KDPE - ECOLI - GREMLIN Contacts

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KDPE - KDP operon transcriptional regulatory protein KdpE

UniProt:	P21866	Sequences: MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATTAPDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGYRFML	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10517
Length:	225 (198)
Sequences:	76539 (55286)
Seq/√Len:	3929.0

ECOLI - KDPE RSTA CPXR BAER ARCA CREB YEDW PHOP CUSR BASR QSEB TORR OMPR PHOB UVRY DCUR DPIA FIMZ YHJB NARL UHPA EVGA RCSB NARP YJJQ YGEK BGLJ BARA YEHT CSGD RCSA TORS RCSC ARCB RSSB CHEB YPDB EVGS NTRC GLRR ZRAR ATOC RCSD
BACSU - YVCP YXDJ YYCF YCBL YVRH BCER YRKP YCLJ CITT PHOP RESD CSSR YKOG MALR YFIK CMPA LIAR DCTR YVFU YDFI DESR DEGU YXJL YBDJ YHCZ YESN CHEB LYTT GLNL NATR SP0A CHEV CCDB
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_R	30_E	3.637	1.00
14_R	32_E	3.051	1.00
18_R	30_E	2.886	1.00
7_V	37_G	2.660	1.00
29_F	46_P	2.651	1.00
34_L	58_G	2.601	1.00
35_Q	57_D	2.591	1.00
33_T	57_D	2.525	1.00
42_A	70_W	2.393	1.00
38_L	66_D	2.339	1.00
58_G	66_D	2.227	1.00
3_N	29_F	2.144	1.00
3_N	27_R	2.124	1.00
190_H	193_R	2.053	1.00
18_R	22_E	1.998	1.00
20_A	105_I	1.941	1.00
51_L	63_F	1.930	1.00
87_K	107_E	1.927	1.00
32_E	36_R	1.883	1.00
173_Q	193_R	1.860	1.00
31_A	40_E	1.852	1.00
155_I	158_R	1.847	1.00
33_T	36_R	1.818	1.00
24_D	109_Q	1.814	1.00
54_G	81_R	1.803	1.00
5_L	31_A	1.776	1.00
84_E	104_G	1.750	1.00
59_D	62_E	1.743	1.00
64_I	75_V	1.707	1.00
77_V	90_A	1.679	1.00
77_V	95_A	1.640	1.00
29_F	40_E	1.600	1.00
195_Y	198_H	1.595	1.00
68_R	96_D	1.557	1.00
133_D	146_G	1.543	1.00
66_D	70_W	1.542	1.00
156_E	202_K	1.540	1.00
66_D	69_Q	1.540	1.00
40_E	44_R	1.526	1.00
34_L	63_F	1.519	1.00
161_A	165_N	1.519	1.00
58_G	62_E	1.502	1.00
21_L	112_L	1.470	1.00
38_L	63_F	1.467	1.00
64_I	77_V	1.461	1.00
51_L	64_I	1.427	1.00
53_L	77_V	1.427	1.00
29_F	44_R	1.411	1.00
48_L	112_L	1.403	1.00
97_D	111_R	1.396	1.00
162_V	179_Q	1.380	1.00
40_E	43_T	1.370	1.00
62_E	65_R	1.362	1.00
49_I	73_V	1.346	1.00
8_E	14_R	1.344	1.00
81_R	86_D	1.342	1.00
41_A	67_L	1.331	1.00
130_K	135_T	1.329	1.00
7_V	55_L	1.328	1.00
76_I	115_A	1.325	1.00
172_T	175_Q	1.294	1.00
31_A	37_G	1.277	1.00
35_Q	58_G	1.274	1.00
96_D	118_R	1.271	1.00
92_D	113_R	1.262	1.00
171_L	179_Q	1.253	1.00
40_E	46_P	1.251	1.00
65_R	93_A	1.247	1.00
38_L	58_G	1.243	1.00
3_N	44_R	1.240	1.00
142_V	149_E	1.232	1.00
39_L	43_T	1.229	1.00
11_Q	32_E	1.202	1.00
53_L	61_I	1.199	1.00
162_V	166_N	1.198	1.00
9_D	52_D	1.198	1.00
35_Q	39_L	1.190	1.00
96_D	115_A	1.174	1.00
26_M	113_R	1.168	1.00
5_L	37_G	1.163	1.00
36_R	39_L	1.158	1.00
83_E	86_D	1.150	1.00
36_R	40_E	1.135	1.00
65_R	89_A	1.115	1.00
5_L	46_P	1.112	1.00
204_E	207_P	1.110	1.00
191_Y	195_Y	1.087	1.00
4_V	26_M	1.087	1.00
48_L	116_L	1.085	1.00
24_D	113_R	1.083	1.00
61_I	89_A	1.076	1.00
162_V	171_L	1.075	1.00
84_E	88_I	1.072	1.00
137_D	140_A	1.071	1.00
157_F	161_A	1.069	1.00
194_I	197_G	1.068	1.00
61_I	90_A	1.057	1.00
25_G	113_R	1.050	1.00
190_H	194_I	1.048	1.00
136_V	164_L	1.042	1.00
135_T	144_H	1.031	1.00
174_R	189_S	1.026	1.00
37_G	41_A	1.024	1.00
7_V	49_I	1.020	1.00
51_L	75_V	1.009	1.00
89_A	93_A	1.008	1.00
162_V	176_L	0.996	1.00
109_Q	113_R	0.994	1.00
17_L	78_L	0.994	1.00
61_I	93_A	0.993	1.00
196_M	200_R	0.987	1.00
107_E	110_A	0.984	1.00
5_L	41_A	0.982	1.00
175_Q	179_Q	0.972	1.00
158_R	161_A	0.964	1.00
49_I	67_L	0.957	1.00
110_A	114_V	0.954	1.00
37_G	63_F	0.948	1.00
6_I	28_V	0.941	1.00
85_S	89_A	0.937	1.00
11_Q	14_R	0.932	1.00
53_L	59_D	0.920	1.00
11_Q	15_R	0.915	1.00
55_L	63_F	0.914	1.00
62_E	66_D	0.912	1.00
5_L	40_E	0.911	1.00
31_A	36_R	0.911	1.00
6_I	17_L	0.909	1.00
39_L	42_A	0.908	1.00
15_R	30_E	0.900	1.00
51_L	77_V	0.899	1.00
38_L	42_A	0.894	1.00
3_N	46_P	0.892	1.00
89_A	92_D	0.891	1.00
171_L	175_Q	0.891	1.00
7_V	31_A	0.888	1.00
17_L	108_L	0.888	1.00
12_A	16_F	0.887	1.00
136_V	157_F	0.886	1.00
88_I	92_D	0.882	1.00
18_R	28_V	0.879	1.00
138_L	161_A	0.875	1.00
154_P	158_R	0.873	1.00
50_I	108_L	0.873	1.00
64_I	95_A	0.868	1.00
153_T	202_K	0.865	1.00
64_I	93_A	0.865	1.00
115_A	118_R	0.862	1.00
26_M	109_Q	0.860	1.00
87_K	100_S	0.857	1.00
76_I	111_R	0.851	1.00
107_E	111_R	0.843	1.00
141_R	158_R	0.839	1.00
189_S	193_R	0.838	1.00
53_L	86_D	0.838	1.00
144_H	149_E	0.837	1.00
63_F	67_L	0.832	1.00
34_L	38_L	0.830	1.00
174_R	178_N	0.827	1.00
50_I	78_L	0.810	1.00
84_E	87_K	0.808	1.00
41_A	73_V	0.807	1.00
88_I	106_G	0.806	1.00
19_T	23_G	0.801	1.00
198_H	201_Q	0.799	1.00
54_G	80_A	0.798	1.00
49_I	75_V	0.797	1.00
190_H	197_G	0.795	1.00
200_R	205_Q	0.790	1.00
65_R	69_Q	0.789	1.00
91_L	111_R	0.787	1.00
15_R	18_R	0.787	1.00
82_S	100_S	0.774	1.00
105_I	109_Q	0.772	1.00
6_I	18_R	0.766	1.00
13_I	103_F	0.765	1.00
76_I	97_D	0.764	1.00
53_L	81_R	0.764	1.00
8_E	55_L	0.764	1.00
197_G	201_Q	0.763	1.00
114_V	117_R	0.762	1.00
128_L	135_T	0.755	1.00
38_L	41_A	0.749	1.00
58_G	63_F	0.748	1.00
103_F	108_L	0.742	1.00
85_S	106_G	0.742	1.00
165_N	179_Q	0.739	1.00
34_L	57_D	0.737	1.00
193_R	196_M	0.734	1.00
7_V	63_F	0.731	1.00
41_A	46_P	0.724	1.00
144_H	147_E	0.714	1.00
86_D	89_A	0.712	1.00
6_I	30_E	0.712	1.00
173_Q	189_S	0.710	1.00
84_E	106_G	0.708	1.00
130_K	133_D	0.706	1.00
3_N	47_D	0.687	1.00
15_R	19_T	0.687	1.00
159_L	163_L	0.684	1.00
141_R	157_F	0.684	1.00
79_S	87_K	0.684	1.00
74_P	96_D	0.679	1.00
50_I	112_L	0.678	1.00
175_Q	178_N	0.678	1.00
51_L	55_L	0.675	1.00
92_D	110_A	0.673	1.00
74_P	116_L	0.671	1.00
104_G	107_E	0.671	1.00
21_L	26_M	0.665	1.00
90_A	95_A	0.663	1.00
42_A	66_D	0.663	1.00
16_F	20_A	0.661	1.00
116_L	119_H	0.655	1.00
194_I	198_H	0.652	1.00
10_E	13_I	0.652	1.00
133_D	145_R	0.648	1.00
67_L	75_V	0.647	1.00
145_R	206_D	0.646	1.00
78_L	103_F	0.645	1.00
41_A	49_I	0.638	1.00
50_I	76_I	0.637	1.00
134_V	145_R	0.636	1.00
14_R	18_R	0.636	1.00
187_E	192_L	0.635	1.00
4_V	21_L	0.633	1.00
162_V	165_N	0.629	1.00
114_V	119_H	0.626	1.00
163_L	196_M	0.624	1.00
10_E	80_A	0.623	1.00
34_L	55_L	0.622	1.00
22_E	27_R	0.614	1.00
87_K	104_G	0.612	1.00
20_A	109_Q	0.612	1.00
41_A	71_S	0.607	1.00
131_F	134_V	0.603	1.00
106_G	110_A	0.602	1.00
41_A	63_F	0.601	1.00
111_R	115_A	0.600	1.00
131_F	164_L	0.599	1.00
68_R	71_S	0.598	1.00
61_I	86_D	0.598	1.00
22_E	28_V	0.596	1.00
130_K	134_V	0.592	1.00
53_L	90_A	0.591	1.00
4_V	48_L	0.591	1.00
119_H	123_T	0.590	1.00
153_T	156_E	0.584	1.00
128_L	137_D	0.582	1.00
7_V	34_L	0.579	1.00
145_R	204_E	0.577	1.00
158_R	162_V	0.574	1.00
52_D	101_K	0.573	1.00
68_R	73_V	0.572	1.00
72_A	122_T	0.571	1.00
133_D	137_D	0.567	1.00
134_V	143_I	0.566	1.00
97_D	114_V	0.563	1.00
9_D	79_S	0.559	1.00
90_A	98_Y	0.555	1.00
38_L	70_W	0.554	1.00
136_V	161_A	0.554	1.00
125_P	128_L	0.551	1.00
145_R	205_Q	0.551	1.00
68_R	74_P	0.550	1.00
74_P	119_H	0.549	1.00
103_F	107_E	0.549	1.00
72_A	121_A	0.547	1.00
13_I	16_F	0.545	1.00
4_V	112_L	0.544	1.00
51_L	67_L	0.544	1.00
145_R	148_E	0.543	1.00
33_T	55_L	0.541	1.00
80_A	102_P	0.540	1.00
166_N	179_Q	0.540	1.00
6_I	14_R	0.539	1.00
165_N	171_L	0.537	1.00
129_V	138_L	0.535	1.00
10_E	102_P	0.534	1.00
138_L	165_N	0.532	1.00
187_E	191_Y	0.529	1.00
67_L	73_V	0.529	1.00
129_V	132_S	0.528	1.00
41_A	70_W	0.527	1.00
20_A	24_D	0.526	1.00
129_V	164_L	0.525	1.00
64_I	68_R	0.525	1.00
92_D	106_G	0.523	1.00
26_M	116_L	0.521	1.00
88_I	91_L	0.520	1.00
163_L	171_L	0.517	1.00
7_V	51_L	0.516	1.00
160_L	163_L	0.516	1.00
155_I	195_Y	0.515	1.00
136_V	143_I	0.511	1.00
137_D	142_V	0.510	1.00
188_H	191_Y	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
4kfcA	2	0.9956	100	0.164	Contact Map
4b09A	2	0.9289	100	0.177	Contact Map
2gwrA	1	0.9822	100	0.181	Contact Map
2oqrA	2	0.9956	100	0.184	Contact Map
3r0jA	2	0.9689	100	0.191	Contact Map
1ys7A	2	0.9911	100	0.199	Contact Map
1kgsA	1	0.9644	100	0.222	Contact Map
1p2fA	1	0.9556	100	0.222	Contact Map
3q9sA	1	0.9333	100	0.242	Contact Map
2hqrA	2	0.9511	100	0.25	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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