YBDJ - BACSU - GREMLIN Contacts

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YBDJ - Uncharacterized transcriptional regulatory protein YbdJ

UniProt:	O31432	Sequences: MKGYRILIVEDDVMIGDLLQKILQREGYRVIWKTDGADVLSVIQKVDLVIMDVMLPGEDGYQMSAKIKKLGLGIPVIFLSARNDMDSKLQGLQIGEDYMVKPFDPRELLLRMRNMLEHHYGTFTQIKHLYIDAVTKKVFNESLHDEVLFTAIERKIFFYLYENRDSILTKEHFFEYLWQLEDRNPNIVNVHIKKIRAKINDQAGEMIENIYGEGYRLNTVVKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	223 (203)
Sequences:	75703 (54009)
Seq/√Len:	3790.7

ECOLI - ARCA YEDW CREB QSEB PHOB PHOP CUSR BASR TORR BAER OMPR CPXR KDPE FIMZ YJJQ CSGD YGEK UVRY NARP RSTA RCSB DPIA DCUR NARL EVGA YHJB BGLJ RCSA TORS RCSC UHPA CHEB ARCB BARA YPDB RSSB NTRC EVGS YEHT GLRR RCSD ZRAR ATOC
BACSU - YBDJ YVRH YKOG YCLJ CSSR PHOP YCBL YRKP RESD YVCP YYCF YXDJ DEGU YFIK BCER YXJL DCTR CMPA CITT LIAR MALR YESN YHCZ YVFU YDFI DESR SP0A CHEB LYTT GLNL NATR CHEV
HALSA - Q9HR09 Q9HNM3 CHEB Q9HRE5 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_G	32_W	3.752	1.00
16_G	34_T	3.328	1.00
20_Q	32_W	3.218	1.00
9_V	39_V	2.755	1.00
37_A	57_G	2.646	1.00
40_L	66_K	2.611	1.00
31_I	46_V	2.582	1.00
44_Q	70_L	2.507	1.00
36_G	58_E	2.481	1.00
35_D	57_G	2.477	1.00
58_E	66_K	2.386	1.00
5_R	31_I	2.180	1.00
5_R	29_R	2.164	1.00
33_K	42_V	2.069	1.00
22_I	105_P	2.056	1.00
20_Q	24_Q	1.983	1.00
88_K	107_E	1.962	1.00
152_I	155_K	1.931	1.00
34_T	38_D	1.930	1.00
64_S	76_V	1.911	1.00
51_M	63_M	1.889	1.00
54_M	82_R	1.887	1.00
186_N	189_N	1.879	1.00
26_E	109_L	1.845	1.00
78_F	91_G	1.817	1.00
7_L	33_K	1.767	1.00
35_D	38_D	1.754	1.00
85_M	104_D	1.734	1.00
66_K	70_L	1.692	1.00
68_K	96_E	1.682	1.00
59_D	62_Q	1.668	1.00
158_F	162_E	1.619	1.00
31_I	42_V	1.612	1.00
58_E	62_Q	1.578	1.00
36_G	63_M	1.554	1.00
97_D	111_R	1.532	1.00
23_L	112_M	1.530	1.00
159_Y	176_Y	1.527	1.00
71_G	74_I	1.516	1.00
4_Y	116_L	1.516	1.00
66_K	69_K	1.510	1.00
128_H	141_E	1.506	1.00
64_S	78_F	1.493	1.00
170_K	189_N	1.475	1.00
43_I	67_I	1.458	1.00
42_V	46_V	1.451	1.00
42_V	45_K	1.431	1.00
82_R	87_S	1.424	1.00
191_H	194_K	1.422	1.00
40_L	63_M	1.416	1.00
62_Q	65_A	1.413	1.00
49_V	74_I	1.399	1.00
153_E	198_K	1.397	1.00
96_E	118_H	1.395	1.00
53_V	78_F	1.378	1.00
37_A	58_E	1.376	1.00
48_L	112_M	1.371	1.00
168_L	176_Y	1.360	1.00
77_I	115_M	1.353	1.00
169_T	172_H	1.346	1.00
159_Y	163_N	1.343	1.00
10_E	16_G	1.328	1.00
65_A	94_I	1.326	1.00
51_M	64_S	1.311	1.00
53_V	61_Y	1.283	1.00
194_K	197_A	1.280	1.00
9_V	55_L	1.257	1.00
41_S	45_K	1.256	1.00
11_D	52_D	1.249	1.00
40_L	58_E	1.243	1.00
96_E	115_M	1.240	1.00
7_L	46_V	1.233	1.00
33_K	39_V	1.217	1.00
125_Q	130_Y	1.215	1.00
13_V	34_T	1.215	1.00
38_D	41_S	1.209	1.00
37_A	41_S	1.197	1.00
28_Y	113_R	1.190	1.00
38_D	42_V	1.185	1.00
65_A	90_Q	1.171	1.00
61_Y	90_Q	1.161	1.00
84_D	87_S	1.158	1.00
7_L	39_V	1.151	1.00
6_I	28_Y	1.136	1.00
27_G	113_R	1.130	1.00
93_Q	113_R	1.126	1.00
109_L	113_R	1.119	1.00
172_H	176_Y	1.109	1.00
132_D	135_T	1.100	1.00
107_E	110_L	1.098	1.00
7_L	42_V	1.088	1.00
43_I	71_G	1.078	1.00
26_E	113_R	1.052	1.00
171_E	185_P	1.039	1.00
154_R	158_F	1.038	1.00
39_V	63_M	1.033	1.00
7_L	43_I	1.032	1.00
155_K	158_F	1.032	1.00
61_Y	91_G	1.031	1.00
90_Q	94_I	1.028	1.00
159_Y	168_L	1.026	1.00
130_Y	139_F	1.019	1.00
40_L	44_Q	1.016	1.00
85_M	89_L	1.014	1.00
190_V	193_K	1.009	1.00
129_L	132_D	1.003	1.00
48_L	116_L	1.000	1.00
110_L	114_N	0.999	1.00
137_K	146_E	0.996	1.00
39_V	43_I	0.995	1.00
89_L	93_Q	0.992	1.00
9_V	49_V	0.988	1.00
86_D	90_Q	0.982	1.00
201_D	209_N	0.973	1.00
49_V	67_I	0.972	1.00
17_D	32_W	0.969	1.00
61_Y	94_I	0.962	1.00
187_I	191_H	0.951	1.00
186_N	190_V	0.951	1.00
13_V	17_D	0.950	1.00
49_V	76_V	0.939	1.00
64_S	94_I	0.938	1.00
19_L	79_L	0.929	1.00
41_S	44_Q	0.929	1.00
51_M	76_V	0.927	1.00
88_K	100_V	0.922	1.00
51_M	78_F	0.922	1.00
85_M	88_K	0.917	1.00
33_K	38_D	0.916	1.00
50_I	108_L	0.913	1.00
90_Q	93_Q	0.913	1.00
53_V	59_D	0.912	1.00
14_M	18_L	0.904	1.00
77_I	111_R	0.903	1.00
8_I	19_L	0.893	1.00
62_Q	66_K	0.886	1.00
9_V	33_K	0.886	1.00
13_V	16_G	0.880	1.00
159_Y	173_F	0.880	1.00
151_A	155_K	0.876	1.00
5_R	46_V	0.874	1.00
8_I	30_V	0.873	1.00
20_Q	30_V	0.867	1.00
17_D	20_Q	0.866	1.00
83_N	100_V	0.858	1.00
168_L	172_H	0.854	1.00
55_L	63_M	0.851	1.00
133_A	158_F	0.850	1.00
115_M	118_H	0.850	1.00
131_I	161_Y	0.849	1.00
75_P	96_E	0.847	1.00
28_Y	109_L	0.839	1.00
53_V	87_S	0.835	1.00
4_Y	28_Y	0.828	1.00
89_L	106_R	0.825	1.00
65_A	69_K	0.820	1.00
43_I	46_V	0.810	1.00
107_E	111_R	0.804	1.00
19_L	108_L	0.801	1.00
114_N	117_E	0.798	1.00
192_I	196_R	0.796	1.00
186_N	193_K	0.794	1.00
4_Y	120_Y	0.793	1.00
5_R	47_D	0.793	1.00
171_E	175_E	0.791	1.00
21_K	25_R	0.790	1.00
129_L	138_V	0.788	1.00
139_F	146_E	0.784	1.00
150_T	198_K	0.784	1.00
63_M	67_I	0.783	1.00
105_P	109_L	0.777	1.00
204_G	212_G	0.775	1.00
193_K	197_A	0.773	1.00
54_M	81_A	0.773	1.00
172_H	175_E	0.763	1.00
58_E	63_M	0.762	1.00
9_V	63_M	0.758	1.00
190_V	194_K	0.758	1.00
201_D	205_E	0.757	1.00
136_K	213_E	0.757	1.00
103_F	108_L	0.755	1.00
50_I	79_L	0.754	1.00
36_G	40_L	0.754	1.00
138_V	142_S	0.753	1.00
53_V	82_R	0.752	1.00
92_L	111_R	0.749	1.00
8_I	20_Q	0.748	1.00
87_S	90_Q	0.748	1.00
202_Q	205_E	0.744	1.00
43_I	74_I	0.741	1.00
129_L	140_N	0.735	1.00
17_D	21_K	0.729	1.00
67_I	72_L	0.727	1.00
44_Q	71_G	0.726	1.00
67_I	76_V	0.723	1.00
162_E	176_Y	0.722	1.00
97_D	114_N	0.716	1.00
104_D	107_E	0.715	1.00
86_D	106_R	0.709	1.00
114_N	119_H	0.708	1.00
200_N	203_A	0.701	1.00
93_Q	110_L	0.698	1.00
139_F	142_S	0.692	1.00
75_P	118_H	0.688	1.00
77_I	97_D	0.688	1.00
44_Q	66_K	0.685	1.00
10_E	55_L	0.685	1.00
36_G	57_G	0.685	1.00
119_H	123_F	0.683	1.00
40_L	43_I	0.683	1.00
116_L	119_H	0.681	1.00
106_R	110_L	0.676	1.00
79_L	103_F	0.675	1.00
170_K	185_P	0.674	1.00
204_G	207_I	0.674	1.00
8_I	32_W	0.669	1.00
50_I	77_I	0.669	1.00
209_N	213_E	0.667	1.00
86_D	89_L	0.663	1.00
126_I	129_L	0.662	1.00
15_I	103_F	0.650	1.00
131_I	154_R	0.649	1.00
85_M	106_R	0.647	1.00
16_G	20_Q	0.640	1.00
73_G	122_T	0.640	1.00
128_H	140_N	0.638	1.00
152_I	191_H	0.636	1.00
80_S	88_K	0.634	1.00
159_Y	162_E	0.633	1.00
111_R	115_M	0.632	1.00
18_L	22_I	0.632	1.00
156_I	160_L	0.628	1.00
43_I	49_V	0.625	1.00
196_R	201_D	0.625	1.00
128_H	132_D	0.623	1.00
50_I	112_M	0.621	1.00
130_Y	142_S	0.619	1.00
61_Y	87_S	0.610	1.00
185_P	189_N	0.609	1.00
12_D	15_I	0.605	1.00
182_D	185_P	0.605	1.00
75_P	116_L	0.602	1.00
68_K	75_P	0.599	1.00
162_E	168_L	0.598	1.00
12_D	81_A	0.595	1.00
46_V	71_G	0.595	1.00
51_M	55_L	0.591	1.00
53_V	91_G	0.591	1.00
68_K	74_I	0.590	1.00
43_I	63_M	0.587	1.00
23_L	28_Y	0.583	1.00
75_P	122_T	0.583	1.00
167_I	213_E	0.582	1.00
81_A	102_P	0.581	1.00
64_S	68_K	0.581	1.00
22_I	109_L	0.579	1.00
204_G	208_E	0.577	1.00
36_G	55_L	0.574	1.00
6_I	23_L	0.570	1.00
24_Q	29_R	0.569	1.00
4_Y	47_D	0.568	1.00
136_K	155_K	0.567	1.00
24_Q	30_V	0.567	1.00
88_K	104_D	0.566	1.00
73_G	121_G	0.566	1.00
189_N	192_I	0.564	1.00
129_L	133_A	0.563	1.00
103_F	107_E	0.562	1.00
89_L	92_L	0.561	1.00
200_N	205_E	0.561	1.00
160_L	192_I	0.559	1.00
15_I	18_L	0.553	1.00
6_I	48_L	0.550	1.00
40_L	70_L	0.548	1.00
110_L	113_R	0.548	1.00
155_K	159_Y	0.543	1.00
125_Q	128_H	0.542	1.00
153_E	156_I	0.540	1.00
205_E	208_E	0.539	1.00
114_N	118_H	0.537	1.00
11_D	80_S	0.535	1.00
80_S	98_Y	0.535	1.00
113_R	117_E	0.534	1.00
67_I	71_G	0.533	1.00
145_D	148_L	0.533	1.00
127_K	130_Y	0.530	1.00
8_I	16_G	0.516	1.00
91_G	98_Y	0.515	1.00
135_T	139_F	0.515	1.00
67_I	74_I	0.515	1.00
33_K	36_G	0.514	1.00
9_V	36_G	0.512	1.00
156_I	177_L	0.511	1.00
35_D	55_L	0.511	1.00
200_N	204_G	0.510	1.00
135_T	138_V	0.509	1.00
146_E	209_N	0.509	1.00
6_I	112_M	0.508	1.00
160_L	163_N	0.508	1.00
9_V	51_M	0.506	1.00
209_N	212_G	0.506	1.00
75_P	119_H	0.502	1.00
163_N	176_Y	0.500	1.00
183_R	188_V	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	0.9552	100	0.275	Contact Map
1ys7A	2	0.9686	100	0.28	Contact Map
2gwrA	1	0.9641	100	0.288	Contact Map
1kgsA	1	0.9507	100	0.298	Contact Map
1p2fA	1	0.9596	100	0.301	Contact Map
4b09A	2	0.9238	100	0.301	Contact Map
3q9sA	1	0.9193	100	0.305	Contact Map
2oqrA	2	0.9552	100	0.311	Contact Map
4kfcA	2	0.9552	100	0.313	Contact Map
2hqrA	2	0.9596	100	0.316	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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