YCBL - BACSU - GREMLIN Contacts

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YCBL - Uncharacterized transcriptional regulatory protein YcbL

UniProt:	P42244	Sequences: MLVEDDHSISEMVDHYLTKEGFGIVHAFDGEEGIRLFQQGSYDLVLLDIMLPKLNGMDFLKIIREKSNIPVLMISAKDGDVDKALGLGFGADDYIAKPFSMIELTARVKAAIRRATQYSAEEPAVNKVIRIHQLAIDIDNVSVLKNGEPLQLTSTEWQLLCLFASNPKKVFTKEQIYRSVWNEEYFDDQNIINVHMRRLREKIEDDPSSPQYIKTLWGIGYKLGEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	226 (199)
Sequences:	74740 (53091)
Seq/√Len:	3763.5

ECOLI - CREB ARCA BAER KDPE RSTA YEDW CPXR OMPR CUSR QSEB PHOP TORR PHOB BASR DPIA FIMZ UVRY DCUR NARL YGEK YHJB EVGA NARP RCSB YJJQ BGLJ UHPA BARA RCSA CSGD RSSB TORS ARCB CHEB RCSC YEHT EVGS YPDB NTRC GLRR ZRAR ATOC RCSD
BACSU - YCBL YVRH YYCF YVCP YRKP YXDJ YKOG PHOP RESD BCER CSSR YCLJ CITT YFIK DCTR MALR CMPA YXJL DEGU LIAR YBDJ YVFU YDFI DESR YHCZ GLNL YESN CHEB LYTT SP0A NATR CHEV
HALSA - CHEB Q9HR09 Q9HNM3 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
10_S	26_H	3.780	1.00
10_S	28_F	3.308	1.00
14_D	26_H	3.223	1.00
3_V	33_G	2.733	1.00
34_I	62_I	2.715	1.00
31_E	53_K	2.626	1.00
25_V	42_Y	2.615	1.00
30_G	54_L	2.454	1.00
54_L	62_I	2.420	1.00
29_D	53_K	2.415	1.00
38_Q	66_K	2.409	1.00
16_Y	101_M	2.135	1.00
14_D	18_T	2.086	1.00
20_E	105_T	2.075	1.00
27_A	36_L	2.020	1.00
50_M	77_K	1.923	1.00
83_K	103_E	1.903	1.00
28_F	32_E	1.893	1.00
190_N	193_N	1.872	1.00
47_L	59_F	1.865	1.00
155_T	158_Q	1.818	1.00
25_V	36_L	1.813	1.00
60_L	71_V	1.786	1.00
29_D	32_E	1.780	1.00
73_M	86_G	1.756	1.00
36_L	40_G	1.723	1.00
62_I	66_K	1.694	1.00
173_K	193_N	1.686	1.00
64_R	92_D	1.681	1.00
80_D	100_S	1.667	1.00
54_L	58_D	1.631	1.00
162_L	179_S	1.621	1.00
73_M	91_A	1.610	1.00
161_C	165_S	1.597	1.00
25_V	40_G	1.594	1.00
30_G	59_F	1.568	1.00
93_D	107_R	1.562	1.00
36_L	39_Q	1.547	1.00
130_R	135_A	1.531	1.00
55_N	58_D	1.519	1.00
17_L	108_V	1.517	1.00
77_K	82_D	1.501	1.00
61_K	89_F	1.467	1.00
195_H	198_R	1.466	1.00
37_F	63_I	1.465	1.00
171_F	179_S	1.465	1.00
62_I	65_E	1.464	1.00
133_Q	146_N	1.449	1.00
45_V	69_I	1.423	1.00
31_E	54_L	1.414	1.00
58_D	61_K	1.404	1.00
172_T	175_Q	1.397	1.00
60_L	73_M	1.396	1.00
44_L	108_V	1.391	1.00
34_I	59_F	1.370	1.00
7_H	28_F	1.365	1.00
72_L	111_A	1.360	1.00
36_L	42_Y	1.296	1.00
49_I	57_M	1.296	1.00
128_V	135_A	1.288	1.00
92_D	114_R	1.275	1.00
4_E	10_S	1.270	1.00
156_E	202_K	1.258	1.00
47_L	60_L	1.252	1.00
34_I	54_L	1.248	1.00
35_R	39_Q	1.247	1.00
162_L	166_N	1.244	1.00
22_F	109_K	1.238	1.00
5_D	48_D	1.213	1.00
92_D	111_A	1.211	1.00
32_E	36_L	1.210	1.00
3_V	51_L	1.198	1.00
32_E	35_R	1.191	1.00
57_M	86_G	1.190	1.00
49_I	73_M	1.186	1.00
27_A	33_G	1.178	1.00
79_G	82_D	1.169	1.00
105_T	109_K	1.157	1.00
175_Q	179_S	1.155	1.00
80_D	84_A	1.154	1.00
137_D	140_N	1.139	1.00
31_E	35_R	1.139	1.00
21_G	109_K	1.137	1.00
57_M	85_L	1.136	1.00
135_A	144_L	1.124	1.00
20_E	109_K	1.113	1.00
88_G	109_K	1.110	1.00
157_W	161_C	1.108	1.00
44_L	112_I	1.103	1.00
85_L	89_F	1.095	1.00
142_S	149_P	1.095	1.00
174_E	189_Q	1.077	1.00
162_L	171_F	1.073	1.00
194_V	197_R	1.064	1.00
106_A	110_A	1.061	1.00
191_I	195_H	1.048	1.00
81_V	85_L	1.046	1.00
103_E	106_A	1.037	1.00
34_I	38_Q	1.036	1.00
84_A	88_G	1.031	1.00
190_N	194_V	1.024	1.00
27_A	32_E	1.014	1.00
158_Q	161_C	1.012	1.00
33_G	59_F	1.010	1.00
138_I	161_C	1.005	1.00
61_K	85_L	1.005	1.00
11_E	26_H	0.986	1.00
83_K	96_A	0.982	1.00
33_G	37_F	0.981	1.00
47_L	71_V	0.971	1.00
57_M	89_F	0.971	1.00
136_I	164_A	0.966	1.00
144_L	149_P	0.966	1.00
13_V	74_I	0.963	1.00
206_D	209_S	0.963	1.00
14_D	24_I	0.951	1.00
154_S	158_Q	0.949	1.00
3_V	27_A	0.948	1.00
130_R	133_Q	0.946	1.00
49_I	55_N	0.945	1.00
7_H	11_E	0.941	1.00
8_S	12_M	0.937	1.00
45_V	63_I	0.935	1.00
60_L	89_F	0.929	1.00
111_A	114_R	0.923	1.00
1_M	27_A	0.920	1.00
58_D	62_I	0.912	1.00
3_V	45_V	0.907	1.00
2_L	13_V	0.904	1.00
196_M	200_R	0.902	1.00
206_D	210_P	0.899	1.00
136_I	157_W	0.898	1.00
46_L	104_L	0.886	1.00
2_L	24_I	0.885	1.00
171_F	175_Q	0.882	1.00
47_L	73_M	0.882	1.00
60_L	91_A	0.881	1.00
22_F	105_T	0.880	1.00
80_D	83_K	0.879	1.00
35_R	38_Q	0.872	1.00
189_Q	193_N	0.867	1.00
11_E	14_D	0.866	1.00
78_D	96_A	0.865	1.00
190_N	197_R	0.861	1.00
7_H	10_S	0.860	1.00
85_L	88_G	0.858	1.00
15_H	19_K	0.853	1.00
51_L	59_F	0.850	1.00
45_V	71_V	0.850	1.00
128_V	137_D	0.844	1.00
162_L	176_I	0.832	1.00
205_D	211_Q	0.831	1.00
198_R	201_E	0.826	1.00
103_E	107_R	0.822	1.00
70_P	92_D	0.820	1.00
197_R	201_E	0.819	1.00
49_I	77_K	0.817	1.00
72_L	107_R	0.813	1.00
101_M	105_T	0.809	1.00
194_V	198_R	0.804	1.00
141_V	158_Q	0.802	1.00
49_I	82_D	0.800	1.00
54_L	59_F	0.797	1.00
59_F	63_I	0.796	1.00
37_F	69_I	0.793	1.00
84_A	102_I	0.786	1.00
74_I	99_F	0.781	1.00
153_T	202_K	0.779	1.00
13_V	104_L	0.778	1.00
173_K	189_Q	0.773	1.00
46_L	74_I	0.773	1.00
61_K	65_E	0.767	1.00
9_I	99_F	0.760	1.00
110_A	113_R	0.760	1.00
82_D	85_L	0.758	1.00
50_M	76_A	0.752	1.00
100_S	103_E	0.750	1.00
81_V	102_I	0.749	1.00
37_F	42_Y	0.748	1.00
110_A	115_A	0.743	1.00
87_L	107_R	0.741	1.00
159_L	163_F	0.741	1.00
174_E	178_R	0.740	1.00
63_I	67_S	0.736	1.00
205_D	215_T	0.732	1.00
162_L	165_S	0.726	1.00
112_I	115_A	0.721	1.00
11_E	15_H	0.721	1.00
30_G	34_I	0.720	1.00
34_I	37_F	0.710	1.00
175_Q	178_R	0.710	1.00
133_Q	145_K	0.705	1.00
144_L	147_G	0.702	1.00
30_G	53_K	0.701	1.00
115_A	119_S	0.698	1.00
200_R	205_D	0.691	1.00
1_M	42_Y	0.689	1.00
41_S	67_S	0.687	1.00
12_M	16_Y	0.683	1.00
86_G	91_A	0.679	1.00
134_L	145_K	0.679	1.00
37_F	45_V	0.677	1.00
70_P	112_I	0.675	1.00
72_L	93_D	0.675	1.00
10_S	14_D	0.674	1.00
38_Q	62_I	0.674	1.00
88_G	106_A	0.673	1.00
18_T	24_I	0.669	1.00
102_I	106_A	0.668	1.00
99_F	104_L	0.668	1.00
46_L	108_V	0.667	1.00
3_V	59_F	0.667	1.00
2_L	14_D	0.666	1.00
129_I	133_Q	0.663	1.00
141_V	157_W	0.659	1.00
129_I	138_I	0.657	1.00
204_E	211_Q	0.655	1.00
2_L	26_H	0.654	1.00
165_S	179_S	0.652	1.00
16_Y	105_T	0.648	1.00
63_I	71_V	0.647	1.00
17_L	22_F	0.647	1.00
165_S	171_F	0.643	1.00
193_N	196_M	0.642	1.00
34_I	66_K	0.641	1.00
204_E	210_P	0.640	1.00
68_N	117_Q	0.632	1.00
30_G	51_L	0.630	1.00
4_E	51_L	0.629	1.00
188_D	191_I	0.627	1.00
46_L	72_L	0.626	1.00
80_D	102_I	0.621	1.00
131_I	135_A	0.621	1.00
107_R	111_A	0.621	1.00
1_M	33_G	0.619	1.00
187_D	192_I	0.619	1.00
37_F	67_S	0.618	1.00
83_K	100_S	0.618	1.00
68_N	118_Y	0.614	1.00
136_I	161_C	0.613	1.00
57_M	82_D	0.613	1.00
211_Q	215_T	0.612	1.00
211_Q	214_K	0.611	1.00
158_Q	162_L	0.611	1.00
206_D	211_Q	0.605	1.00
145_K	204_E	0.604	1.00
16_Y	20_E	0.602	1.00
49_I	86_G	0.600	1.00
129_I	164_A	0.597	1.00
64_R	70_P	0.594	1.00
93_D	110_A	0.592	1.00
155_T	195_H	0.591	1.00
210_P	213_I	0.591	1.00
133_Q	137_D	0.590	1.00
64_R	69_I	0.587	1.00
6_D	76_A	0.584	1.00
163_F	196_M	0.583	1.00
75_S	83_K	0.579	1.00
48_D	97_K	0.576	1.00
106_A	109_K	0.574	1.00
145_K	206_D	0.571	1.00
60_L	64_R	0.570	1.00
22_F	112_I	0.569	1.00
6_D	9_I	0.567	1.00
99_F	103_E	0.567	1.00
145_K	148_E	0.564	1.00
32_E	53_K	0.562	1.00
137_D	142_S	0.558	1.00
70_P	114_R	0.557	1.00
81_V	84_A	0.555	1.00
18_T	23_G	0.552	1.00
47_L	51_L	0.547	1.00
9_I	12_M	0.545	1.00
166_N	179_S	0.540	1.00
138_I	165_S	0.540	1.00
37_F	66_K	0.539	1.00
37_F	59_F	0.538	1.00
109_K	113_R	0.532	1.00
145_K	205_D	0.531	1.00
12_M	15_H	0.530	1.00
44_L	111_A	0.529	1.00
63_I	69_I	0.528	1.00
29_D	51_L	0.527	1.00
38_Q	67_S	0.523	1.00
131_I	164_A	0.519	1.00
84_A	87_L	0.519	1.00
136_I	143_V	0.518	1.00
78_D	98_P	0.517	1.00
130_R	134_L	0.514	1.00
131_I	134_L	0.510	1.00
114_R	118_Y	0.510	1.00
70_P	115_A	0.509	1.00
3_V	47_L	0.508	1.00
15_H	18_T	0.508	1.00
153_T	156_E	0.508	1.00
33_G	45_V	0.506	1.00
75_S	97_K	0.504	1.00
160_L	163_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
2gwrA	1	0.9646	100	0.161	Contact Map
2oqrA	2	0.9823	100	0.176	Contact Map
4b09A	2	0.9115	100	0.178	Contact Map
3r0jA	2	0.9513	100	0.178	Contact Map
1ys7A	2	0.9779	100	0.182	Contact Map
4kfcA	2	0.9735	100	0.185	Contact Map
1kgsA	1	0.9469	100	0.205	Contact Map
1p2fA	1	0.9336	100	0.228	Contact Map
2hqrA	2	0.9381	100	0.23	Contact Map
3q9sA	1	0.9115	100	0.23	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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