PHOP - ECOLI - GREMLIN Contacts

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PHOP - Transcriptional regulatory protein PhoP

UniProt:	P23836	Sequences: MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRRNSGLASQVISLPPFQVDLSRRELSINDEVIKLTAFEYTIMETLIRNNGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQYPQEVITTVRGQGYLFELR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10731
Length:	223 (206)
Sequences:	81998 (58357)
Seq/√Len:	4065.9

ECOLI - PHOP CUSR YEDW QSEB PHOB BASR CREB ARCA OMPR KDPE RSTA BAER TORR CPXR UVRY FIMZ YHJB EVGA NARL NARP YJJQ YGEK DPIA DCUR RCSB BGLJ RCSA UHPA CSGD BARA TORS RCSC RSSB ARCB YPDB EVGS CHEB YEHT NTRC GLRR ZRAR ATOC RCSD CHEY
BACSU - YKOG YVRH PHOP YXDJ YVCP BCER YCBL YYCF YCLJ CSSR RESD YRKP CITT YFIK YXJL CMPA DCTR DEGU LIAR MALR YVFU YHCZ YBDJ DESR YDFI YESN LYTT GLNL NATR SP0A CHEB CHEV SP0F CCDB CHEY
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_R	29_D	3.860	1.00
13_R	31_E	3.405	1.00
17_K	29_D	3.365	1.00
6_V	36_A	2.879	1.00
37_D	65_R	2.822	1.00
34_K	56_D	2.622	1.00
28_D	45_P	2.537	1.00
33_A	57_E	2.524	1.00
41_N	69_N	2.417	1.00
57_E	65_R	2.397	1.00
32_D	56_D	2.349	1.00
30_A	39_Y	2.122	1.00
19_Q	105_I	2.074	1.00
23_A	109_M	2.069	1.00
17_K	21_Q	2.026	1.00
2_R	26_Q	2.014	1.00
53_G	81_R	1.955	1.00
31_E	35_E	1.919	1.00
50_V	62_L	1.916	1.00
188_H	191_D	1.894	1.00
63_I	75_I	1.887	1.00
87_K	107_E	1.885	1.00
39_Y	43_H	1.818	1.00
28_D	39_Y	1.811	1.00
77_V	90_V	1.785	1.00
32_D	35_E	1.781	1.00
28_D	43_H	1.772	1.00
2_R	28_D	1.768	1.00
4_L	30_A	1.759	1.00
65_R	69_N	1.758	1.00
77_V	95_A	1.725	1.00
67_R	96_D	1.701	1.00
64_R	93_A	1.673	1.00
153_F	156_T	1.656	1.00
33_A	62_L	1.640	1.00
84_W	104_H	1.629	1.00
57_E	61_S	1.629	1.00
58_D	61_S	1.608	1.00
97_D	111_R	1.607	1.00
171_K	191_D	1.578	1.00
159_E	163_R	1.534	1.00
39_Y	42_E	1.531	1.00
40_L	66_W	1.512	1.00
65_R	68_S	1.506	1.00
48_A	73_L	1.458	1.00
81_R	86_D	1.458	1.00
20_I	112_M	1.456	1.00
169_V	177_Q	1.454	1.00
63_I	77_V	1.445	1.00
193_L	196_R	1.440	1.00
160_T	177_Q	1.439	1.00
34_K	57_E	1.426	1.00
194_M	198_R	1.413	1.00
170_S	173_S	1.379	1.00
160_T	164_N	1.371	1.00
37_D	62_L	1.369	1.00
61_S	64_R	1.369	1.00
96_D	118_R	1.366	1.00
39_Y	45_P	1.336	1.00
96_D	115_L	1.334	1.00
131_P	144_N	1.329	1.00
47_I	112_M	1.318	1.00
10_A	31_E	1.308	1.00
76_L	115_L	1.294	1.00
52_L	60_L	1.291	1.00
37_D	57_E	1.287	1.00
70_D	73_L	1.271	1.00
7_E	13_R	1.262	1.00
60_L	90_V	1.259	1.00
6_V	54_L	1.247	1.00
25_H	113_Q	1.223	1.00
50_V	63_I	1.219	1.00
38_Y	42_E	1.209	1.00
4_L	45_P	1.194	1.00
89_E	93_A	1.193	1.00
30_A	36_A	1.189	1.00
109_M	113_Q	1.175	1.00
35_E	38_Y	1.171	1.00
35_E	39_Y	1.170	1.00
8_D	51_D	1.168	1.00
52_L	77_V	1.163	1.00
60_L	89_E	1.160	1.00
154_E	200_K	1.149	1.00
83_S	86_D	1.144	1.00
2_R	43_H	1.138	1.00
4_L	36_A	1.129	1.00
34_K	38_Y	1.125	1.00
173_S	177_Q	1.118	1.00
155_Y	159_E	1.104	1.00
84_W	88_V	1.092	1.00
23_A	113_Q	1.091	1.00
4_L	39_Y	1.080	1.00
135_D	138_R	1.079	1.00
110_A	114_A	1.071	1.00
189_T	193_L	1.067	1.00
88_V	92_S	1.066	1.00
140_E	147_V	1.065	1.00
24_G	113_Q	1.055	1.00
36_A	62_L	1.052	1.00
37_D	41_N	1.050	1.00
64_R	89_E	1.049	1.00
107_E	110_A	1.046	1.00
3_V	25_H	1.041	1.00
172_D	187_S	1.035	1.00
203_A	212_T	1.034	1.00
30_A	35_E	1.034	1.00
47_I	116_M	1.029	1.00
156_T	159_E	1.026	1.00
192_V	195_G	1.023	1.00
14_H	29_D	1.020	1.00
92_S	113_Q	0.994	1.00
85_Q	89_E	0.993	1.00
188_H	192_V	0.992	1.00
48_A	66_W	0.981	1.00
5_V	16_L	0.980	1.00
157_I	161_L	0.979	1.00
160_T	169_V	0.973	1.00
36_A	40_L	0.972	1.00
10_A	14_H	0.967	1.00
17_K	27_V	0.962	1.00
87_K	100_T	0.958	1.00
48_A	75_I	0.956	1.00
134_V	162_I	0.956	1.00
6_V	30_A	0.952	1.00
4_L	40_L	0.942	1.00
169_V	173_S	0.940	1.00
11_L	15_H	0.939	1.00
52_L	58_D	0.935	1.00
60_L	93_A	0.928	1.00
84_W	87_K	0.926	1.00
74_P	96_D	0.925	1.00
63_I	93_A	0.920	1.00
50_V	77_V	0.917	1.00
16_L	78_L	0.916	1.00
76_L	111_R	0.913	1.00
38_Y	41_N	0.913	1.00
63_I	95_A	0.906	1.00
14_H	17_K	0.905	1.00
133_Q	142_S	0.905	1.00
50_V	75_I	0.897	1.00
61_S	65_R	0.894	1.00
6_V	48_A	0.889	1.00
89_E	92_S	0.885	1.00
49_I	108_V	0.879	1.00
128_S	133_Q	0.868	1.00
152_A	156_T	0.865	1.00
107_E	111_R	0.848	1.00
136_L	159_E	0.843	1.00
5_V	27_V	0.840	1.00
82_E	100_T	0.840	1.00
52_L	86_D	0.837	1.00
10_A	13_R	0.830	1.00
62_L	66_W	0.819	1.00
18_V	22_D	0.818	1.00
74_P	122_L	0.815	1.00
74_P	118_R	0.809	1.00
115_L	118_R	0.807	1.00
40_L	70_D	0.803	1.00
105_I	109_M	0.796	1.00
64_R	68_S	0.793	1.00
134_V	155_Y	0.793	1.00
25_H	109_M	0.792	1.00
189_T	194_M	0.789	1.00
40_L	73_L	0.788	1.00
52_L	81_R	0.786	1.00
187_S	191_D	0.786	1.00
188_H	195_G	0.785	1.00
86_D	89_E	0.783	1.00
142_S	147_V	0.781	1.00
40_L	45_P	0.778	1.00
54_L	62_L	0.776	1.00
160_T	174_L	0.775	1.00
49_I	112_M	0.768	1.00
12_L	103_F	0.767	1.00
104_H	107_E	0.765	1.00
33_A	37_D	0.763	1.00
103_F	108_V	0.762	1.00
173_S	176_L	0.762	1.00
14_H	18_V	0.761	1.00
192_V	196_R	0.760	1.00
97_D	114_A	0.760	1.00
57_E	62_L	0.759	1.00
6_V	62_L	0.755	1.00
78_L	103_F	0.747	1.00
88_V	106_E	0.747	1.00
172_D	176_L	0.744	1.00
190_I	194_M	0.742	1.00
160_T	163_R	0.732	1.00
16_L	108_V	0.731	1.00
66_W	75_I	0.730	1.00
130_P	134_V	0.726	1.00
203_A	208_E	0.725	1.00
33_A	56_D	0.723	1.00
114_A	117_R	0.719	1.00
204_Q	208_E	0.717	1.00
49_I	78_L	0.715	1.00
196_R	199_K	0.714	1.00
111_R	115_L	0.709	1.00
85_Q	106_E	0.708	1.00
204_Q	207_Q	0.708	1.00
119_N	123_A	0.705	1.00
134_V	141_L	0.703	1.00
53_G	80_A	0.698	1.00
72_S	122_L	0.683	1.00
41_N	65_R	0.680	1.00
195_G	199_K	0.678	1.00
139_R	156_T	0.677	1.00
116_M	119_N	0.675	1.00
44_I	70_D	0.673	1.00
91_L	111_R	0.672	1.00
40_L	48_A	0.670	1.00
37_D	40_L	0.668	1.00
114_A	119_N	0.665	1.00
15_H	19_Q	0.663	1.00
2_R	46_D	0.662	1.00
151_T	200_K	0.661	1.00
33_A	54_L	0.661	1.00
49_I	76_L	0.661	1.00
74_P	116_M	0.658	1.00
199_K	202_Q	0.658	1.00
5_V	17_K	0.650	1.00
106_E	110_A	0.648	1.00
156_T	160_T	0.644	1.00
13_R	17_K	0.643	1.00
67_R	74_P	0.643	1.00
19_Q	109_M	0.634	1.00
202_Q	205_Y	0.634	1.00
9_N	80_A	0.632	1.00
41_N	70_D	0.632	1.00
163_R	177_Q	0.630	1.00
85_Q	88_V	0.629	1.00
60_L	86_D	0.628	1.00
76_L	97_D	0.626	1.00
142_S	145_D	0.623	1.00
90_V	95_A	0.623	1.00
7_E	54_L	0.623	1.00
113_Q	117_R	0.622	1.00
194_M	197_L	0.621	1.00
5_V	29_D	0.620	1.00
66_W	71_V	0.620	1.00
37_D	69_N	0.620	1.00
21_Q	27_V	0.618	1.00
207_Q	210_I	0.617	1.00
9_N	12_L	0.617	1.00
92_S	110_A	0.617	1.00
151_T	154_E	0.615	1.00
202_Q	208_E	0.613	1.00
143_I	146_E	0.609	1.00
207_Q	215_G	0.609	1.00
87_K	104_H	0.608	1.00
171_K	187_S	0.608	1.00
63_I	67_R	0.603	1.00
185_R	190_I	0.600	1.00
103_F	107_E	0.596	1.00
205_Y	208_E	0.594	1.00
131_P	135_D	0.593	1.00
84_W	106_E	0.588	1.00
12_L	15_H	0.587	1.00
163_R	169_V	0.587	1.00
110_A	113_Q	0.584	1.00
208_E	211_T	0.584	1.00
158_M	161_L	0.579	1.00
198_R	203_A	0.575	1.00
74_P	119_N	0.572	1.00
161_L	164_N	0.564	1.00
135_D	140_E	0.564	1.00
186_E	189_T	0.564	1.00
139_R	155_Y	0.563	1.00
67_R	73_L	0.558	1.00
19_Q	23_A	0.557	1.00
50_V	54_L	0.551	1.00
52_L	90_V	0.548	1.00
3_V	47_I	0.547	1.00
20_I	25_H	0.546	1.00
66_W	73_L	0.544	1.00
51_D	101_K	0.544	1.00
80_A	102_P	0.542	1.00
193_L	197_L	0.542	1.00
79_T	87_K	0.541	1.00
164_N	177_Q	0.539	1.00
118_R	122_L	0.538	1.00
88_V	91_L	0.538	1.00
5_V	13_R	0.537	1.00
195_G	198_R	0.535	1.00
50_V	66_W	0.535	1.00
191_D	194_M	0.534	1.00
72_S	121_G	0.534	1.00
151_T	161_L	0.531	1.00
35_E	56_D	0.530	1.00
111_R	114_A	0.530	1.00
3_V	20_I	0.529	1.00
74_P	115_L	0.529	1.00
185_R	189_T	0.525	1.00
114_A	118_R	0.521	1.00
8_D	79_T	0.521	1.00
134_V	159_E	0.517	1.00
130_P	133_Q	0.516	1.00
207_Q	211_T	0.516	1.00
204_Q	209_V	0.515	1.00
189_T	196_R	0.513	1.00
161_L	194_M	0.512	1.00
32_D	54_L	0.509	1.00
40_L	62_L	0.508	1.00
6_V	33_A	0.508	1.00
211_T	214_R	0.507	1.00
82_E	102_P	0.507	1.00
136_L	139_R	0.506	1.00
79_T	101_K	0.506	1.00
18_V	21_Q	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	0.9865	100	0.19	Contact Map
3r0jA	2	0.9776	100	0.191	Contact Map
1ys7A	2	0.9955	100	0.193	Contact Map
1kgsA	1	0.9776	100	0.198	Contact Map
4kfcA	2	0.9865	100	0.209	Contact Map
4b09A	2	0.9327	100	0.217	Contact Map
2oqrA	2	0.9865	100	0.218	Contact Map
2hqrA	2	0.9686	100	0.219	Contact Map
1p2fA	1	0.9596	100	0.242	Contact Map
3q9sA	1	0.9372	100	0.245	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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