1.00
126_E	240_S	0.617	1.00
36_I	40_E	0.615	1.00
12_I	17_S	0.614	1.00
93_L	296_T	0.610	1.00
295_L	298_Q	0.609	1.00
206_N	234_N	0.609	1.00
220_R	225_L	0.605	1.00
147_S	281_R	0.602	1.00
18_F	54_S	0.597	1.00
108_P	111_K	0.595	1.00
143_L	301_M	0.593	1.00
300_F	304_S	0.590	1.00
108_P	112_Q	0.590	1.00
21_A	25_L	0.589	1.00
99_A	128_D	0.588	1.00
145_V	304_S	0.587	1.00
7_E	72_I	0.586	1.00
80_R	84_E	0.586	1.00
4_K	38_K	0.585	1.00
195_R	198_C	0.585	1.00
106_F	109_L	0.583	1.00
163_E	281_R	0.582	1.00
93_L	143_L	0.581	1.00
213_K	240_S	0.581	1.00
218_F	222_V	0.581	1.00
43_L	64_F	0.578	1.00
136_T	286_V	0.575	1.00
31_S	34_Q	0.574	1.00
226_C	233_P	0.574	1.00
63_R	82_M	0.571	1.00
221_T	224_D	0.570	1.00
4_K	8_Y	0.568	1.00
9_A	61_G	0.568	1.00
126_E	241_H	0.568	1.00
167_L	209_F	0.565	1.00
245_A	249_V	0.563	1.00
30_P	34_Q	0.562	1.00
250_A	267_D	0.561	1.00
165_V	257_M	0.561	1.00
90_G	121_E	0.558	1.00
161_L	283_L	0.558	1.00
172_E	271_I	0.557	1.00
239_T	244_T	0.557	1.00
223_L	226_C	0.556	1.00
287_F	298_Q	0.555	1.00
48_F	57_L	0.555	1.00
28_A	34_Q	0.553	1.00
43_L	82_M	0.553	1.00
136_T	155_L	0.553	1.00
270_V	275_I	0.550	1.00
267_D	270_V	0.545	1.00
248_L	254_G	0.545	1.00
72_I	76_D	0.545	1.00
57_L	65_I	0.544	1.00
117_Y	120_V	0.544	1.00
45_L	49_H	0.544	1.00
214_E	238_K	0.540	1.00
173_K	255_V	0.539	1.00
84_E	89_I	0.535	1.00
101_T	105_L	0.535	1.00
91_H	119_H	0.531	1.00
169_V	271_I	0.531	1.00
110_L	122_V	0.529	1.00
96_G	125_V	0.529	1.00
43_L	46_T	0.529	1.00
156_S	290_N	0.526	1.00
200_P	277_S	0.522	1.00
13_A	62_R	0.522	1.00
160_L	285_F	0.520	1.00
258_A	263_R	0.520	1.00
66_E	81_E	0.519	1.00
198_C	203_M	0.517	1.00
174_Q	196_Q	0.517	1.00
8_Y	36_I	0.516	1.00
175_R	199_V	0.514	1.00
168_A	266_K	0.511	1.00
8_Y	21_A	0.510	1.00
148_L	157_I	0.509	1.00
274_S	277_S	0.507	1.00
46_T	60_H	0.507	1.00
103_R	241_H	0.507	1.00
18_F	29_Q	0.506	1.00
16_Q	55_V	0.505	1.00
81_E	84_E	0.504	1.00
80_R	83_Q	0.504	1.00
134_K	140_E	0.503	1.00
242_I	259_P	0.501	1.00
27_I	35_Q	0.501	1.00
175_R	196_Q	0.501	1.00
266_K	271_I	0.500	1.00
198_C	274_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
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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	0.8981	100	0.149	Contact Map
2h98A	2	0.6512	100	0.16	Contact Map
1al3A	1	0.6821	100	0.161	Contact Map
2esnA	3	0.8951	100	0.161	Contact Map
4x6gA	4	0.9259	100	0.163	Contact Map
1uthA	2	0.6914	100	0.163	Contact Map
3fzvA	4	0.8765	100	0.167	Contact Map
2h9bA	2	0.6512	100	0.169	Contact Map
3fxqA	3	0.892	100	0.17	Contact Map
3szpA	3	0.8858	100	0.188	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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