XTMA - BACSU - GREMLIN Contacts

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XTMA - PBSX phage terminase small subunit

UniProt:	P39785	Sequences: MKTQQREQALAIYQQHQGKITNRAIADTIGVSAKTIGIWKKQDKWKEALFSASKNEQKQRPINNDELNERQRLFCLYYVKSFNATQSAIKAGYSPDSAHVTGSRLLKNEKVAAEIRRIKKEMVNEMFIEAMDVLQVYIKIAFADITDYVTFGKKEVQAVGKSGPLFDEDDNPIMKEISFVDVKDSGLVDGTIVTEAKLGKEGIAIKLADKMKALEKLSLYFDLFPDQFKQKIENEKLKLAKQKAEKTDDSQEPIEIMIKRKERKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	265 (243)
Sequences:	170 (132)
Seq/√Len:	8.5

BACSU - XTMA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
101_T	109_E	4.705	0.99
104_R	109_E	3.907	0.97
22_N	37_G	3.703	0.96
38_I	42_Q	3.420	0.94
107_K	110_K	3.343	0.94
197_K	204_A	3.237	0.92
99_H	107_K	3.055	0.90
88_A	93_Y	3.004	0.89
99_H	110_K	2.909	0.87
103_S	110_K	2.733	0.84
22_N	34_K	2.584	0.80
114_E	117_R	2.514	0.78
88_A	95_P	2.481	0.77
146_T	190_G	2.416	0.75
84_A	102_G	2.383	0.74
25_I	39_W	2.332	0.73
33_A	37_G	2.269	0.70
135_Q	139_K	2.230	0.69
26_A	40_K	2.196	0.68
35_T	38_I	2.107	0.64
12_I	19_K	2.086	0.64
9_A	12_I	2.021	0.61
23_R	33_A	1.934	0.57
31_V	36_I	1.895	0.56
100_V	110_K	1.824	0.53
24_A	27_D	1.813	0.52
105_L	109_E	1.805	0.52
101_T	104_R	1.767	0.50
12_I	43_D	1.725	0.49
12_I	16_H	1.724	0.49
25_I	36_I	1.718	0.48
37_G	42_Q	1.692	0.47
12_I	20_I	1.673	0.46
29_I	36_I	1.672	0.46
29_I	32_S	1.646	0.45
9_A	43_D	1.646	0.45
88_A	101_T	1.645	0.45
22_N	29_I	1.628	0.45
136_V	139_K	1.614	0.44
215_E	219_L	1.599	0.43
29_I	39_W	1.583	0.43
155_E	174_M	1.530	0.40
103_S	107_K	1.527	0.40
154_K	181_D	1.514	0.40
84_A	106_L	1.474	0.38
97_S	104_R	1.451	0.37
225_P	228_F	1.437	0.37
32_S	39_W	1.436	0.37
9_A	38_I	1.432	0.37
36_I	39_W	1.430	0.36
28_T	37_G	1.404	0.35
29_I	43_D	1.393	0.35
26_A	45_W	1.386	0.35
22_N	33_A	1.380	0.35
12_I	38_I	1.376	0.34
134_L	216_K	1.375	0.34
19_K	43_D	1.362	0.34
13_Y	17_Q	1.349	0.33
22_N	38_I	1.344	0.33
102_G	106_L	1.332	0.33
33_A	38_I	1.320	0.32
10_L	14_Q	1.305	0.32
101_T	105_L	1.301	0.32
20_I	36_I	1.296	0.31
39_W	43_D	1.290	0.31
21_T	42_Q	1.270	0.30
15_Q	29_I	1.269	0.30
34_K	37_G	1.255	0.30
16_H	28_T	1.248	0.30
36_I	53_S	1.245	0.30
234_N	238_K	1.243	0.30
21_T	38_I	1.235	0.29
29_I	37_G	1.231	0.29
28_T	31_V	1.231	0.29
9_A	29_I	1.230	0.29
130_A	134_L	1.227	0.29
29_I	38_I	1.225	0.29
239_L	248_D	1.222	0.29
77_Y	90_K	1.217	0.29
195_E	206_K	1.215	0.29
9_A	16_H	1.207	0.28
229_K	233_E	1.203	0.28
19_K	38_I	1.202	0.28
28_T	42_Q	1.199	0.28
95_P	101_T	1.199	0.28
89_I	95_P	1.194	0.28
89_I	93_Y	1.192	0.28
13_Y	16_H	1.186	0.28
16_H	29_I	1.174	0.27
36_I	40_K	1.171	0.27
68_N	71_Q	1.163	0.27
20_I	29_I	1.163	0.27
64_N	93_Y	1.152	0.26
35_T	42_Q	1.131	0.26
227_Q	231_K	1.129	0.26
32_S	36_I	1.127	0.26
21_T	34_K	1.126	0.26
16_H	43_D	1.126	0.26
97_S	109_E	1.104	0.25
224_F	235_E	1.103	0.25
199_G	202_G	1.099	0.25
210_K	219_L	1.099	0.25
36_I	43_D	1.098	0.25
20_I	34_K	1.093	0.25
22_N	46_K	1.085	0.24
25_I	29_I	1.084	0.24
9_A	13_Y	1.083	0.24
77_Y	81_S	1.081	0.24
26_A	36_I	1.081	0.24
28_T	33_A	1.077	0.24
28_T	38_I	1.073	0.24
12_I	29_I	1.073	0.24
160_G	163_G	1.067	0.24
12_I	39_W	1.061	0.24
86_Q	89_I	1.060	0.24
86_Q	139_K	1.060	0.24
29_I	33_A	1.055	0.23
85_T	102_G	1.041	0.23
119_K	132_D	1.032	0.23
37_G	46_K	1.027	0.23
22_N	42_Q	1.027	0.23
137_Y	211_M	1.012	0.22
33_A	36_I	1.012	0.22
153_K	176_E	1.008	0.22
10_L	43_D	1.007	0.22
81_S	86_Q	1.004	0.22
10_L	36_I	0.996	0.22
21_T	25_I	0.993	0.22
208_A	211_M	0.988	0.21
13_Y	43_D	0.987	0.21
16_H	20_I	0.986	0.21
19_K	22_N	0.983	0.21
20_I	28_T	0.980	0.21
10_L	16_H	0.975	0.21
100_V	109_E	0.972	0.21
224_F	232_I	0.970	0.21
25_I	33_A	0.970	0.21
13_Y	18_G	0.969	0.21
212_K	215_E	0.962	0.21
23_R	36_I	0.955	0.20
75_C	90_K	0.950	0.20
152_G	178_S	0.950	0.20
21_T	43_D	0.948	0.20
10_L	29_I	0.945	0.20
28_T	36_I	0.933	0.20
20_I	25_I	0.931	0.20
25_I	40_K	0.925	0.20
16_H	32_S	0.924	0.20
243_K	247_T	0.916	0.19
7_E	43_D	0.915	0.19
100_V	103_S	0.912	0.19
38_I	43_D	0.910	0.19
111_V	187_L	0.907	0.19
133_V	221_F	0.907	0.19
23_R	37_G	0.906	0.19
12_I	21_T	0.905	0.19
15_Q	33_A	0.904	0.19
142_F	214_L	0.902	0.19
49_L	52_A	0.901	0.19
15_Q	28_T	0.893	0.19
18_G	22_N	0.889	0.19
23_R	38_I	0.882	0.19
225_P	230_Q	0.881	0.19
25_I	43_D	0.873	0.18
12_I	42_Q	0.870	0.18
23_R	42_Q	0.866	0.18
16_H	31_V	0.865	0.18
239_L	244_A	0.857	0.18
93_Y	101_T	0.856	0.18
233_E	240_A	0.853	0.18
143_A	149_V	0.845	0.18
21_T	37_G	0.842	0.18
20_I	33_A	0.838	0.17
10_L	38_I	0.836	0.17
16_H	22_N	0.835	0.17
9_A	15_Q	0.835	0.17
13_Y	29_I	0.835	0.17
26_A	39_W	0.828	0.17
10_L	15_Q	0.824	0.17
58_K	200_K	0.821	0.17
194_T	206_K	0.820	0.17
16_H	19_K	0.820	0.17
133_V	235_E	0.820	0.17
9_A	39_W	0.819	0.17
40_K	45_W	0.817	0.17
8_Q	25_I	0.814	0.17
17_Q	20_I	0.814	0.17
15_Q	20_I	0.812	0.17
32_S	38_I	0.810	0.17
12_I	17_Q	0.799	0.17
35_T	40_K	0.793	0.16
226_D	229_K	0.791	0.16
19_K	25_I	0.789	0.16
134_L	225_P	0.787	0.16
25_I	28_T	0.786	0.16
8_Q	11_A	0.784	0.16
22_N	45_W	0.783	0.16
14_Q	18_G	0.782	0.16
26_A	31_V	0.781	0.16
210_K	232_I	0.780	0.16
101_T	108_N	0.772	0.16
23_R	50_F	0.770	0.16
31_V	47_E	0.765	0.16
22_N	28_T	0.762	0.16
12_I	15_Q	0.760	0.16
241_K	245_E	0.760	0.16
33_A	42_Q	0.759	0.16
20_I	26_A	0.759	0.16
140_I	211_M	0.752	0.15
159_V	163_G	0.752	0.15
94_S	101_T	0.750	0.15
115_I	140_I	0.746	0.15
240_A	244_A	0.740	0.15
22_N	40_K	0.738	0.15
159_V	173_I	0.737	0.15
88_A	104_R	0.737	0.15
23_R	34_K	0.737	0.15
22_N	39_W	0.737	0.15
27_D	32_S	0.736	0.15
242_Q	245_E	0.735	0.15
82_F	137_Y	0.735	0.15
22_N	25_I	0.734	0.15
10_L	39_W	0.733	0.15
160_G	166_F	0.732	0.15
15_Q	26_A	0.727	0.15
7_E	38_I	0.727	0.15
210_K	224_F	0.726	0.15
230_Q	235_E	0.725	0.15
159_V	162_S	0.722	0.15
43_D	49_L	0.721	0.15
143_A	220_Y	0.720	0.15
28_T	32_S	0.720	0.15
26_A	29_I	0.718	0.15
11_A	18_G	0.717	0.15
106_L	109_E	0.715	0.15
134_L	224_F	0.713	0.15
81_S	90_K	0.712	0.15
10_L	22_N	0.712	0.15
124_N	128_I	0.706	0.14
159_V	166_F	0.706	0.14
10_L	31_V	0.698	0.14
125_E	131_M	0.696	0.14
75_C	78_Y	0.695	0.14
28_T	47_E	0.693	0.14
167_D	170_D	0.692	0.14
61_P	65_D	0.689	0.14
12_I	25_I	0.681	0.14
235_E	238_K	0.680	0.14
192_I	219_L	0.677	0.14
15_Q	22_N	0.677	0.14
22_N	47_E	0.672	0.14
216_K	228_F	0.670	0.14
45_W	56_E	0.669	0.14
32_S	43_D	0.669	0.14
9_A	36_I	0.668	0.14
22_N	26_A	0.667	0.14
12_I	36_I	0.664	0.14
102_G	109_E	0.663	0.14
225_P	235_E	0.662	0.14
18_G	36_I	0.662	0.14
136_V	191_T	0.661	0.14
134_L	138_I	0.661	0.14
21_T	33_A	0.660	0.14
9_A	31_V	0.658	0.13
37_G	47_E	0.657	0.13
221_F	225_P	0.655	0.13
227_Q	234_N	0.655	0.13
17_Q	21_T	0.652	0.13
134_L	235_E	0.650	0.13
148_Y	190_G	0.648	0.13
34_K	50_F	0.639	0.13
7_E	10_L	0.631	0.13
20_I	38_I	0.630	0.13
79_V	115_I	0.629	0.13
11_A	22_N	0.627	0.13
239_L	243_K	0.627	0.13
230_Q	237_L	0.622	0.13
10_L	21_T	0.620	0.13
19_K	36_I	0.620	0.13
16_H	35_T	0.619	0.13
31_V	38_I	0.619	0.13
15_Q	32_S	0.613	0.13
19_K	24_A	0.612	0.13
97_S	106_L	0.612	0.13
227_Q	230_Q	0.609	0.13
71_Q	91_A	0.606	0.12
10_L	18_G	0.596	0.12
39_W	45_W	0.594	0.12
22_N	36_I	0.593	0.12
12_I	28_T	0.591	0.12
12_I	22_N	0.590	0.12
20_I	39_W	0.586	0.12
13_Y	49_L	0.586	0.12
137_Y	209_D	0.586	0.12
17_Q	25_I	0.586	0.12
134_L	227_Q	0.584	0.12
23_R	52_A	0.583	0.12
29_I	45_W	0.579	0.12
145_I	151_F	0.578	0.12
29_I	40_K	0.574	0.12
18_G	49_L	0.572	0.12
180_V	203_I	0.572	0.12
134_L	228_F	0.572	0.12
143_A	213_A	0.570	0.12
178_S	188_V	0.569	0.12
12_I	37_G	0.566	0.12
14_Q	38_I	0.566	0.12
11_A	29_I	0.565	0.12
32_S	41_K	0.563	0.12
232_I	236_K	0.561	0.12
178_S	182_V	0.560	0.12
103_S	109_E	0.558	0.12
12_I	31_V	0.557	0.12
153_K	184_D	0.557	0.12
235_E	243_K	0.557	0.12
216_K	219_L	0.556	0.12
81_S	132_D	0.555	0.12
48_A	55_N	0.553	0.12
24_A	35_T	0.553	0.12
64_N	75_C	0.552	0.12
11_A	34_K	0.552	0.12
139_K	220_Y	0.551	0.12
7_E	12_I	0.549	0.11
126_M	227_Q	0.548	0.11
133_V	225_P	0.548	0.11
9_A	33_A	0.545	0.11
46_K	49_L	0.545	0.11
42_Q	46_K	0.544	0.11
242_Q	246_K	0.542	0.11
119_K	127_F	0.540	0.11
196_A	201_E	0.537	0.11
11_A	43_D	0.535	0.11
182_V	187_L	0.535	0.11
140_I	213_A	0.535	0.11
9_A	26_A	0.535	0.11
17_Q	43_D	0.534	0.11
13_Y	32_S	0.529	0.11
13_Y	19_K	0.525	0.11
26_A	32_S	0.525	0.11
228_F	232_I	0.522	0.11
15_Q	38_I	0.522	0.11
19_K	35_T	0.520	0.11
161_K	165_L	0.518	0.11
122_M	130_A	0.518	0.11
100_V	106_L	0.517	0.11
18_G	38_I	0.516	0.11
20_I	31_V	0.513	0.11
11_A	51_S	0.513	0.11
12_I	32_S	0.512	0.11
136_V	214_L	0.512	0.11
130_A	139_K	0.512	0.11
18_G	37_G	0.510	0.11
9_A	25_I	0.510	0.11
171_N	200_K	0.510	0.11
125_E	139_K	0.509	0.11
238_K	242_Q	0.504	0.11
88_A	99_H	0.502	0.11
228_F	237_L	0.502	0.11
9_A	22_N	0.501	0.11
179_F	183_K	0.501	0.11
178_S	183_K	0.501	0.11
16_H	38_I	0.501	0.11
15_Q	31_V	0.500	0.11
209_D	217_L	0.500	0.11

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
3zqpA	3	0.2906	100	0.685	Contact Map
2cmpA	1	0.2075	99.8	0.794	Contact Map
2ao9A	7	0.3774	96.7	0.928	Contact Map
2x48A	1	0.1585	96.2	0.932	Contact Map
2elhA	1	0.2566	96	0.933	Contact Map
1k78A	1	0.3925	95.7	0.935	Contact Map
2m8eA	1	0.1962	95.7	0.935	Contact Map
1tc3C	1	0.1849	95.4	0.936	Contact Map
3zqoA	5	0.2189	95.2	0.937	Contact Map
2jn6A	1	0.3509	95	0.938	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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