RSTA - ECOLI - GREMLIN Contacts

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RSTA - Transcriptional regulatory protein RstA

UniProt:	P52108	Sequences: MNTIVFVEDDAEVGSLIAAYLAKHDMQVTVEPRGDQAEETILRENPDLVLLDIMLPGKDGMTICRDLRAKWSGPIVLLTSLDSDMNHILALEMGACDYILKTTPPAVLLARLRLHLRQNEQATLTKGLQETSLTPYKALHFGTLTIDPINRVVTLANTEISLSTADFELLWELATHAGQIMDRDALLKNLRGVSYDGLDRSVDVAISRLRKKLLDNAAEPYRIKTVRNKGYLFAPHAWE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13190
Length:	239 (204)
Sequences:	68454 (48210)
Seq/√Len:	3375.4

ECOLI - RSTA KDPE CPXR ARCA BAER YEDW OMPR CREB TORR PHOP CUSR QSEB BASR PHOB DCUR UVRY DPIA UHPA YHJB EVGA YJJQ FIMZ NARL RCSB NARP BARA YEHT YGEK BGLJ CSGD ARCB RCSC TORS RCSA RSSB CHEB YPDB EVGS NTRC GLRR ATOC ZRAR RCSD
BACSU - YXDJ YVCP YYCF YVRH YCBL BCER CITT RESD YCLJ PHOP YRKP CSSR YKOG MALR YFIK DCTR CMPA YDFI LIAR YVFU DESR DEGU YXJL CHEB YESN YHCZ YBDJ LYTT NATR SP0A GLNL CHEV
HALSA - CHEB Q9HR09 Q9HNM3 BAT Q9HRE5 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
14_G	30_V	3.701	1.00
14_G	32_P	3.145	1.00
18_A	30_V	3.048	1.00
7_V	37_A	2.721	1.00
35_D	57_G	2.597	1.00
38_E	66_D	2.516	1.00
33_R	57_G	2.461	1.00
29_T	46_P	2.454	1.00
34_G	58_K	2.409	1.00
58_K	66_D	2.364	1.00
42_L	70_K	2.344	1.00
18_A	22_A	2.125	1.00
3_T	29_T	2.123	1.00
20_Y	105_P	2.039	1.00
3_T	27_Q	2.036	1.00
24_H	109_L	1.992	1.00
31_E	40_T	1.961	1.00
87_H	107_V	1.940	1.00
165_A	168_E	1.933	1.00
200_R	203_D	1.919	1.00
32_P	36_Q	1.826	1.00
54_M	81_L	1.815	1.00
33_R	36_Q	1.807	1.00
51_L	63_I	1.796	1.00
77_L	90_A	1.773	1.00
64_C	75_I	1.760	1.00
84_D	104_P	1.751	1.00
68_R	96_C	1.709	1.00
143_T	156_A	1.703	1.00
183_R	203_D	1.641	1.00
29_T	40_T	1.637	1.00
5_V	31_E	1.636	1.00
172_E	189_N	1.604	1.00
171_W	175_T	1.589	1.00
77_L	95_A	1.585	1.00
21_L	112_L	1.582	1.00
58_K	62_T	1.578	1.00
66_D	70_K	1.565	1.00
59_D	62_T	1.556	1.00
34_G	63_I	1.529	1.00
205_A	208_R	1.500	1.00
166_D	212_K	1.496	1.00
81_L	86_N	1.494	1.00
40_T	44_E	1.488	1.00
66_D	69_A	1.467	1.00
181_M	189_N	1.458	1.00
97_D	111_R	1.456	1.00
40_T	43_R	1.442	1.00
29_T	44_E	1.437	1.00
49_V	73_G	1.431	1.00
76_V	115_H	1.431	1.00
35_D	58_K	1.411	1.00
48_L	112_L	1.403	1.00
41_I	67_L	1.393	1.00
182_D	185_A	1.386	1.00
38_E	63_I	1.383	1.00
62_T	65_R	1.380	1.00
64_C	77_L	1.359	1.00
11_A	32_P	1.345	1.00
140_H	145_T	1.325	1.00
53_I	77_L	1.305	1.00
51_L	64_C	1.292	1.00
8_E	14_G	1.279	1.00
65_R	93_M	1.274	1.00
39_E	43_R	1.269	1.00
7_V	55_L	1.263	1.00
96_C	118_Q	1.261	1.00
53_I	61_M	1.256	1.00
152_V	159_E	1.247	1.00
26_M	113_R	1.240	1.00
9_D	52_D	1.237	1.00
147_D	150_N	1.232	1.00
40_T	46_P	1.222	1.00
138_A	145_T	1.218	1.00
38_E	58_K	1.218	1.00
92_E	113_R	1.209	1.00
36_Q	39_E	1.207	1.00
83_S	86_N	1.190	1.00
5_V	46_P	1.170	1.00
35_D	39_E	1.169	1.00
145_T	154_T	1.166	1.00
172_E	181_M	1.164	1.00
31_E	37_A	1.158	1.00
25_D	113_R	1.157	1.00
36_Q	40_T	1.153	1.00
61_M	89_L	1.143	1.00
216_N	220_P	1.128	1.00
172_E	176_H	1.124	1.00
5_V	37_A	1.116	1.00
185_A	189_N	1.112	1.00
48_L	116_L	1.112	1.00
84_D	88_I	1.110	1.00
3_T	44_E	1.110	1.00
61_M	90_A	1.106	1.00
24_H	113_R	1.100	1.00
204_V	207_S	1.093	1.00
109_L	113_R	1.086	1.00
146_I	174_A	1.081	1.00
184_D	199_D	1.065	1.00
148_P	171_W	1.033	1.00
167_F	171_W	1.031	1.00
85_M	89_L	1.028	1.00
61_M	93_M	1.024	1.00
4_I	26_M	1.020	1.00
107_V	110_A	1.014	1.00
65_R	89_L	1.008	1.00
89_L	93_M	1.006	1.00
96_C	115_H	1.005	1.00
5_V	40_T	0.996	1.00
137_K	149_I	0.988	1.00
110_A	114_L	0.981	1.00
172_E	186_L	0.978	1.00
17_I	78_L	0.977	1.00
31_E	36_Q	0.976	1.00
115_H	118_Q	0.974	1.00
7_V	49_V	0.974	1.00
37_A	41_I	0.963	1.00
216_N	219_E	0.957	1.00
18_A	28_V	0.955	1.00
51_L	75_I	0.954	1.00
41_I	71_W	0.953	1.00
6_F	17_I	0.949	1.00
140_H	143_T	0.948	1.00
181_M	185_A	0.947	1.00
88_I	92_E	0.945	1.00
168_E	171_W	0.944	1.00
38_E	42_L	0.938	1.00
87_H	100_L	0.928	1.00
200_R	204_V	0.926	1.00
37_A	63_I	0.925	1.00
53_I	59_D	0.920	1.00
5_V	41_I	0.920	1.00
7_V	31_E	0.913	1.00
154_T	159_E	0.909	1.00
146_I	167_F	0.908	1.00
201_S	205_A	0.905	1.00
206_I	210_R	0.905	1.00
64_C	93_M	0.905	1.00
12_E	16_L	0.903	1.00
138_A	147_D	0.902	1.00
164_T	168_E	0.898	1.00
62_T	66_D	0.894	1.00
49_V	67_L	0.894	1.00
163_S	212_K	0.893	1.00
15_S	30_V	0.884	1.00
11_A	15_S	0.883	1.00
26_M	109_L	0.879	1.00
39_E	42_L	0.869	1.00
91_L	111_R	0.863	1.00
82_D	100_L	0.858	1.00
6_F	28_V	0.857	1.00
200_R	207_S	0.857	1.00
19_A	23_K	0.855	1.00
64_C	95_A	0.850	1.00
11_A	14_G	0.850	1.00
88_I	106_A	0.843	1.00
55_L	63_I	0.832	1.00
17_I	108_L	0.826	1.00
45_N	71_W	0.822	1.00
151_R	168_E	0.822	1.00
215_D	221_Y	0.821	1.00
51_L	77_L	0.820	1.00
199_D	203_D	0.820	1.00
50_L	78_L	0.815	1.00
50_L	108_L	0.814	1.00
84_D	87_H	0.808	1.00
215_D	224_K	0.806	1.00
89_L	92_E	0.805	1.00
207_S	211_K	0.801	1.00
53_I	81_L	0.799	1.00
107_V	111_R	0.798	1.00
15_S	18_A	0.792	1.00
63_I	67_L	0.792	1.00
85_M	106_A	0.787	1.00
3_T	46_P	0.784	1.00
53_I	86_N	0.779	1.00
208_R	211_K	0.777	1.00
49_V	75_I	0.769	1.00
54_M	80_S	0.766	1.00
175_T	189_N	0.764	1.00
74_P	96_C	0.762	1.00
105_P	109_L	0.760	1.00
114_L	119_N	0.754	1.00
34_G	38_E	0.753	1.00
58_K	63_I	0.750	1.00
76_V	97_D	0.748	1.00
184_D	188_K	0.747	1.00
41_I	73_G	0.746	1.00
65_R	69_A	0.742	1.00
76_V	111_R	0.735	1.00
86_N	89_L	0.732	1.00
183_R	199_D	0.721	1.00
172_E	175_T	0.713	1.00
6_F	18_A	0.711	1.00
41_I	46_P	0.709	1.00
78_L	103_T	0.709	1.00
114_L	117_R	0.705	1.00
38_E	41_I	0.705	1.00
42_L	71_W	0.699	1.00
154_T	157_N	0.699	1.00
84_D	106_A	0.697	1.00
21_L	26_M	0.692	1.00
214_L	220_P	0.692	1.00
175_T	181_M	0.691	1.00
103_T	108_L	0.690	1.00
72_S	121_Q	0.689	1.00
6_F	30_V	0.689	1.00
3_T	47_D	0.688	1.00
15_S	19_A	0.685	1.00
34_G	57_G	0.682	1.00
139_L	148_P	0.681	1.00
8_E	55_L	0.681	1.00
13_V	103_T	0.680	1.00
92_E	110_A	0.678	1.00
16_L	20_Y	0.676	1.00
7_V	63_I	0.675	1.00
90_A	95_A	0.674	1.00
104_P	107_V	0.674	1.00
204_V	208_R	0.669	1.00
41_I	49_V	0.668	1.00
173_L	206_I	0.662	1.00
20_Y	109_L	0.662	1.00
214_L	221_Y	0.659	1.00
210_R	215_D	0.656	1.00
151_R	167_F	0.655	1.00
143_T	155_L	0.652	1.00
14_G	18_A	0.651	1.00
22_A	28_V	0.649	1.00
185_A	188_K	0.649	1.00
4_I	48_L	0.647	1.00
144_L	155_L	0.644	1.00
87_H	104_P	0.643	1.00
22_A	27_Q	0.643	1.00
116_L	119_N	0.642	1.00
197_G	202_V	0.632	1.00
74_P	116_L	0.631	1.00
4_I	21_L	0.629	1.00
106_A	110_A	0.620	1.00
165_A	205_A	0.618	1.00
119_N	123_T	0.616	1.00
10_D	13_V	0.615	1.00
53_I	90_A	0.614	1.00
42_L	66_D	0.613	1.00
10_D	80_S	0.611	1.00
143_T	147_D	0.609	1.00
147_D	152_V	0.609	1.00
26_M	116_L	0.601	1.00
170_L	221_Y	0.601	1.00
68_R	73_G	0.600	1.00
38_E	70_K	0.600	1.00
72_S	122_A	0.592	1.00
79_T	87_H	0.590	1.00
155_L	216_N	0.587	1.00
50_L	112_L	0.586	1.00
52_D	101_K	0.583	1.00
214_L	218_A	0.583	1.00
170_L	209_L	0.583	1.00
139_L	174_A	0.583	1.00
148_P	175_T	0.583	1.00
155_L	158_T	0.581	1.00
146_I	171_W	0.581	1.00
203_D	206_I	0.576	1.00
4_I	112_L	0.569	1.00
34_G	55_L	0.565	1.00
172_E	190_L	0.563	1.00
137_K	148_P	0.562	1.00
9_D	79_T	0.562	1.00
103_T	107_V	0.560	1.00
139_L	143_T	0.555	1.00
137_K	141_F	0.554	1.00
219_E	222_R	0.553	1.00
36_Q	57_G	0.551	1.00
61_M	86_N	0.551	1.00
155_L	214_L	0.548	1.00
146_I	153_V	0.547	1.00
168_E	172_E	0.545	1.00
51_L	55_L	0.543	1.00
155_L	215_D	0.543	1.00
50_L	76_V	0.543	1.00
206_I	218_A	0.543	1.00
141_F	174_A	0.542	1.00
169_L	173_L	0.541	1.00
64_C	68_R	0.540	1.00
20_Y	24_H	0.538	1.00
67_L	71_W	0.536	1.00
139_L	142_G	0.534	1.00
82_D	102_T	0.532	1.00
166_D	208_R	0.531	1.00
48_L	115_H	0.531	1.00
111_R	115_H	0.531	1.00
41_I	63_I	0.529	1.00
67_L	75_I	0.529	1.00
68_R	74_P	0.520	1.00
16_L	19_A	0.518	1.00
198_L	201_S	0.517	1.00
144_L	153_V	0.515	1.00
88_I	91_L	0.514	1.00
141_F	145_T	0.512	1.00
79_T	101_K	0.512	1.00
6_F	14_G	0.510	1.00
97_D	114_L	0.510	1.00
33_R	55_L	0.507	1.00
110_A	113_R	0.507	1.00
67_L	73_G	0.507	1.00
68_R	71_W	0.504	1.00
187_L	196_D	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	0.9289	100	0.208	Contact Map
2oqrA	2	0.9456	100	0.22	Contact Map
4kfcA	2	0.9372	100	0.221	Contact Map
4b09A	2	0.8912	100	0.225	Contact Map
3r0jA	2	0.9163	100	0.23	Contact Map
1ys7A	2	0.9414	100	0.23	Contact Map
1kgsA	1	0.9121	100	0.253	Contact Map
1p2fA	1	0.8996	100	0.267	Contact Map
3q9sA	1	0.8787	100	0.275	Contact Map
2hqrA	2	0.9121	100	0.285	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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