YCNK - BACSU - GREMLIN Contacts

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YCNK - HTH-type transcriptional repressor YcnK

UniProt:	P94433	Sequences: MLPINRQQHILKWLKEEGSLRISDISARFGVSEMTVYRDVNQLVQSNQVIKTAGGITLPVRTPQTDHMCSYCLKPVNQAHSVQLITVNQDIEQLCCAHCAFLRYADKTEEVSHLICRDFLLQTTVSAGSAYFVVNAELNLHCCQPQAIPFATLDHAERFQKGFGGAVCTFDQALEDMLQDRKKRCTCTKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	190 (172)
Sequences:	104 (89)
Seq/√Len:	6.8

BACSU - YCNK

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_E	28_R	3.176	0.86
153_L	157_E	2.540	0.70
95_C	98_H	2.285	0.61
51_K	172_Q	2.081	0.54
119_F	163_F	2.017	0.51
98_H	102_L	2.009	0.51
126_S	152_T	1.940	0.49
35_T	38_R	1.906	0.47
13_W	36_V	1.867	0.46
74_K	142_C	1.734	0.41
98_H	146_Q	1.721	0.40
29_F	36_V	1.720	0.40
26_S	33_E	1.716	0.40
165_G	170_F	1.716	0.40
96_C	99_C	1.712	0.40
88_N	176_D	1.704	0.40
37_Y	74_K	1.704	0.40
128_G	172_Q	1.700	0.40
34_M	38_R	1.694	0.39
82_V	104_Y	1.690	0.39
96_C	146_Q	1.689	0.39
66_D	76_V	1.679	0.39
136_A	140_L	1.664	0.38
95_C	146_Q	1.633	0.37
14_L	67_H	1.626	0.37
95_C	173_A	1.605	0.36
116_C	136_A	1.592	0.36
92_E	103_R	1.583	0.35
106_D	131_Y	1.575	0.35
51_K	134_V	1.555	0.35
116_C	119_F	1.547	0.34
69_C	72_C	1.528	0.34
96_C	163_F	1.522	0.33
83_Q	86_T	1.516	0.33
116_C	140_L	1.506	0.33
92_E	124_T	1.492	0.32
95_C	99_C	1.491	0.32
114_L	137_E	1.478	0.32
136_A	149_P	1.465	0.32
166_A	176_D	1.456	0.31
116_C	130_A	1.442	0.31
18_G	28_R	1.432	0.30
121_L	166_A	1.424	0.30
167_V	171_D	1.406	0.30
22_I	26_S	1.387	0.29
76_V	133_V	1.383	0.29
136_A	141_H	1.380	0.29
49_V	56_I	1.357	0.28
124_T	146_Q	1.343	0.28
95_C	102_L	1.328	0.27
12_K	129_S	1.323	0.27
99_C	146_Q	1.318	0.27
82_V	162_G	1.298	0.26
130_A	136_A	1.282	0.26
47_N	54_G	1.279	0.26
127_A	172_Q	1.275	0.26
70_S	135_N	1.274	0.26
16_E	62_T	1.272	0.26
161_K	167_V	1.270	0.26
10_I	35_T	1.254	0.25
132_F	170_F	1.250	0.25
118_D	150_F	1.246	0.25
70_S	82_V	1.232	0.24
78_Q	159_F	1.228	0.24
32_S	39_D	1.220	0.24
100_A	132_F	1.220	0.24
88_N	108_T	1.218	0.24
68_M	76_V	1.209	0.24
12_K	131_Y	1.202	0.24
57_T	171_D	1.200	0.24
31_V	39_D	1.183	0.23
22_I	25_I	1.176	0.23
10_I	13_W	1.168	0.23
137_E	167_V	1.150	0.22
64_Q	88_N	1.149	0.22
100_A	105_A	1.148	0.22
25_I	83_Q	1.130	0.22
26_S	32_S	1.130	0.22
13_W	26_S	1.129	0.22
10_I	23_S	1.125	0.22
150_F	159_F	1.122	0.22
23_S	161_K	1.116	0.21
74_K	140_L	1.114	0.21
96_C	162_G	1.107	0.21
18_G	180_D	1.105	0.21
176_D	181_R	1.102	0.21
38_R	142_C	1.102	0.21
121_L	129_S	1.092	0.21
31_V	34_M	1.092	0.21
56_I	85_I	1.089	0.21
61_R	117_R	1.082	0.21
98_H	170_F	1.081	0.20
67_H	73_L	1.076	0.20
99_C	102_L	1.075	0.20
98_H	181_R	1.070	0.20
33_E	38_R	1.065	0.20
19_S	25_I	1.063	0.20
135_N	146_Q	1.060	0.20
35_T	39_D	1.051	0.20
96_C	145_P	1.038	0.19
59_P	152_T	1.030	0.19
98_H	163_F	1.023	0.19
125_V	136_A	1.019	0.19
133_V	160_Q	1.016	0.19
114_L	128_G	0.993	0.18
13_W	28_R	0.993	0.18
64_Q	93_Q	0.988	0.18
14_L	25_I	0.981	0.18
140_L	149_P	0.981	0.18
129_S	157_E	0.975	0.18
45_Q	172_Q	0.967	0.18
168_C	183_K	0.965	0.18
101_F	176_D	0.963	0.18
133_V	167_V	0.958	0.18
18_G	29_F	0.956	0.18
69_C	150_F	0.954	0.18
72_C	150_F	0.954	0.18
96_C	102_L	0.951	0.17
57_T	177_M	0.946	0.17
105_A	157_E	0.945	0.17
23_S	28_R	0.940	0.17
71_Y	102_L	0.934	0.17
11_L	17_E	0.933	0.17
21_R	24_D	0.928	0.17
20_L	23_S	0.916	0.17
157_E	161_K	0.915	0.17
23_S	29_F	0.912	0.17
116_C	141_H	0.907	0.17
32_S	38_R	0.900	0.16
119_F	150_F	0.898	0.16
20_L	28_R	0.898	0.16
16_E	48_Q	0.895	0.16
51_K	165_G	0.893	0.16
23_S	44_V	0.891	0.16
145_P	163_F	0.880	0.16
151_A	155_H	0.879	0.16
12_K	30_G	0.878	0.16
31_V	36_V	0.878	0.16
84_L	97_A	0.867	0.16
14_L	158_R	0.866	0.16
34_M	145_P	0.856	0.15
34_M	39_D	0.848	0.15
19_S	28_R	0.847	0.15
79_A	148_I	0.846	0.15
13_W	25_I	0.833	0.15
96_C	142_C	0.831	0.15
29_F	109_E	0.823	0.15
103_R	146_Q	0.820	0.15
154_D	158_R	0.819	0.15
147_A	182_K	0.818	0.15
48_Q	108_T	0.814	0.15
123_T	151_A	0.814	0.15
19_S	23_S	0.814	0.15
30_G	63_P	0.809	0.15
169_T	172_Q	0.807	0.15
26_S	31_V	0.805	0.15
70_S	86_T	0.799	0.14
142_C	163_F	0.796	0.14
102_L	173_A	0.791	0.14
58_L	161_K	0.785	0.14
16_E	20_L	0.782	0.14
32_S	35_T	0.782	0.14
38_R	43_L	0.780	0.14
140_L	146_Q	0.773	0.14
133_V	141_H	0.771	0.14
132_F	177_M	0.761	0.14
25_I	133_V	0.757	0.14
24_D	175_E	0.754	0.14
91_I	133_V	0.752	0.14
42_Q	169_T	0.752	0.14
121_L	172_Q	0.751	0.14
59_P	149_P	0.751	0.14
149_P	182_K	0.750	0.14
103_R	116_C	0.748	0.13
29_F	129_S	0.747	0.13
25_I	86_T	0.739	0.13
38_R	145_P	0.729	0.13
47_N	131_Y	0.729	0.13
99_C	162_G	0.727	0.13
52_T	91_I	0.718	0.13
72_C	118_D	0.711	0.13
69_C	118_D	0.711	0.13
66_D	182_K	0.706	0.13
69_C	156_A	0.705	0.13
72_C	156_A	0.705	0.13
60_V	167_V	0.703	0.13
98_H	145_P	0.693	0.13
101_F	171_D	0.689	0.12
71_Y	89_Q	0.689	0.12
114_L	127_A	0.686	0.12
35_T	40_V	0.686	0.12
120_L	163_F	0.685	0.12
56_I	64_Q	0.681	0.12
84_L	166_A	0.678	0.12
87_V	171_D	0.677	0.12
135_N	170_F	0.677	0.12
61_R	65_T	0.675	0.12
81_S	115_I	0.673	0.12
125_V	138_L	0.671	0.12
114_L	160_Q	0.671	0.12
42_Q	45_Q	0.667	0.12
115_I	161_K	0.662	0.12
138_L	177_M	0.661	0.12
102_L	146_Q	0.660	0.12
142_C	162_G	0.657	0.12
130_A	144_Q	0.649	0.12
35_T	54_G	0.647	0.12
45_Q	90_D	0.647	0.12
14_L	127_A	0.637	0.12
134_V	180_D	0.636	0.12
114_L	133_V	0.631	0.12
43_L	165_G	0.631	0.12
78_Q	148_I	0.629	0.12
60_V	88_N	0.626	0.11
61_R	101_F	0.618	0.11
110_E	178_L	0.618	0.11
102_L	163_F	0.613	0.11
35_T	47_N	0.607	0.11
73_L	94_L	0.601	0.11
157_E	169_T	0.598	0.11
130_A	149_P	0.595	0.11
14_L	22_I	0.594	0.11
92_E	146_Q	0.591	0.11
12_K	76_V	0.590	0.11
141_H	148_I	0.590	0.11
119_F	162_G	0.588	0.11
34_M	142_C	0.582	0.11
24_D	110_E	0.577	0.11
40_V	164_G	0.574	0.11
32_S	37_Y	0.572	0.11
89_Q	117_R	0.561	0.11
14_L	62_T	0.558	0.10
54_G	164_G	0.555	0.10
114_L	131_Y	0.552	0.10
145_P	162_G	0.551	0.10
17_E	29_F	0.545	0.10
23_S	26_S	0.544	0.10
136_A	148_I	0.535	0.10
76_V	174_L	0.534	0.10
100_A	142_C	0.534	0.10
95_C	162_G	0.534	0.10
119_F	164_G	0.527	0.10
127_A	165_G	0.522	0.10
117_R	140_L	0.522	0.10
80_H	86_T	0.521	0.10
31_V	35_T	0.520	0.10
12_K	177_M	0.519	0.10
80_H	173_A	0.518	0.10
38_R	54_G	0.518	0.10
94_L	157_E	0.510	0.10
78_Q	136_A	0.507	0.10
65_T	100_A	0.506	0.10
93_Q	122_Q	0.506	0.10
83_Q	109_E	0.505	0.10
67_H	149_P	0.504	0.10
102_L	148_I	0.503	0.10
30_G	149_P	0.502	0.10
78_Q	141_H	0.500	0.10

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
2hpuA	1	0.5737	100	0.553	Contact Map
2l0kA	1	0.3947	98	0.868	Contact Map
4a0zA	2	0.8474	97.9	0.871	Contact Map
2w48A	3	0.8895	97.8	0.875	Contact Map
1oyiA	1	0.3263	97.7	0.877	Contact Map
1b4aA	5	0.7053	97.4	0.884	Contact Map
1j5yA	4	0.7316	97.3	0.887	Contact Map
1xmkA	1	0.3789	97.1	0.889	Contact Map
2heoA	1	0.3053	97.1	0.89	Contact Map
2vxzA	1	0.7105	97.1	0.89	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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