YKOG - BACSU - GREMLIN Contacts

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YKOG - Uncharacterized transcriptional regulatory protein YkoG

UniProt:	O34903	Sequences: MEKGHILIVEDEEKIARVLQLELEYEGYSVTIKHNGTEGLDAAAEGGYSLVLLDVMLPGLSGLEVLRRLRKTDSQTPVILLTARDSIPDKVTGLDIGANDYVTKPFEIEELLARIRAALRQNGTKTEDIGTFLTYDDLRVNEKTREVRRGDKEVELTPREFDLLVYMLKHPQQVLTREQILSSVWGFDYIGDTNVVDVYIRYIRKKLDYPYEKQLIHTIRGVGYAIKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	228 (207)
Sequences:	79943 (56836)
Seq/√Len:	3950.3

ECOLI - CREB ARCA PHOP CUSR BAER YEDW OMPR QSEB KDPE BASR PHOB RSTA TORR FIMZ CPXR YGEK DPIA RCSB NARP NARL EVGA YHJB UVRY YJJQ DCUR BGLJ CSGD RCSA TORS BARA UHPA RSSB CHEB RCSC ARCB NTRC YPDB YEHT EVGS ZRAR GLRR ATOC RCSD CHEY
BACSU - YKOG YVRH YCBL BCER PHOP YXDJ YCLJ RESD YVCP CSSR YYCF YRKP DEGU DCTR YFIK CITT YXJL YBDJ CMPA MALR LIAR YVFU YHCZ YDFI DESR SP0A YESN GLNL LYTT CHEB NATR CHEV SP0F
HALSA - Q9HR09 CHEB Q9HRE5 Q9HNM3 BAT O51970 Q9HP91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_A	32_I	3.754	1.00
16_A	34_H	3.304	1.00
20_Q	32_I	3.262	1.00
9_V	39_G	2.809	1.00
40_L	68_R	2.709	1.00
37_T	59_G	2.587	1.00
31_T	48_Y	2.537	1.00
36_G	60_L	2.468	1.00
44_A	72_T	2.396	1.00
35_N	59_G	2.362	1.00
60_L	68_R	2.361	1.00
5_H	31_T	2.243	1.00
5_H	29_S	2.129	1.00
22_E	108_I	2.112	1.00
33_K	42_A	2.072	1.00
20_Q	24_E	2.052	1.00
26_E	112_L	2.017	1.00
56_M	84_R	1.944	1.00
34_H	38_E	1.926	1.00
90_K	110_E	1.880	1.00
53_L	65_V	1.875	1.00
194_N	197_D	1.845	1.00
31_T	42_A	1.821	1.00
66_L	78_V	1.792	1.00
7_L	33_K	1.778	1.00
35_N	38_E	1.773	1.00
80_L	93_G	1.752	1.00
68_R	72_T	1.709	1.00
159_R	162_D	1.693	1.00
70_R	99_N	1.675	1.00
80_L	98_A	1.667	1.00
67_R	96_I	1.640	1.00
42_A	46_G	1.638	1.00
31_T	46_G	1.635	1.00
87_I	107_E	1.617	1.00
36_G	65_V	1.610	1.00
60_L	64_E	1.585	1.00
177_R	197_D	1.576	1.00
100_D	114_R	1.560	1.00
61_S	64_E	1.556	1.00
4_G	119_L	1.553	1.00
42_A	45_E	1.515	1.00
166_Y	183_S	1.501	1.00
68_R	71_K	1.483	1.00
43_A	69_L	1.482	1.00
165_V	169_K	1.478	1.00
23_L	115_I	1.467	1.00
84_R	89_D	1.442	1.00
199_Y	202_Y	1.433	1.00
66_L	80_L	1.429	1.00
137_D	150_G	1.418	1.00
51_V	76_T	1.417	1.00
175_L	183_S	1.402	1.00
37_T	60_L	1.379	1.00
64_E	67_R	1.372	1.00
50_L	115_I	1.357	1.00
40_L	65_V	1.355	1.00
176_T	179_Q	1.340	1.00
13_E	34_H	1.334	1.00
42_A	48_Y	1.326	1.00
99_N	121_Q	1.300	1.00
79_I	118_A	1.294	1.00
10_E	16_A	1.288	1.00
55_V	63_L	1.274	1.00
11_D	54_D	1.270	1.00
5_H	46_G	1.260	1.00
99_N	118_A	1.251	1.00
63_L	93_G	1.239	1.00
53_L	66_L	1.239	1.00
41_D	45_E	1.237	1.00
73_D	76_T	1.233	1.00
40_L	60_L	1.229	1.00
166_Y	170_H	1.227	1.00
9_V	57_L	1.217	1.00
28_Y	116_R	1.213	1.00
38_E	41_D	1.210	1.00
55_V	80_L	1.196	1.00
146_E	153_E	1.189	1.00
6_I	28_Y	1.170	1.00
7_L	48_Y	1.166	1.00
200_I	204_R	1.166	1.00
37_T	41_D	1.162	1.00
160_E	206_K	1.161	1.00
141_N	144_T	1.159	1.00
33_K	39_G	1.159	1.00
38_E	42_A	1.158	1.00
92_T	96_I	1.158	1.00
86_S	89_D	1.152	1.00
112_L	116_R	1.145	1.00
7_L	39_G	1.118	1.00
139_R	148_R	1.111	1.00
63_L	92_T	1.106	1.00
209_Y	218_T	1.105	1.00
26_E	116_R	1.092	1.00
87_I	91_V	1.092	1.00
179_Q	183_S	1.065	1.00
198_V	201_R	1.064	1.00
27_G	116_R	1.050	1.00
39_G	65_V	1.043	1.00
95_D	116_R	1.033	1.00
33_K	38_E	1.027	1.00
7_L	42_A	1.026	1.00
4_G	28_Y	1.024	1.00
113_A	117_A	1.016	1.00
50_L	119_L	1.015	1.00
195_V	199_Y	1.013	1.00
91_V	95_D	1.007	1.00
40_L	44_A	1.004	1.00
17_R	32_I	0.994	1.00
39_G	43_A	0.991	1.00
166_Y	175_L	0.991	1.00
110_E	113_A	0.991	1.00
67_R	92_T	0.989	1.00
162_D	165_V	0.987	1.00
140_V	168_L	0.986	1.00
8_I	19_L	0.983	1.00
161_F	165_V	0.979	1.00
51_V	69_L	0.977	1.00
88_P	92_T	0.975	1.00
13_E	17_R	0.975	1.00
20_Q	30_V	0.972	1.00
194_N	198_V	0.958	1.00
53_L	78_V	0.957	1.00
90_K	103_T	0.954	1.00
178_E	193_T	0.953	1.00
14_K	18_V	0.951	1.00
7_L	43_A	0.940	1.00
9_V	33_K	0.932	1.00
63_L	96_I	0.930	1.00
175_L	179_Q	0.928	1.00
148_R	153_E	0.925	1.00
159_R	185_W	0.921	1.00
55_V	61_S	0.918	1.00
19_L	81_L	0.915	1.00
66_L	98_A	0.907	1.00
9_V	51_V	0.902	1.00
64_E	68_R	0.902	1.00
41_D	44_A	0.901	1.00
142_E	165_V	0.901	1.00
66_L	96_I	0.896	1.00
132_F	139_R	0.893	1.00
53_L	80_L	0.890	1.00
51_V	78_V	0.888	1.00
5_H	49_S	0.882	1.00
92_T	95_D	0.879	1.00
87_I	90_K	0.878	1.00
52_L	111_L	0.877	1.00
13_E	16_A	0.876	1.00
8_I	30_V	0.874	1.00
209_Y	214_Q	0.874	1.00
17_R	20_Q	0.859	1.00
79_I	114_R	0.857	1.00
55_V	89_D	0.857	1.00
118_A	121_Q	0.850	1.00
28_Y	112_L	0.842	1.00
158_P	162_D	0.841	1.00
85_D	103_T	0.836	1.00
21_L	25_Y	0.834	1.00
140_V	161_F	0.830	1.00
5_H	48_Y	0.829	1.00
208_D	214_Q	0.828	1.00
77_P	99_N	0.819	1.00
65_V	69_L	0.818	1.00
57_L	65_V	0.817	1.00
163_L	167_M	0.817	1.00
202_Y	205_K	0.809	1.00
43_A	73_D	0.807	1.00
110_E	114_R	0.804	1.00
67_R	71_K	0.800	1.00
194_N	201_R	0.795	1.00
108_I	112_L	0.788	1.00
193_T	197_D	0.788	1.00
148_R	151_D	0.787	1.00
178_E	182_S	0.783	1.00
43_A	76_T	0.783	1.00
91_V	109_E	0.782	1.00
15_I	106_F	0.781	1.00
43_A	48_Y	0.775	1.00
166_Y	180_I	0.773	1.00
19_L	111_L	0.772	1.00
36_G	40_L	0.770	1.00
60_L	65_V	0.769	1.00
55_V	84_R	0.763	1.00
89_D	92_T	0.763	1.00
52_L	115_I	0.760	1.00
107_E	110_E	0.759	1.00
117_A	120_R	0.753	1.00
145_R	162_D	0.748	1.00
52_L	81_L	0.743	1.00
56_M	83_A	0.741	1.00
9_V	65_V	0.733	1.00
88_P	109_E	0.729	1.00
179_Q	182_S	0.723	1.00
81_L	106_F	0.721	1.00
17_R	21_L	0.718	1.00
201_R	205_K	0.716	1.00
157_T	206_K	0.716	1.00
36_G	59_G	0.715	1.00
4_G	123_G	0.706	1.00
141_N	146_E	0.702	1.00
106_F	111_L	0.696	1.00
94_L	114_R	0.691	1.00
119_L	122_N	0.690	1.00
177_R	193_T	0.688	1.00
44_A	68_R	0.686	1.00
36_G	57_L	0.684	1.00
40_L	43_A	0.683	1.00
166_Y	169_K	0.681	1.00
69_L	78_V	0.678	1.00
18_V	22_E	0.677	1.00
93_G	98_A	0.671	1.00
22_E	112_L	0.670	1.00
211_Y	214_Q	0.663	1.00
198_V	202_Y	0.662	1.00
8_I	32_I	0.661	1.00
117_A	122_N	0.660	1.00
114_R	118_A	0.659	1.00
122_N	126_T	0.659	1.00
16_A	20_Q	0.658	1.00
138_L	149_R	0.656	1.00
169_K	183_S	0.656	1.00
109_E	113_A	0.654	1.00
10_E	57_L	0.649	1.00
95_D	113_A	0.647	1.00
52_L	79_I	0.645	1.00
69_L	74_S	0.644	1.00
8_I	20_Q	0.644	1.00
182_S	185_W	0.643	1.00
100_D	117_A	0.641	1.00
70_R	77_P	0.641	1.00
77_P	121_Q	0.641	1.00
204_R	209_Y	0.640	1.00
79_I	100_D	0.635	1.00
191_G	196_V	0.635	1.00
47_G	73_D	0.631	1.00
43_A	51_V	0.628	1.00
6_I	23_L	0.627	1.00
6_I	50_L	0.625	1.00
145_R	161_F	0.625	1.00
24_E	30_V	0.621	1.00
77_P	119_L	0.621	1.00
137_D	149_R	0.620	1.00
149_R	152_K	0.619	1.00
213_K	216_I	0.618	1.00
169_K	175_L	0.614	1.00
40_L	72_T	0.614	1.00
208_D	213_K	0.612	1.00
90_K	107_E	0.609	1.00
12_E	15_I	0.608	1.00
4_G	49_S	0.608	1.00
23_L	28_Y	0.606	1.00
12_E	83_A	0.604	1.00
44_A	73_D	0.603	1.00
11_D	82_T	0.600	1.00
15_I	18_V	0.598	1.00
106_F	110_E	0.595	1.00
87_I	109_E	0.592	1.00
113_A	116_R	0.592	1.00
55_V	93_G	0.592	1.00
75_Q	125_K	0.588	1.00
63_L	89_D	0.585	1.00
54_D	104_K	0.582	1.00
70_R	76_T	0.579	1.00
53_L	57_L	0.579	1.00
66_L	70_R	0.577	1.00
131_T	143_K	0.573	1.00
116_R	120_R	0.572	1.00
75_Q	124_T	0.572	1.00
82_T	90_K	0.571	1.00
195_V	200_I	0.569	1.00
162_D	166_Y	0.565	1.00
181_L	185_W	0.563	1.00
22_E	26_E	0.561	1.00
192_D	195_V	0.561	1.00
82_T	104_K	0.559	1.00
77_P	122_N	0.553	1.00
53_L	69_L	0.553	1.00
208_D	211_Y	0.552	1.00
140_V	165_V	0.552	1.00
197_D	200_I	0.549	1.00
167_M	200_I	0.546	1.00
77_P	125_K	0.546	1.00
38_E	59_G	0.543	1.00
164_L	167_M	0.541	1.00
88_P	91_V	0.540	1.00
132_F	141_N	0.539	1.00
43_A	65_V	0.538	1.00
214_Q	217_H	0.535	1.00
8_I	16_A	0.532	1.00
213_K	217_H	0.531	1.00
91_V	94_L	0.531	1.00
82_T	101_Y	0.529	1.00
11_D	57_L	0.529	1.00
149_R	208_D	0.527	1.00
69_L	76_T	0.523	1.00
18_V	21_L	0.523	1.00
128_D	131_T	0.522	1.00
191_G	195_V	0.521	1.00
135_Y	168_L	0.515	1.00
149_R	209_Y	0.514	1.00
35_N	57_L	0.513	1.00
157_T	160_E	0.513	1.00
83_A	105_P	0.510	1.00
177_R	181_L	0.507	1.00
153_E	218_T	0.506	1.00
24_E	29_S	0.505	1.00
159_R	199_Y	0.505	1.00
133_L	142_E	0.503	1.00
6_I	115_I	0.500	1.00
135_Y	138_L	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
1ys7A	2	0.9868	100	0.168	Contact Map
3r0jA	2	0.9693	100	0.183	Contact Map
1kgsA	1	0.9561	100	0.198	Contact Map
2gwrA	1	0.9693	100	0.202	Contact Map
4b09A	2	0.9167	100	0.206	Contact Map
2oqrA	2	0.9825	100	0.207	Contact Map
4kfcA	2	0.9781	100	0.226	Contact Map
2hqrA	2	0.943	100	0.232	Contact Map
3q9sA	1	0.9211	100	0.237	Contact Map
1p2fA	1	0.9474	100	0.248	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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