XhoI - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

XhoI - Restriction endonuclease XhoI

PFAM:	PF04555	Sequences: KQIESGKADQGERGAVTGGKQMDGFIALVRDLLVEAGLPEAEIHTKRALELPGYFRPTKEWDLLVVHDGQLVAAIEFKSQVGPSFGNNFNNRTEEAIGSATDLWTAYREGAFGPSPRPWLGYLMLLEDCPKSRRPVRVREPHFPVFPEFKGASYAKRYELLCRKLVRERLYDAACFLTSPRSAGLTGEYSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	191 (189)
Sequences:	1439 (927)
Seq/√Len:	67.4
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_D	133_R	5.042	1.00
155_A	178_T	4.433	1.00
156_K	159_E	4.431	1.00
29_V	77_F	4.080	1.00
111_A	146_F	4.029	1.00
117_R	172_D	3.546	1.00
126_L	155_A	2.896	1.00
9_D	17_T	2.792	1.00
125_L	179_S	2.642	1.00
131_K	134_R	2.560	1.00
101_T	170_L	2.451	1.00
85_F	129_C	2.421	1.00
93_T	161_L	2.399	1.00
55_F	105_T	2.362	1.00
105_T	108_R	2.314	1.00
148_E	164_K	2.292	1.00
97_I	101_T	2.243	1.00
80_Q	158_Y	2.163	1.00
20_K	23_D	2.105	1.00
180_P	183_A	2.071	1.00
97_I	161_L	1.997	1.00
146_F	164_K	1.996	1.00
108_R	168_E	1.954	1.00
33_L	65_V	1.926	1.00
54_Y	164_K	1.831	1.00
93_T	97_I	1.820	1.00
166_V	173_A	1.818	1.00
18_G	21_Q	1.812	1.00
50_E	60_E	1.737	1.00
7_K	10_Q	1.733	1.00
34_V	40_E	1.722	1.00
13_R	17_T	1.713	1.00
123_L	175_C	1.712	1.00
30_R	34_V	1.694	0.99
83_P	129_C	1.651	0.99
130_P	134_R	1.644	0.99
44_H	142_H	1.633	0.99
12_E	15_A	1.625	0.99
105_T	168_E	1.584	0.99
119_W	172_D	1.549	0.99
103_L	120_L	1.546	0.99
83_P	127_E	1.530	0.99
82_G	127_E	1.478	0.99
39_P	42_E	1.450	0.98
42_E	67_H	1.437	0.98
159_E	163_R	1.408	0.98
85_F	127_E	1.361	0.98
89_F	93_T	1.359	0.98
21_Q	119_W	1.343	0.97
6_G	9_D	1.335	0.97
117_R	169_R	1.333	0.97
183_A	186_T	1.333	0.97
57_P	89_F	1.331	0.97
22_M	79_S	1.328	0.97
140_E	150_K	1.320	0.97
110_G	167_R	1.299	0.97
23_D	26_I	1.292	0.97
80_Q	124_M	1.274	0.96
6_G	17_T	1.269	0.96
147_P	150_K	1.264	0.96
156_K	160_L	1.259	0.96
104_W	117_R	1.252	0.96
47_R	60_E	1.237	0.96
152_A	156_K	1.236	0.96
55_F	170_L	1.203	0.95
89_F	158_Y	1.201	0.95
71_L	143_F	1.190	0.95
104_W	169_R	1.184	0.95
26_I	63_L	1.151	0.94
6_G	10_Q	1.140	0.93
144_P	150_K	1.110	0.92
27_A	45_T	1.088	0.92
58_T	163_R	1.086	0.92
182_S	186_T	1.077	0.91
49_L	60_E	1.067	0.91
55_F	101_T	1.053	0.90
2_Q	10_Q	1.043	0.90
126_L	178_T	1.019	0.89
104_W	107_Y	1.008	0.88
81_V	85_F	1.002	0.88
31_D	35_E	0.981	0.87
133_R	178_T	0.974	0.86
114_P	163_R	0.971	0.86
38_L	122_Y	0.957	0.85
58_T	162_C	0.954	0.85
41_A	160_L	0.950	0.85
22_M	125_L	0.947	0.85
13_R	19_G	0.946	0.85
15_A	18_G	0.945	0.85
163_R	167_R	0.935	0.84
167_R	170_L	0.928	0.84
124_M	176_F	0.924	0.83
138_V	145_V	0.923	0.83
2_Q	5_S	0.922	0.83
3_I	27_A	0.915	0.83
10_Q	14_G	0.894	0.81
124_M	163_R	0.893	0.81
115_S	122_Y	0.889	0.81
100_A	104_W	0.888	0.81
84_S	87_N	0.866	0.79
12_E	181_R	0.865	0.79
21_Q	33_L	0.860	0.79
117_R	170_L	0.859	0.79
101_T	161_L	0.852	0.78
32_L	35_E	0.848	0.78
183_A	188_E	0.848	0.78
178_T	190_S	0.841	0.77
9_D	13_R	0.839	0.77
59_K	76_E	0.836	0.77
80_Q	86_G	0.835	0.77
138_V	152_A	0.827	0.76
180_P	188_E	0.827	0.76
148_E	160_L	0.823	0.76
5_S	8_A	0.820	0.75
156_K	163_R	0.819	0.75
150_K	188_E	0.819	0.75
140_E	145_V	0.818	0.75
185_L	188_E	0.814	0.75
74_A	99_S	0.812	0.75
84_S	91_N	0.812	0.75
54_Y	115_S	0.811	0.74
100_A	170_L	0.807	0.74
185_L	189_Y	0.798	0.73
80_Q	122_Y	0.797	0.73
3_I	8_A	0.794	0.73
15_A	21_Q	0.793	0.73
26_I	30_R	0.788	0.72
54_Y	58_T	0.775	0.71
2_Q	8_A	0.774	0.71
63_L	110_G	0.772	0.71
113_G	116_P	0.771	0.71
43_I	63_L	0.767	0.70
10_Q	17_T	0.767	0.70
58_T	140_E	0.765	0.70
43_I	46_K	0.759	0.69
16_V	19_G	0.758	0.69
6_G	14_G	0.757	0.69
44_H	66_V	0.757	0.69
80_Q	83_P	0.755	0.69
56_R	59_K	0.754	0.69
39_P	45_T	0.753	0.69
122_Y	176_F	0.752	0.69
28_L	38_L	0.750	0.69
170_L	175_C	0.749	0.68
11_G	17_T	0.743	0.68
74_A	124_M	0.740	0.68
184_G	189_Y	0.740	0.68
32_L	41_A	0.734	0.67
31_D	34_V	0.734	0.67
104_W	158_Y	0.734	0.67
127_E	181_R	0.733	0.67
72_V	165_L	0.730	0.66
14_G	17_T	0.726	0.66
76_E	92_R	0.726	0.66
140_E	144_P	0.724	0.66
30_R	40_E	0.723	0.66
87_N	94_E	0.721	0.66
60_E	99_S	0.721	0.66
91_N	95_E	0.709	0.64
110_G	174_A	0.699	0.63
57_P	161_L	0.699	0.63
2_Q	6_G	0.697	0.63
38_L	65_V	0.696	0.63
75_I	155_A	0.691	0.62
27_A	31_D	0.690	0.62
155_A	159_E	0.689	0.62
131_K	185_L	0.689	0.62
133_R	190_S	0.688	0.62
39_P	46_K	0.687	0.62
104_W	120_L	0.687	0.62
128_D	190_S	0.686	0.62
54_Y	105_T	0.684	0.61
26_I	77_F	0.681	0.61
36_A	124_M	0.676	0.61
77_F	125_L	0.676	0.61
130_P	133_R	0.674	0.60
85_F	132_S	0.671	0.60
56_R	98_G	0.670	0.60
33_L	175_C	0.670	0.60
55_F	74_A	0.667	0.60
99_S	171_Y	0.666	0.59
110_G	135_P	0.664	0.59
28_L	177_L	0.663	0.59
54_Y	124_M	0.663	0.59
88_N	92_R	0.660	0.59
38_L	72_V	0.656	0.58
126_L	176_F	0.655	0.58
60_E	103_L	0.653	0.58
90_N	98_G	0.651	0.58
138_V	151_G	0.646	0.57
105_T	114_P	0.642	0.57
45_T	63_L	0.642	0.57
103_L	112_F	0.639	0.56
86_G	91_N	0.638	0.56
116_P	119_W	0.637	0.56
39_P	67_H	0.635	0.56
7_K	39_P	0.634	0.56
176_F	180_P	0.634	0.56
126_L	158_Y	0.633	0.56
80_Q	176_F	0.633	0.56
105_T	109_E	0.631	0.55
75_I	147_P	0.631	0.55
41_A	67_H	0.631	0.55
77_F	124_M	0.630	0.55
159_E	176_F	0.630	0.55
63_L	164_K	0.629	0.55
55_F	137_R	0.626	0.55
177_L	180_P	0.625	0.55
182_S	190_S	0.625	0.55
78_K	91_N	0.624	0.55
75_I	115_S	0.619	0.54
72_V	116_P	0.616	0.54
29_V	75_I	0.612	0.53
29_V	170_L	0.611	0.53
53_G	161_L	0.608	0.53
132_S	153_S	0.608	0.53
22_M	123_L	0.607	0.52
180_P	190_S	0.607	0.52
50_E	139_R	0.607	0.52
127_E	158_Y	0.604	0.52
39_P	114_P	0.603	0.52
59_K	78_K	0.601	0.52
56_R	76_E	0.599	0.52
29_V	79_S	0.598	0.51
44_H	64_L	0.593	0.51
161_L	165_L	0.593	0.51
80_Q	89_F	0.589	0.50
84_S	94_E	0.586	0.50
77_F	103_L	0.586	0.50
166_V	174_A	0.585	0.50
80_Q	87_N	0.584	0.50
16_V	81_V	0.584	0.50
34_V	41_A	0.583	0.50
93_T	136_V	0.582	0.50
111_A	122_Y	0.581	0.49
65_V	74_A	0.580	0.49
42_E	68_D	0.578	0.49
101_T	105_T	0.578	0.49
64_L	103_L	0.577	0.49
30_R	107_Y	0.576	0.49
9_D	12_E	0.575	0.49
33_L	73_A	0.574	0.49
80_Q	93_T	0.573	0.48
136_V	152_A	0.573	0.48
96_A	99_S	0.572	0.48
114_P	167_R	0.561	0.47
92_R	95_E	0.560	0.47
114_P	150_K	0.559	0.47
175_C	190_S	0.559	0.47
30_R	45_T	0.558	0.47
179_S	184_G	0.555	0.46
57_P	85_F	0.554	0.46
23_D	27_A	0.553	0.46
80_Q	104_W	0.551	0.46
68_D	185_L	0.549	0.46
76_E	94_E	0.547	0.45
78_K	86_G	0.544	0.45
136_V	177_L	0.543	0.45
136_V	140_E	0.539	0.44
180_P	184_G	0.533	0.44
31_D	63_L	0.532	0.44
48_A	166_V	0.530	0.43
149_F	160_L	0.529	0.43
15_A	20_K	0.527	0.43
38_L	119_W	0.527	0.43
105_T	162_C	0.526	0.43
56_R	94_E	0.525	0.43
116_P	151_G	0.524	0.43
31_D	46_K	0.524	0.43
93_T	156_K	0.523	0.43
125_L	150_K	0.521	0.42
66_V	143_F	0.519	0.42
57_P	138_V	0.516	0.42
123_L	177_L	0.513	0.41
186_T	190_S	0.513	0.41
28_L	35_E	0.506	0.41
101_T	154_Y	0.506	0.41
60_E	74_A	0.506	0.41
41_A	144_P	0.505	0.40
75_I	159_E	0.505	0.40
113_G	167_R	0.503	0.40
29_V	63_L	0.501	0.40
57_P	162_C	0.500	0.40
55_F	168_E	0.500	0.40

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
2wcwA	2	0.6492	14.2	0.966	Contact Map
1j3gA	1	0.3822	8.6	0.969	Contact Map
3mtxA	1	0.4136	7.3	0.97	Contact Map
1t8hA	1	0.3822	5.8	0.972	Contact Map
4b94A	1	0.3613	5.1	0.972	Contact Map
4qbnA	2	0.4607	4.9	0.973	Contact Map
3h1tA	1	0.7801	4.7	0.973	Contact Map
4bzjA	2	0.7277	4.7	0.973	Contact Map
4knkA	1	0.4084	4.5	0.973	Contact Map
3ld2A	1	0.6649	4.5	0.973	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.

Page generated in 0.0072 seconds.