YOKF - BACSU - GREMLIN Contacts

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YOKF - SPBc2 prophage-derived endonuclease YokF

UniProt:	O32001	Sequences: MKKVLLGFAAFTLSLSLAACSSNDSEKVSTEKETPQASTDVEKKTEQKESTKEKTADKSKEKDKKELVDVTLDRAVDGDTIKVTYNGNVDTVRYLLIDTPETKKPNSCVQPYGEDASKRNKELVNSGKLQLEFDKGDRRDKYGRLLAYVYVDGKSVQETLLKEGLARVAYVYEPNTKYIDQFKKDEQEAKSEKLSIWSKNGYVTDRGFNGCVKEKTTAVKKATTSKPAATQPTTPKASSETSTTTEKEASSETTGGTETFKNCTELRKKYPNGVPSSHPAYQSKMDRDHDNYACER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	296 (244)
Sequences:	184 (171)
Seq/√Len:	10.9

BACSU - YOKF YNCB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
266_L	270_Y	3.017	0.94
266_L	269_K	2.847	0.93
123_L	156_V	2.783	0.92
235_P	241_T	2.632	0.89
79_D	101_E	2.622	0.89
83_V	131_L	2.528	0.87
270_Y	273_G	2.502	0.86
266_L	271_P	2.493	0.86
82_K	91_T	2.435	0.85
266_L	273_G	2.262	0.80
202_Y	207_G	2.252	0.80
94_Y	157_Q	2.238	0.79
72_L	126_S	2.219	0.79
155_S	182_F	2.200	0.78
93_R	142_Y	2.171	0.77
96_L	196_I	2.151	0.77
271_P	274_V	2.129	0.76
263_C	273_G	2.111	0.75
131_L	149_V	2.037	0.72
90_D	139_R	2.017	0.72
101_E	144_R	2.013	0.71
72_L	129_L	2.008	0.71
9_A	21_S	1.983	0.70
102_T	113_G	1.934	0.68
101_E	142_Y	1.929	0.68
263_C	267_R	1.857	0.65
93_R	101_E	1.831	0.64
231_Q	235_P	1.787	0.62
262_N	270_Y	1.784	0.62
126_S	129_L	1.761	0.61
119_R	123_L	1.753	0.60
67_L	130_Q	1.739	0.60
159_T	162_K	1.718	0.59
79_D	98_D	1.713	0.58
187_Q	190_K	1.702	0.58
231_Q	234_T	1.700	0.58
72_L	127_G	1.650	0.55
10_A	16_S	1.647	0.55
96_L	171_V	1.646	0.55
103_K	117_S	1.636	0.55
98_D	101_E	1.623	0.54
120_N	156_V	1.621	0.54
260_F	271_P	1.605	0.53
109_V	114_E	1.605	0.53
124_V	129_L	1.557	0.51
75_A	126_S	1.534	0.50
93_R	98_D	1.506	0.49
44_K	52_K	1.495	0.48
126_S	157_Q	1.493	0.48
204_T	207_G	1.467	0.47
263_C	266_L	1.460	0.46
75_A	129_L	1.440	0.45
266_L	272_N	1.427	0.45
92_V	143_G	1.410	0.44
166_A	197_W	1.394	0.43
92_V	147_A	1.390	0.43
111_P	168_V	1.385	0.43
242_S	251_S	1.374	0.42
234_T	254_T	1.368	0.42
257_T	263_C	1.357	0.42
113_G	142_Y	1.352	0.41
102_T	109_V	1.350	0.41
11_F	19_A	1.340	0.41
244_T	266_L	1.337	0.41
269_K	273_G	1.335	0.40
104_K	108_C	1.332	0.40
13_L	16_S	1.313	0.39
79_D	144_R	1.300	0.39
263_C	274_V	1.300	0.39
148_Y	178_Y	1.290	0.38
119_R	165_L	1.280	0.38
242_S	272_N	1.279	0.38
119_R	163_E	1.279	0.38
120_N	178_Y	1.273	0.38
251_S	272_N	1.272	0.38
99_T	102_T	1.263	0.37
262_N	266_L	1.263	0.37
93_R	140_D	1.255	0.37
262_N	271_P	1.252	0.37
164_G	189_A	1.232	0.36
95_L	153_G	1.222	0.35
161_L	182_F	1.213	0.35
243_T	263_C	1.213	0.35
237_A	240_E	1.212	0.35
237_A	257_T	1.212	0.35
243_T	251_S	1.210	0.35
266_L	274_V	1.209	0.35
14_S	24_D	1.206	0.35
264_T	270_Y	1.204	0.35
262_N	267_R	1.199	0.34
148_Y	168_V	1.196	0.34
267_R	273_G	1.194	0.34
232_P	257_T	1.191	0.34
120_N	124_V	1.189	0.34
112_Y	195_S	1.180	0.34
232_P	235_P	1.177	0.33
270_Y	274_V	1.176	0.33
226_K	229_A	1.175	0.33
104_K	107_S	1.173	0.33
167_R	196_I	1.169	0.33
109_V	118_K	1.169	0.33
161_L	185_D	1.162	0.33
15_L	60_K	1.160	0.33
244_T	251_S	1.158	0.33
186_E	190_K	1.156	0.33
148_Y	197_W	1.151	0.32
264_T	271_P	1.139	0.32
99_T	109_V	1.139	0.32
50_S	53_E	1.126	0.31
263_C	275_P	1.121	0.31
147_A	169_A	1.115	0.31
85_Y	133_F	1.115	0.31
9_A	12_T	1.110	0.31
148_Y	174_P	1.105	0.30
262_N	273_G	1.100	0.30
54_K	58_K	1.098	0.30
124_V	156_V	1.094	0.30
231_Q	241_T	1.093	0.30
246_E	270_Y	1.088	0.30
112_Y	178_Y	1.087	0.30
165_L	175_N	1.087	0.30
11_F	76_V	1.086	0.30
262_N	272_N	1.084	0.30
96_L	197_W	1.083	0.30
235_P	257_T	1.080	0.29
14_S	20_C	1.077	0.29
242_S	245_T	1.073	0.29
243_T	247_K	1.072	0.29
187_Q	191_S	1.068	0.29
97_I	163_E	1.055	0.28
83_V	129_L	1.055	0.28
271_P	275_P	1.055	0.28
115_D	124_V	1.040	0.28
94_Y	108_C	1.035	0.28
96_L	148_Y	1.034	0.28
82_K	172_Y	1.026	0.27
94_Y	159_T	1.025	0.27
78_G	101_E	1.021	0.27
264_T	273_G	1.019	0.27
97_I	160_L	1.014	0.27
260_F	265_E	1.014	0.27
243_T	266_L	1.006	0.27
82_K	89_V	1.004	0.26
245_T	248_E	0.995	0.26
70_V	124_V	0.985	0.26
267_R	271_P	0.980	0.26
107_S	165_L	0.975	0.25
241_T	251_S	0.966	0.25
237_A	256_G	0.966	0.25
270_Y	275_P	0.965	0.25
263_C	272_N	0.960	0.25
14_S	22_S	0.958	0.25
132_E	177_K	0.958	0.25
267_R	274_V	0.947	0.24
113_G	144_R	0.944	0.24
105_P	109_V	0.942	0.24
104_K	112_Y	0.941	0.24
263_C	271_P	0.941	0.24
79_D	93_R	0.941	0.24
98_D	142_Y	0.935	0.24
133_F	147_A	0.934	0.24
234_T	257_T	0.934	0.24
171_V	196_I	0.929	0.24
260_F	270_Y	0.926	0.24
158_E	196_I	0.926	0.24
203_V	207_G	0.918	0.23
167_R	202_Y	0.917	0.23
231_Q	257_T	0.914	0.23
11_F	21_S	0.913	0.23
96_L	198_S	0.908	0.23
10_A	46_E	0.902	0.23
77_D	101_E	0.901	0.23
111_P	148_Y	0.901	0.23
264_T	267_R	0.898	0.23
113_G	117_S	0.897	0.23
46_E	49_E	0.895	0.23
111_P	132_E	0.892	0.23
233_T	257_T	0.883	0.22
247_K	251_S	0.881	0.22
244_T	272_N	0.878	0.22
263_C	269_K	0.877	0.22
101_E	113_G	0.876	0.22
94_Y	162_K	0.867	0.22
14_S	19_A	0.866	0.22
101_E	140_D	0.864	0.22
9_A	13_L	0.863	0.22
167_R	207_G	0.862	0.22
186_E	197_W	0.858	0.21
262_N	274_V	0.851	0.21
134_D	146_L	0.848	0.21
244_T	270_Y	0.845	0.21
152_D	165_L	0.845	0.21
243_T	248_E	0.845	0.21
97_I	188_E	0.843	0.21
182_F	197_W	0.842	0.21
264_T	268_K	0.842	0.21
132_E	148_Y	0.839	0.21
124_V	157_Q	0.833	0.21
96_L	202_Y	0.832	0.21
243_T	272_N	0.830	0.21
95_L	138_R	0.821	0.20
10_A	24_D	0.818	0.20
240_E	256_G	0.816	0.20
103_K	107_S	0.815	0.20
72_L	124_V	0.811	0.20
96_L	169_A	0.811	0.20
49_E	53_E	0.804	0.20
10_A	13_L	0.802	0.20
242_S	248_E	0.799	0.20
94_Y	120_N	0.798	0.20
148_Y	166_A	0.789	0.19
92_V	123_L	0.788	0.19
93_R	144_R	0.785	0.19
245_T	251_S	0.780	0.19
96_L	168_V	0.779	0.19
232_P	241_T	0.773	0.19
76_V	103_K	0.772	0.19
244_T	253_T	0.769	0.19
168_V	186_E	0.768	0.19
139_R	161_L	0.768	0.19
10_A	14_S	0.766	0.19
133_F	175_N	0.764	0.19
130_Q	152_D	0.763	0.18
155_S	161_L	0.759	0.18
77_D	144_R	0.759	0.18
96_L	179_I	0.753	0.18
241_T	257_T	0.753	0.18
15_L	23_N	0.749	0.18
225_S	230_T	0.747	0.18
110_Q	167_R	0.746	0.18
98_D	144_R	0.744	0.18
175_N	200_N	0.742	0.18
93_R	113_G	0.737	0.18
45_T	51_T	0.732	0.18
272_N	275_P	0.730	0.18
24_D	42_E	0.717	0.17
251_S	254_T	0.716	0.17
196_I	203_V	0.715	0.17
179_I	183_K	0.712	0.17
129_L	195_S	0.702	0.17
169_A	179_I	0.702	0.17
79_D	142_Y	0.699	0.17
233_T	251_S	0.697	0.17
124_V	127_G	0.696	0.17
226_K	230_T	0.692	0.17
233_T	236_K	0.690	0.16
140_D	144_R	0.689	0.16
77_D	142_Y	0.689	0.16
48_K	51_T	0.687	0.16
233_T	239_S	0.687	0.16
96_L	203_V	0.684	0.16
72_L	75_A	0.684	0.16
242_S	246_E	0.679	0.16
51_T	57_D	0.677	0.16
17_L	20_C	0.674	0.16
10_A	17_L	0.673	0.16
112_Y	186_E	0.667	0.16
133_F	138_R	0.665	0.16
110_Q	176_T	0.663	0.16
239_S	245_T	0.662	0.16
47_Q	55_T	0.662	0.16
105_P	174_P	0.660	0.16
258_E	263_C	0.659	0.16
86_N	158_E	0.656	0.16
96_L	138_R	0.654	0.16
70_V	119_R	0.654	0.16
98_D	147_A	0.653	0.16
99_T	113_G	0.648	0.15
175_N	180_D	0.646	0.15
94_Y	141_K	0.643	0.15
120_N	155_S	0.643	0.15
139_R	186_E	0.640	0.15
72_L	92_V	0.639	0.15
241_T	269_K	0.639	0.15
157_Q	161_L	0.638	0.15
167_R	203_V	0.636	0.15
43_K	47_Q	0.630	0.15
243_T	262_N	0.629	0.15
129_L	157_Q	0.628	0.15
102_T	105_P	0.625	0.15
236_K	251_S	0.621	0.15
135_K	176_T	0.621	0.15
13_L	19_A	0.621	0.15
43_K	48_K	0.620	0.15
243_T	270_Y	0.620	0.15
49_E	58_K	0.616	0.15
151_V	154_K	0.615	0.15
10_A	21_S	0.608	0.14
173_E	176_T	0.608	0.14
92_V	145_L	0.608	0.14
91_T	120_N	0.607	0.14
161_L	166_A	0.601	0.14
9_A	14_S	0.596	0.14
76_V	178_Y	0.596	0.14
181_Q	184_K	0.595	0.14
44_K	47_Q	0.594	0.14
236_K	247_K	0.594	0.14
56_A	63_D	0.593	0.14
148_Y	182_F	0.591	0.14
95_L	152_D	0.589	0.14
261_K	265_E	0.584	0.14
152_D	158_E	0.583	0.14
95_L	151_V	0.583	0.14
140_D	149_V	0.583	0.14
108_C	186_E	0.581	0.14
124_V	269_K	0.581	0.14
97_I	102_T	0.581	0.14
125_N	190_K	0.578	0.14
239_S	257_T	0.575	0.14
131_L	134_D	0.575	0.14
100_P	164_G	0.573	0.14
50_S	57_D	0.572	0.14
254_T	272_N	0.571	0.14
110_Q	208_F	0.569	0.14
132_E	178_Y	0.566	0.13
256_G	271_P	0.565	0.13
117_S	121_K	0.559	0.13
110_Q	153_G	0.559	0.13
155_S	174_P	0.559	0.13
13_L	18_A	0.558	0.13
95_L	182_F	0.557	0.13
102_T	176_T	0.557	0.13
130_Q	175_N	0.553	0.13
257_T	266_L	0.553	0.13
15_L	21_S	0.553	0.13
242_S	254_T	0.552	0.13
100_P	115_D	0.552	0.13
167_R	186_E	0.551	0.13
44_K	49_E	0.550	0.13
92_V	149_V	0.550	0.13
16_S	19_A	0.549	0.13
49_E	56_A	0.548	0.13
158_E	181_Q	0.548	0.13
150_Y	155_S	0.543	0.13
92_V	169_A	0.542	0.13
72_L	95_L	0.536	0.13
15_L	45_T	0.536	0.13
83_V	161_L	0.536	0.13
87_G	100_P	0.535	0.13
81_I	145_L	0.535	0.13
72_L	157_Q	0.534	0.13
19_A	162_K	0.533	0.13
240_E	259_T	0.532	0.13
120_N	126_S	0.531	0.13
147_A	208_F	0.528	0.13
19_A	215_K	0.527	0.13
248_E	273_G	0.526	0.13
243_T	271_P	0.525	0.13
44_K	48_K	0.524	0.13
269_K	274_V	0.524	0.13
147_A	163_E	0.521	0.12
46_E	51_T	0.518	0.12
254_T	260_F	0.517	0.12
137_D	185_D	0.515	0.12
119_R	122_E	0.515	0.12
70_V	81_I	0.514	0.12
42_E	49_E	0.510	0.12
74_R	82_K	0.509	0.12
130_Q	155_S	0.509	0.12
169_A	202_Y	0.508	0.12
250_S	274_V	0.507	0.12
132_E	168_V	0.507	0.12
153_G	183_K	0.505	0.12
129_L	194_L	0.504	0.12
141_K	145_L	0.503	0.12
103_K	108_C	0.500	0.12

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
4eqpA	1	0.4324	100	0.597	Contact Map
4qmgA	3	0.6622	100	0.639	Contact Map
3bdlA	2	0.7365	100	0.643	Contact Map
2wacA	1	0.6284	99.9	0.752	Contact Map
2hqxA	2	0.2027	99.9	0.753	Contact Map
4b9wA	2	0.5304	97	0.92	Contact Map
4q5yA	2	0.5304	86.9	0.946	Contact Map
4b9xA	1	0.5507	85.5	0.947	Contact Map
3zbiC	1	0.0912	81.8	0.95	Contact Map
3ntkA	1	0.5236	77.2	0.952	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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