YCLJ - BACSU - GREMLIN Contacts

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YCLJ - Uncharacterized transcriptional regulatory protein YclJ

UniProt:	P94413	Sequences: MKILMIEDNVSVCTMTEMFFFKEGFEAEFVHDGLEGYQRFTEENWDLIILDIMLPSMDGVTICRKIRETSTVPIIMLTAKDTESDQVIGFEMGADDYVTKPFSPLTLVARIKAVIRRYKATGKAVIDEDMIETECFTINKKTREVLLNGEPVENLTPKEFDLLYYLVQNPRQVFSREQLLEQVWGYQFYGDERTVDVHIKRLRKKLASEDKPFLYTVWGVGYKFDED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	227 (207)
Sequences:	78776 (56560)
Seq/√Len:	3931.2

ECOLI - ARCA YEDW RSTA CREB KDPE TORR BAER CUSR PHOP QSEB OMPR BASR CPXR PHOB UVRY DPIA DCUR EVGA YJJQ YHJB FIMZ RCSB NARP YGEK NARL BARA UHPA BGLJ CHEB YEHT RSSB RCSC TORS CSGD RCSA ARCB YPDB NTRC GLRR ZRAR ATOC EVGS RCSD CHEY
BACSU - YCLJ YXDJ YVRH YVCP BCER YYCF YCBL PHOP YRKP CSSR RESD YKOG CITT YFIK YBDJ DCTR MALR DEGU YDFI CMPA LIAR YXJL YVFU DESR YHCZ GLNL CHEB YESN LYTT SP0A NATR CHEV SP0F CHEY CCDB
HALSA - CHEB Q9HR09 Q9HNM3 Q9HRE5 BAT O51970 Q9HP91 F2Z6H5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_C	29_F	3.770	1.00
13_C	31_H	3.395	1.00
17_E	29_F	3.320	1.00
6_I	36_G	2.830	1.00
37_Y	65_K	2.785	1.00
34_L	56_S	2.586	1.00
28_E	45_W	2.472	1.00
33_G	57_M	2.454	1.00
41_T	69_T	2.401	1.00
57_M	65_K	2.400	1.00
32_D	56_S	2.332	1.00
30_V	39_R	2.113	1.00
19_F	104_P	2.045	1.00
17_E	21_F	2.038	1.00
2_K	26_E	1.993	1.00
53_M	80_K	1.934	1.00
86_Q	106_T	1.922	1.00
23_E	108_V	1.903	1.00
63_C	74_I	1.893	1.00
50_L	62_I	1.882	1.00
31_H	35_E	1.866	1.00
193_R	196_D	1.861	1.00
76_M	89_G	1.829	1.00
158_K	161_D	1.794	1.00
28_E	39_R	1.770	1.00
2_K	28_E	1.757	1.00
39_R	43_E	1.746	1.00
32_D	35_E	1.727	1.00
65_K	69_T	1.725	1.00
76_M	94_A	1.725	1.00
4_L	30_V	1.723	1.00
28_E	43_E	1.704	1.00
67_R	95_D	1.667	1.00
83_E	103_S	1.648	1.00
33_G	62_I	1.595	1.00
58_D	61_T	1.591	1.00
64_R	92_M	1.570	1.00
96_D	110_R	1.562	1.00
57_M	61_T	1.561	1.00
135_C	148_N	1.547	1.00
39_R	42_E	1.533	1.00
164_Y	168_Q	1.520	1.00
40_F	66_I	1.519	1.00
65_K	68_E	1.490	1.00
20_F	111_I	1.470	1.00
165_Y	182_Q	1.468	1.00
174_F	182_Q	1.451	1.00
80_K	85_D	1.450	1.00
48_I	72_V	1.447	1.00
198_H	201_R	1.445	1.00
95_D	117_R	1.435	1.00
63_C	76_M	1.433	1.00
34_L	57_M	1.413	1.00
37_Y	62_I	1.393	1.00
61_T	64_R	1.371	1.00
176_R	196_D	1.365	1.00
165_Y	169_N	1.364	1.00
39_R	45_W	1.348	1.00
175_S	178_Q	1.321	1.00
47_L	111_I	1.319	1.00
75_I	114_V	1.316	1.00
95_D	114_V	1.313	1.00
52_I	60_V	1.307	1.00
10_V	31_H	1.272	1.00
7_E	13_C	1.257	1.00
6_I	54_L	1.250	1.00
37_Y	57_M	1.236	1.00
38_Q	42_E	1.229	1.00
8_D	51_D	1.225	1.00
159_E	205_K	1.224	1.00
52_I	76_M	1.218	1.00
25_F	112_K	1.215	1.00
50_L	63_C	1.198	1.00
35_E	39_R	1.183	1.00
35_E	38_Q	1.181	1.00
108_V	112_K	1.178	1.00
30_V	36_G	1.176	1.00
34_L	38_Q	1.174	1.00
4_L	45_W	1.170	1.00
201_R	204_K	1.166	1.00
82_T	85_D	1.158	1.00
137_T	146_L	1.150	1.00
60_V	89_G	1.150	1.00
60_V	88_I	1.144	1.00
139_N	142_T	1.139	1.00
88_I	92_M	1.137	1.00
4_L	36_G	1.124	1.00
130_M	137_T	1.114	1.00
83_E	87_V	1.107	1.00
132_E	137_T	1.086	1.00
144_E	151_P	1.079	1.00
2_K	43_E	1.072	1.00
3_I	25_F	1.072	1.00
36_G	62_I	1.072	1.00
4_L	39_R	1.070	1.00
37_Y	41_T	1.069	1.00
64_R	88_I	1.057	1.00
87_V	91_E	1.054	1.00
24_G	112_K	1.049	1.00
109_A	113_A	1.049	1.00
106_T	109_A	1.044	1.00
161_D	164_Y	1.039	1.00
165_Y	174_F	1.036	1.00
178_Q	182_Q	1.034	1.00
14_T	29_F	1.032	1.00
140_K	164_Y	1.021	1.00
47_L	115_I	1.017	1.00
91_E	112_K	1.012	1.00
30_V	35_E	1.012	1.00
197_V	200_K	1.008	1.00
5_M	16_T	0.997	1.00
84_S	88_I	0.987	1.00
36_G	40_F	0.982	1.00
160_F	164_Y	0.973	1.00
146_L	151_P	0.965	1.00
138_I	167_V	0.963	1.00
48_I	66_I	0.962	1.00
23_E	112_K	0.958	1.00
4_L	40_F	0.957	1.00
48_I	74_I	0.951	1.00
199_I	203_R	0.950	1.00
208_S	216_T	0.948	1.00
60_V	92_M	0.948	1.00
86_Q	99_T	0.948	1.00
193_R	197_V	0.947	1.00
10_V	14_T	0.946	1.00
174_F	178_Q	0.945	1.00
143_R	220_V	0.942	1.00
83_E	86_Q	0.939	1.00
6_I	48_I	0.938	1.00
17_E	27_A	0.934	1.00
11_S	15_M	0.932	1.00
52_I	58_D	0.928	1.00
61_T	65_K	0.927	1.00
88_I	91_E	0.925	1.00
6_I	30_V	0.924	1.00
73_P	95_D	0.924	1.00
50_L	74_I	0.911	1.00
38_Q	41_T	0.909	1.00
177_E	192_E	0.908	1.00
194_T	198_H	0.903	1.00
50_L	76_M	0.903	1.00
63_C	92_M	0.898	1.00
75_I	110_R	0.898	1.00
63_C	94_A	0.896	1.00
16_T	77_L	0.894	1.00
14_T	17_E	0.887	1.00
114_V	117_R	0.882	1.00
151_P	154_N	0.873	1.00
190_G	194_T	0.872	1.00
49_I	107_L	0.871	1.00
5_M	27_A	0.859	1.00
157_P	161_D	0.847	1.00
52_I	85_D	0.844	1.00
18_M	22_K	0.842	1.00
10_V	13_C	0.841	1.00
193_R	200_K	0.841	1.00
81_D	99_T	0.838	1.00
25_F	108_V	0.837	1.00
64_R	68_E	0.834	1.00
208_S	212_P	0.831	1.00
40_F	70_S	0.829	1.00
54_L	62_I	0.822	1.00
129_D	141_K	0.818	1.00
62_I	66_I	0.816	1.00
162_L	166_L	0.812	1.00
138_I	160_F	0.805	1.00
104_P	108_V	0.804	1.00
73_P	121_T	0.801	1.00
106_T	110_R	0.800	1.00
87_V	105_L	0.790	1.00
40_F	45_W	0.788	1.00
85_D	88_I	0.785	1.00
57_M	62_I	0.783	1.00
209_E	212_P	0.776	1.00
44_N	70_S	0.773	1.00
146_L	149_G	0.773	1.00
40_F	72_V	0.773	1.00
177_E	181_E	0.770	1.00
14_T	18_M	0.770	1.00
49_I	111_I	0.769	1.00
73_P	117_R	0.768	1.00
132_E	135_C	0.763	1.00
102_F	107_L	0.761	1.00
16_T	107_L	0.753	1.00
52_I	80_K	0.753	1.00
113_A	116_R	0.752	1.00
103_S	106_T	0.748	1.00
165_Y	179_L	0.747	1.00
49_I	77_L	0.747	1.00
156_T	205_K	0.745	1.00
96_D	113_A	0.744	1.00
216_T	220_V	0.744	1.00
12_V	102_F	0.743	1.00
33_G	37_Y	0.737	1.00
77_L	102_F	0.736	1.00
6_I	62_I	0.732	1.00
197_V	201_R	0.720	1.00
71_T	121_T	0.719	1.00
33_G	56_S	0.719	1.00
53_M	79_A	0.715	1.00
66_I	74_I	0.713	1.00
200_K	204_K	0.712	1.00
115_I	118_Y	0.711	1.00
90_F	110_R	0.711	1.00
147_L	150_E	0.710	1.00
130_M	139_N	0.710	1.00
207_A	210_D	0.706	1.00
113_A	118_Y	0.706	1.00
178_Q	181_E	0.705	1.00
84_S	105_L	0.704	1.00
136_F	147_L	0.698	1.00
41_T	65_K	0.696	1.00
67_R	73_P	0.694	1.00
91_E	109_A	0.686	1.00
89_G	94_A	0.685	1.00
5_M	17_E	0.685	1.00
37_Y	40_F	0.684	1.00
143_R	161_D	0.682	1.00
40_F	48_I	0.678	1.00
15_M	19_F	0.676	1.00
143_R	160_F	0.673	1.00
105_L	109_A	0.671	1.00
2_K	46_D	0.663	1.00
165_Y	168_Q	0.662	1.00
118_Y	122_G	0.661	1.00
13_C	17_E	0.659	1.00
33_G	54_L	0.653	1.00
75_I	96_D	0.652	1.00
37_Y	69_T	0.650	1.00
110_R	114_V	0.642	1.00
19_F	108_V	0.640	1.00
49_I	75_I	0.640	1.00
190_G	195_V	0.635	1.00
5_M	29_F	0.635	1.00
83_E	105_L	0.628	1.00
168_Q	182_Q	0.628	1.00
7_E	54_L	0.625	1.00
168_Q	174_F	0.623	1.00
192_E	196_D	0.623	1.00
67_R	72_V	0.618	1.00
203_R	208_S	0.618	1.00
112_K	116_R	0.617	1.00
73_P	115_I	0.613	1.00
86_Q	103_S	0.611	1.00
176_R	180_L	0.610	1.00
60_V	85_D	0.607	1.00
78_T	86_Q	0.606	1.00
73_P	118_Y	0.605	1.00
212_P	215_Y	0.602	1.00
63_C	67_R	0.597	1.00
21_F	27_A	0.597	1.00
166_L	199_I	0.597	1.00
84_S	87_V	0.597	1.00
9_N	79_A	0.596	1.00
50_L	54_L	0.596	1.00
176_R	192_E	0.596	1.00
102_F	106_T	0.596	1.00
12_V	15_M	0.593	1.00
158_K	198_H	0.586	1.00
9_N	12_V	0.585	1.00
161_D	165_Y	0.581	1.00
41_T	70_S	0.581	1.00
175_S	180_L	0.580	1.00
66_I	72_V	0.578	1.00
109_A	112_K	0.572	1.00
71_T	120_A	0.571	1.00
211_K	219_G	0.568	1.00
40_F	62_I	0.564	1.00
52_I	89_G	0.564	1.00
135_C	147_L	0.560	1.00
79_A	101_P	0.555	1.00
198_H	202_L	0.553	1.00
87_V	90_F	0.552	1.00
156_T	159_E	0.551	1.00
20_F	25_F	0.548	1.00
191_D	194_T	0.547	1.00
5_M	13_C	0.545	1.00
147_L	209_E	0.544	1.00
145_V	152_V	0.544	1.00
35_E	56_S	0.543	1.00
131_I	140_K	0.543	1.00
113_A	117_R	0.540	1.00
207_A	212_P	0.536	1.00
3_I	47_L	0.535	1.00
25_F	115_I	0.534	1.00
3_I	20_F	0.532	1.00
50_L	66_I	0.530	1.00
165_Y	178_Q	0.529	1.00
81_D	101_P	0.528	1.00
19_F	23_E	0.525	1.00
162_L	167_V	0.524	1.00
145_V	149_G	0.518	1.00
138_I	164_Y	0.517	1.00
8_D	78_T	0.517	1.00
199_I	202_L	0.516	1.00
2_K	45_W	0.514	1.00
130_M	135_C	0.513	1.00
91_E	96_D	0.508	1.00
51_D	100_K	0.508	1.00
6_I	33_G	0.507	1.00
21_F	26_E	0.505	1.00
67_R	70_S	0.504	1.00
180_L	183_V	0.504	1.00
32_D	54_L	0.503	1.00
111_I	115_I	0.502	1.00
117_R	121_T	0.502	1.00
189_Y	194_T	0.502	1.00
159_E	162_L	0.501	1.00
18_M	21_F	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
3r0jA	2	0.9604	100	0.19	Contact Map
2gwrA	1	0.9648	100	0.2	Contact Map
4b09A	2	0.9119	100	0.204	Contact Map
1ys7A	2	0.9824	100	0.205	Contact Map
2oqrA	2	0.9824	100	0.208	Contact Map
4kfcA	2	0.9736	100	0.222	Contact Map
1kgsA	1	0.9515	100	0.224	Contact Map
2hqrA	2	0.9427	100	0.252	Contact Map
1p2fA	1	0.9339	100	0.254	Contact Map
3q9sA	1	0.9163	100	0.257	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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