LIGT - ECOLI - GREMLIN Contacts

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LIGT - 2'-5'-RNA ligase

UniProt:	P37025	Sequences: MSEPQRLFFAIDLPAEIREQIIHWRATHFPPEAGRPVAADNLHLTLAFLGEVSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQLANMLRSQAARSGCFQSNRPFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTLYASSFARGRTRYTPLKRWALTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12330
Length:	176 (168)
Sequences:	2303 (1787)
Seq/√Len:	137.9

ECOLI - LIGT
BACSU - YTLP YJCG
SULSO - Q97Z91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_G	89_W	3.445	1.00
153_T	168_P	3.408	1.00
47_A	107_R	3.396	1.00
151_E	171_R	3.334	1.00
72_F	149_V	3.178	1.00
158_S	167_T	3.113	1.00
12_D	155_Y	3.000	1.00
9_F	64_A	2.937	1.00
34_G	129_L	2.935	1.00
21_I	90_L	2.857	1.00
80_G	91_G	2.747	1.00
60_L	110_A	2.707	1.00
156_A	167_T	2.604	1.00
156_A	169_L	2.359	1.00
10_A	155_Y	2.308	1.00
11_I	149_V	2.228	1.00
9_F	49_L	2.223	1.00
159_F	164_T	2.168	1.00
5_Q	51_E	2.122	1.00
25_R	42_L	2.117	1.00
7_L	52_V	2.101	1.00
77_D	93_R	2.044	1.00
9_F	106_L	1.975	1.00
5_Q	156_A	1.968	1.00
73_T	146_S	1.958	1.00
64_A	106_L	1.938	1.00
73_T	148_A	1.928	1.00
76_L	90_L	1.890	1.00
49_L	110_A	1.824	1.00
14_P	147_Y	1.803	1.00
152_F	172_W	1.799	1.00
47_A	117_Q	1.799	1.00
65_G	170_K	1.792	1.00
155_Y	168_P	1.765	1.00
103_A	107_R	1.726	1.00
75_T	146_S	1.713	1.00
61_S	170_K	1.617	1.00
168_P	171_R	1.597	1.00
53_S	56_K	1.590	1.00
67_I	152_F	1.572	1.00
19_E	39_A	1.533	1.00
69_Q	105_M	1.499	1.00
160_A	163_R	1.493	1.00
7_L	154_L	1.486	1.00
82_W	89_W	1.455	1.00
14_P	17_I	1.451	1.00
37_V	164_T	1.434	1.00
41_N	166_Y	1.407	1.00
153_T	171_R	1.386	1.00
68_R	152_F	1.383	1.00
160_A	165_R	1.378	1.00
94_Q	97_R	1.367	1.00
90_L	128_L	1.364	1.00
46_L	152_F	1.301	1.00
107_R	117_Q	1.287	1.00
34_G	131_D	1.266	1.00
41_N	164_T	1.255	1.00
106_L	110_A	1.181	1.00
13_L	155_Y	1.180	1.00
13_L	18_R	1.167	0.99
36_P	129_L	1.163	0.99
38_A	41_N	1.152	0.99
76_L	126_I	1.150	0.99
82_W	91_G	1.101	0.99
56_K	59_A	1.096	0.99
37_V	130_R	1.095	0.99
111_A	117_Q	1.082	0.99
57_E	61_S	1.080	0.99
64_A	152_F	1.077	0.99
130_R	159_F	1.041	0.99
20_Q	145_W	1.040	0.99
7_L	49_L	1.032	0.99
6_R	130_R	1.027	0.99
159_F	166_Y	1.025	0.99
85_S	131_D	1.010	0.98
115_C	118_S	1.005	0.98
15_A	18_R	1.002	0.98
154_L	172_W	0.999	0.98
69_Q	174_L	0.998	0.98
109_Q	113_S	0.991	0.98
18_R	39_A	0.985	0.98
61_S	172_W	0.980	0.98
6_R	48_F	0.967	0.98
13_L	147_Y	0.958	0.98
64_A	154_L	0.944	0.98
47_A	103_A	0.930	0.97
49_L	52_V	0.929	0.97
103_A	124_P	0.924	0.97
12_D	153_T	0.918	0.97
49_L	115_C	0.913	0.97
49_L	106_L	0.903	0.97
6_R	157_S	0.902	0.97
47_A	106_L	0.891	0.97
5_Q	54_A	0.889	0.97
52_V	56_K	0.888	0.96
130_R	157_S	0.883	0.96
52_V	57_E	0.874	0.96
11_I	72_F	0.870	0.96
38_A	163_R	0.855	0.96
86_R	131_D	0.853	0.96
46_L	102_L	0.847	0.95
170_K	173_A	0.843	0.95
83_L	86_R	0.838	0.95
17_I	147_Y	0.836	0.95
110_A	113_S	0.829	0.95
44_L	92_M	0.815	0.94
88_V	129_L	0.811	0.94
41_N	157_S	0.798	0.94
75_T	93_R	0.790	0.93
76_L	92_M	0.788	0.93
37_V	42_L	0.786	0.93
126_I	129_L	0.781	0.93
46_L	103_A	0.780	0.93
47_A	110_A	0.779	0.93
151_E	174_L	0.778	0.93
48_F	130_R	0.775	0.93
11_I	46_L	0.761	0.92
11_I	152_F	0.760	0.92
94_Q	100_I	0.759	0.92
59_A	112_R	0.757	0.92
74_L	99_L	0.749	0.91
6_R	51_E	0.744	0.91
35_R	132_A	0.742	0.91
101_Q	105_M	0.741	0.91
9_F	154_L	0.740	0.91
35_R	130_R	0.727	0.90
60_L	64_A	0.718	0.90
150_T	173_A	0.711	0.89
87_V	130_R	0.705	0.89
64_A	172_W	0.697	0.88
76_L	147_Y	0.695	0.88
7_L	50_G	0.694	0.88
53_S	57_E	0.693	0.88
34_G	132_A	0.692	0.88
100_I	124_P	0.688	0.88
103_A	121_P	0.687	0.88
20_Q	23_H	0.686	0.87
63_L	106_L	0.684	0.87
65_G	172_W	0.680	0.87
29_F	64_A	0.675	0.87
63_L	109_Q	0.668	0.86
35_R	38_A	0.668	0.86
132_A	165_R	0.667	0.86
11_I	99_L	0.665	0.86
77_D	141_P	0.664	0.86
51_E	159_F	0.662	0.86
136_V	139_P	0.662	0.86
77_D	143_F	0.660	0.85
21_I	128_L	0.656	0.85
67_I	105_M	0.655	0.85
21_I	42_L	0.653	0.85
9_F	47_A	0.649	0.84
9_F	152_F	0.647	0.84
58_K	61_S	0.643	0.84
130_R	164_T	0.642	0.84
68_R	71_G	0.637	0.83
12_D	18_R	0.636	0.83
63_L	110_A	0.636	0.83
33_A	135_A	0.631	0.83
56_K	115_C	0.629	0.83
161_R	164_T	0.615	0.81
9_F	60_L	0.613	0.81
72_F	99_L	0.613	0.81
66_R	109_Q	0.611	0.81
34_G	126_I	0.610	0.81
21_I	76_L	0.607	0.80
74_L	92_M	0.606	0.80
22_I	42_L	0.606	0.80
68_R	105_M	0.606	0.80
109_Q	112_R	0.604	0.80
103_A	122_F	0.600	0.79
44_L	126_I	0.597	0.79
77_D	144_N	0.596	0.79
23_H	104_N	0.593	0.79
52_V	60_L	0.592	0.79
74_L	147_Y	0.591	0.78
9_F	110_A	0.588	0.78
97_R	100_I	0.587	0.78
55_E	59_A	0.583	0.78
19_E	23_H	0.582	0.77
97_R	101_Q	0.581	0.77
78_D	145_W	0.581	0.77
33_A	157_S	0.578	0.77
47_A	115_C	0.578	0.77
72_F	102_L	0.577	0.77
61_S	65_G	0.575	0.77
23_H	27_T	0.574	0.76
9_F	172_W	0.572	0.76
59_A	62_L	0.572	0.76
12_D	168_P	0.571	0.76
88_V	126_I	0.570	0.76
59_A	63_L	0.567	0.76
159_F	162_G	0.560	0.75
24_W	143_F	0.558	0.74
66_R	112_R	0.555	0.74
149_V	152_F	0.555	0.74
77_D	97_R	0.555	0.74
76_L	144_N	0.555	0.74
79_A	142_G	0.552	0.74
160_A	164_T	0.551	0.74
20_Q	142_G	0.551	0.74
74_L	96_P	0.550	0.73
70_P	98_G	0.550	0.73
98_G	101_Q	0.550	0.73
158_S	165_R	0.550	0.73
105_M	109_Q	0.549	0.73
15_A	39_A	0.549	0.73
32_E	129_L	0.548	0.73
132_A	157_S	0.546	0.73
100_I	104_N	0.546	0.73
13_L	126_I	0.544	0.73
22_I	25_R	0.543	0.72
35_R	164_T	0.543	0.72
36_P	88_V	0.542	0.72
11_I	147_Y	0.535	0.71
37_V	41_N	0.534	0.71
135_A	138_I	0.533	0.71
106_L	109_Q	0.530	0.71
110_A	116_F	0.529	0.71
37_V	127_T	0.528	0.70
92_M	145_W	0.528	0.70
62_L	173_A	0.527	0.70
77_D	90_L	0.526	0.70
103_A	110_A	0.526	0.70
16_E	20_Q	0.525	0.70
61_S	64_A	0.524	0.70
56_K	116_F	0.521	0.69
131_D	164_T	0.520	0.69
10_A	153_T	0.519	0.69
52_V	115_C	0.519	0.69
63_L	112_R	0.517	0.69
122_F	164_T	0.517	0.69
110_A	115_C	0.516	0.69
49_L	60_L	0.516	0.69
79_A	90_L	0.516	0.69
34_G	42_L	0.513	0.68
135_A	140_P	0.513	0.68
152_F	174_L	0.513	0.68
5_Q	57_E	0.513	0.68
151_E	173_A	0.513	0.68
7_L	169_L	0.512	0.68
34_G	41_N	0.509	0.68
75_T	173_A	0.508	0.67
132_A	163_R	0.508	0.67
49_L	172_W	0.507	0.67
17_I	76_L	0.506	0.67
66_R	105_M	0.506	0.67
57_E	169_L	0.505	0.67
102_L	152_F	0.504	0.67
69_Q	101_Q	0.503	0.67
48_F	166_Y	0.501	0.66
84_R	133_S	0.500	0.66

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
4qakA	1	0.9886	100	0.202	Contact Map
1iuhA	1	0.9659	100	0.252	Contact Map
1vgjA	1	0.9659	100	0.272	Contact Map
3j4qA	1	0.9773	100	0.301	Contact Map
2vfkA	1	0.983	100	0.331	Contact Map
1jh6A	5	0.9375	100	0.394	Contact Map
4h7wA	1	0.9261	100	0.394	Contact Map
2d4gA	2	0.9034	100	0.396	Contact Map
2fsqA	1	0.8864	96.9	0.848	Contact Map
2xmiA	1	0.8864	49.9	0.923	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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