CPXR - ECOLI - GREMLIN Contacts

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CPXR - Transcriptional regulatory protein CpxR

UniProt:	P0AE88	Sequences: MNKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLDDSIDLLLLDVMMPKKNGIDTLKALRQTHQTPVIMLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILRRSHWSEQQQNNDNGSPTLEVDALVLNPGRQEASFDGQTLELTGTEFTLLYLLAQHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDRKDGHPWFKTLRGRGYLMVSAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10020
Length:	232 (200)
Sequences:	77101 (55248)
Seq/√Len:	3906.6

ECOLI - CPXR RSTA KDPE ARCA BAER YEDW OMPR TORR CREB BASR CUSR QSEB PHOP PHOB DCUR UVRY DPIA FIMZ UHPA NARP NARL YHJB YJJQ CSGD YGEK EVGA RCSB BARA BGLJ TORS YEHT RCSA RSSB RCSC ARCB CHEB YPDB EVGS NTRC ATOC GLRR ZRAR RCSD
BACSU - YRKP YVCP YXDJ YYCF YVRH YCBL RESD CSSR PHOP CITT BCER YCLJ MALR YFIK YKOG DCTR LIAR CMPA YDFI YVFU DEGU YBDJ DESR YXJL YHCZ CHEB YESN GLNL LYTT NATR SP0A 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
14_T	30_V	3.805	1.00
14_T	32_H	3.335	1.00
18_K	30_V	3.289	1.00
38_L	65_A	2.780	1.00
7_V	37_A	2.765	1.00
35_E	56_K	2.556	1.00
29_I	45_I	2.464	1.00
34_G	57_K	2.409	1.00
57_K	65_A	2.395	1.00
33_D	56_K	2.304	1.00
42_D	69_T	2.278	1.00
24_E	108_V	2.154	1.00
20_L	104_D	2.138	1.00
3_K	29_I	2.132	1.00
31_A	40_L	2.076	1.00
18_K	22_E	2.040	1.00
53_M	80_R	1.945	1.00
3_K	27_N	1.940	1.00
32_H	36_Q	1.867	1.00
86_R	106_E	1.827	1.00
50_L	62_T	1.810	1.00
195_R	198_D	1.808	1.00
29_I	40_L	1.805	1.00
33_D	36_Q	1.775	1.00
76_M	89_G	1.745	1.00
67_R	95_D	1.727	1.00
160_T	163_T	1.725	1.00
65_A	69_T	1.724	1.00
64_K	92_L	1.717	1.00
63_L	74_V	1.710	1.00
5_L	31_A	1.686	1.00
178_R	198_D	1.678	1.00
83_E	103_N	1.611	1.00
96_D	110_R	1.611	1.00
34_G	62_T	1.597	1.00
76_M	94_A	1.587	1.00
57_K	61_D	1.586	1.00
166_Y	170_Q	1.572	1.00
167_L	184_E	1.520	1.00
21_L	111_I	1.515	1.00
176_V	184_E	1.478	1.00
135_E	140_V	1.474	1.00
41_L	66_L	1.470	1.00
58_N	61_D	1.468	1.00
80_R	85_D	1.453	1.00
48_L	72_T	1.450	1.00
65_A	68_Q	1.435	1.00
177_S	180_H	1.428	1.00
35_E	57_K	1.428	1.00
200_H	203_N	1.426	1.00
11_R	32_H	1.380	1.00
40_L	45_I	1.377	1.00
63_L	76_M	1.365	1.00
138_A	151_D	1.359	1.00
47_L	111_I	1.327	1.00
75_I	114_I	1.321	1.00
40_L	43_D	1.315	1.00
61_D	64_K	1.313	1.00
38_L	62_T	1.303	1.00
60_I	89_G	1.295	1.00
52_V	60_I	1.283	1.00
95_D	117_R	1.280	1.00
95_D	114_I	1.269	1.00
161_E	207_K	1.269	1.00
171_H	174_Q	1.263	1.00
26_F	112_R	1.254	1.00
180_H	184_E	1.243	1.00
162_F	166_Y	1.233	1.00
38_L	57_K	1.223	1.00
133_T	140_V	1.219	1.00
5_L	45_I	1.218	1.00
167_L	171_H	1.215	1.00
108_V	112_R	1.213	1.00
7_V	54_M	1.207	1.00
88_L	92_L	1.207	1.00
8_D	14_T	1.196	1.00
140_V	149_S	1.187	1.00
211_R	215_H	1.186	1.00
9_D	51_D	1.172	1.00
36_Q	40_L	1.169	1.00
31_A	37_A	1.167	1.00
36_Q	39_D	1.160	1.00
82_S	85_D	1.159	1.00
60_I	88_L	1.156	1.00
50_L	63_L	1.144	1.00
24_E	112_R	1.120	1.00
142_N	145_R	1.116	1.00
5_L	37_A	1.105	1.00
83_E	87_V	1.105	1.00
179_E	194_D	1.095	1.00
35_E	39_D	1.089	1.00
52_V	76_M	1.078	1.00
47_L	115_L	1.077	1.00
25_G	112_R	1.076	1.00
39_D	43_D	1.073	1.00
5_L	40_L	1.066	1.00
199_M	202_S	1.052	1.00
109_A	113_A	1.047	1.00
167_L	176_V	1.045	1.00
31_A	36_Q	1.038	1.00
195_R	199_M	1.031	1.00
4_I	26_F	1.027	1.00
106_E	109_A	1.025	1.00
87_V	91_E	1.021	1.00
84_L	88_L	1.016	1.00
91_E	112_R	1.015	1.00
18_K	28_V	1.004	1.00
38_L	42_D	0.997	1.00
6_L	17_L	0.996	1.00
37_A	41_L	0.993	1.00
147_E	154_T	0.990	1.00
159_G	163_T	0.986	1.00
86_R	99_P	0.981	1.00
15_S	30_V	0.981	1.00
143_P	166_Y	0.977	1.00
11_R	15_S	0.965	1.00
163_T	166_Y	0.965	1.00
141_L	169_A	0.965	1.00
37_A	62_T	0.964	1.00
64_K	88_L	0.958	1.00
52_V	58_N	0.950	1.00
48_L	66_L	0.949	1.00
17_L	77_L	0.936	1.00
7_V	31_A	0.933	1.00
60_I	92_L	0.930	1.00
50_L	74_V	0.927	1.00
5_L	41_L	0.922	1.00
164_L	168_L	0.918	1.00
141_L	162_F	0.910	1.00
176_V	180_H	0.909	1.00
12_E	16_L	0.905	1.00
196_A	200_H	0.900	1.00
63_L	92_L	0.894	1.00
50_L	76_M	0.891	1.00
114_I	117_R	0.887	1.00
149_S	154_T	0.885	1.00
81_G	99_P	0.874	1.00
49_L	107_L	0.870	1.00
63_L	94_A	0.858	1.00
83_E	86_R	0.856	1.00
7_V	48_L	0.855	1.00
167_L	181_L	0.843	1.00
39_D	42_D	0.838	1.00
15_S	18_K	0.837	1.00
144_G	174_Q	0.836	1.00
73_P	95_D	0.834	1.00
61_D	65_A	0.833	1.00
13_L	102_F	0.829	1.00
19_E	23_M	0.827	1.00
135_E	138_A	0.822	1.00
75_I	110_R	0.821	1.00
11_R	14_T	0.821	1.00
26_F	108_V	0.816	1.00
52_V	85_D	0.816	1.00
62_T	66_L	0.815	1.00
174_Q	180_H	0.812	1.00
201_I	205_R	0.810	1.00
132_P	144_G	0.807	1.00
104_D	108_V	0.807	1.00
48_L	74_V	0.803	1.00
194_D	198_D	0.803	1.00
210_D	216_P	0.803	1.00
88_L	91_E	0.802	1.00
41_L	72_T	0.802	1.00
178_R	194_D	0.796	1.00
195_R	202_S	0.796	1.00
6_L	28_V	0.796	1.00
199_M	203_N	0.794	1.00
180_H	183_Q	0.786	1.00
203_N	206_R	0.778	1.00
106_E	110_R	0.777	1.00
202_S	206_R	0.776	1.00
167_L	170_Q	0.774	1.00
85_D	88_L	0.774	1.00
57_K	62_T	0.761	1.00
52_V	80_R	0.760	1.00
179_E	183_Q	0.754	1.00
64_K	68_Q	0.750	1.00
15_S	19_E	0.748	1.00
49_L	111_I	0.747	1.00
209_P	215_H	0.745	1.00
54_M	62_T	0.745	1.00
49_L	77_L	0.745	1.00
146_Q	163_T	0.745	1.00
34_G	38_L	0.744	1.00
103_N	106_E	0.744	1.00
77_L	102_F	0.742	1.00
113_A	118_S	0.739	1.00
41_L	45_I	0.739	1.00
133_T	142_N	0.739	1.00
158_T	207_K	0.738	1.00
3_K	46_D	0.736	1.00
87_V	105_R	0.734	1.00
66_L	70_H	0.730	1.00
113_A	116_R	0.730	1.00
115_L	118_S	0.723	1.00
20_L	108_V	0.720	1.00
7_V	62_T	0.713	1.00
84_L	105_R	0.713	1.00
210_D	219_K	0.708	1.00
17_L	107_L	0.702	1.00
3_K	45_I	0.695	1.00
118_S	122_E	0.689	1.00
139_L	150_F	0.687	1.00
34_G	56_K	0.687	1.00
163_T	167_L	0.684	1.00
53_M	79_A	0.676	1.00
90_L	110_R	0.675	1.00
38_L	41_L	0.668	1.00
38_L	69_T	0.665	1.00
89_G	94_A	0.664	1.00
209_P	216_P	0.664	1.00
67_R	73_P	0.658	1.00
205_R	210_D	0.655	1.00
192_P	197_I	0.654	1.00
66_L	74_V	0.652	1.00
22_E	28_V	0.649	1.00
198_D	201_I	0.647	1.00
16_L	20_L	0.643	1.00
6_L	30_V	0.642	1.00
102_F	107_L	0.638	1.00
86_R	103_N	0.637	1.00
41_L	48_L	0.634	1.00
34_G	54_M	0.632	1.00
91_E	109_A	0.629	1.00
14_T	18_K	0.628	1.00
105_R	109_A	0.626	1.00
149_S	152_G	0.626	1.00
60_I	85_D	0.626	1.00
42_D	65_A	0.623	1.00
71_Q	121_S	0.622	1.00
71_Q	120_W	0.620	1.00
168_L	201_I	0.619	1.00
10_D	79_A	0.619	1.00
73_P	115_L	0.616	1.00
4_I	47_L	0.613	1.00
110_R	114_I	0.606	1.00
146_Q	162_F	0.605	1.00
4_I	21_L	0.604	1.00
21_L	26_F	0.602	1.00
75_I	96_D	0.602	1.00
6_L	18_K	0.602	1.00
83_E	105_R	0.600	1.00
141_L	166_Y	0.597	1.00
73_P	117_R	0.597	1.00
143_P	170_Q	0.596	1.00
170_Q	176_V	0.596	1.00
174_Q	184_E	0.592	1.00
170_Q	184_E	0.590	1.00
49_L	75_I	0.588	1.00
102_F	106_E	0.587	1.00
73_P	118_S	0.586	1.00
138_A	150_F	0.586	1.00
193_F	196_A	0.585	1.00
150_F	153_Q	0.581	1.00
150_F	211_R	0.581	1.00
109_A	112_R	0.580	1.00
67_R	72_T	0.576	1.00
96_D	113_A	0.576	1.00
160_T	200_H	0.575	1.00
150_F	209_P	0.571	1.00
51_D	100_K	0.568	1.00
8_D	54_M	0.566	1.00
171_H	184_E	0.565	1.00
215_H	218_F	0.563	1.00
174_Q	181_L	0.562	1.00
112_R	116_R	0.559	1.00
9_D	78_T	0.559	1.00
141_L	148_A	0.558	1.00
52_V	89_G	0.557	1.00
63_L	67_R	0.555	1.00
50_L	66_L	0.555	1.00
165_L	216_P	0.553	1.00
142_N	147_E	0.548	1.00
36_Q	56_K	0.548	1.00
158_T	161_E	0.544	1.00
20_L	24_E	0.544	1.00
50_L	54_M	0.543	1.00
150_F	210_D	0.542	1.00
87_V	90_L	0.541	1.00
84_L	87_V	0.537	1.00
81_G	101_P	0.537	1.00
41_L	69_T	0.531	1.00
22_E	27_N	0.528	1.00
138_A	142_N	0.522	1.00
66_L	72_T	0.522	1.00
9_D	54_M	0.520	1.00
16_L	19_E	0.519	1.00
13_L	16_L	0.517	1.00
211_R	217_W	0.513	1.00
26_F	115_L	0.510	1.00
73_P	121_S	0.510	1.00
10_D	13_L	0.509	1.00
111_I	115_L	0.508	1.00
105_R	108_V	0.507	1.00
19_E	22_E	0.506	1.00
134_L	143_P	0.502	1.00
78_T	86_R	0.501	1.00
178_R	201_I	0.500	1.00
44_S	70_H	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	0.9526	100	0.229	Contact Map
4b09A	2	0.9052	100	0.231	Contact Map
4kfcA	2	0.9612	100	0.231	Contact Map
2oqrA	2	0.9698	100	0.235	Contact Map
3r0jA	2	0.9397	100	0.245	Contact Map
1ys7A	2	0.9655	100	0.249	Contact Map
1p2fA	1	0.9267	100	0.254	Contact Map
1kgsA	1	0.9353	100	0.269	Contact Map
3q9sA	1	0.9009	100	0.287	Contact Map
2hqrA	2	0.9267	100	0.298	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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